uganda development case study

Employment creation potential, labor skills requirements, and skill gaps for young people: A Uganda case study

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Madina m. guloba , mmg madina m. guloba senior research fellow - economic policy research centre in uganda medard kakuru , mk medard kakuru research analyst - economic policy research centre in uganda sarah n. ssewanyana , and sns sarah n. ssewanyana executive director - economic policy research centre in uganda jakob rauschendorfer jr jakob rauschendorfer country economist - international growth centre.

August 3, 2021

Introduction

Over the course of the last decade, Uganda’s economic growth has ranked among sub-Saharan Africa’s strongest; indeed, the country’s annualized average growth rate was 5.4 percent between 2010 and 2019 (World Bank, 2020). Despite this impressive growth, there has been limited creation of productive and decent jobs 1 to both absorb the burgeoning labor force and improve livelihoods. The population growth rate (recorded at 3.1 percent per year) has consistently remained higher than the jobs creation rate necessary for absorbing persons joining the labor market, resulting in increasing unemployment and pervasive underemployment rates. Moreover, where jobs have been created, few young Ugandans (especially young women) have benefited from such opportunities. Indeed, a study conducted by the EPRC (2018) finds that, while the economy grew by 4.5 percent in 2016/17, this growth was largely driven by the services sector, 2 but services, in turn, contribute a mere 15 percent to total employment. In addition, due to severe skill gaps, Ugandan youth are largely engaged in low-value services (e.g., petty trade, food vending, etc.), and only few are able to secure employment in high value-added economic activities like agro-processing, horticulture, or tourism.

Uganda’s economy-wide unemployment rate declined to 9.2 percent in 2016/17 from 11.1 percent in 2012/13. Among youth 3 (who represent 21.6 percent of Uganda’s population), unemployment declined to 16.8 percent in 2016/17 from 20.3 percent in 2012/13, however, with less progress recorded for female youth. Underemployment, a critical development challenge faced by the youth, is widespread in Uganda and can partly be explained by low skills among job seekers (at 1 percent), time (at 43.6 percent) as well as wage-related aspects (at 30.2 percent) (UBOS 2018). At the same time, inequality of opportunity is also growing. Even among the employed youth, 21 percent are classified as poor due to the precarious jobs in which they are engaged, especially if they work in the informal sector.

In this regard, informality, underemployment, and unemployment persist in the country’s labor market; as a result, many Ugandans are engaged in “vulnerable employment.” 4 Vulnerable employment is often characterized by inadequate earnings, low productivity, and difficult conditions of work that undermine workers’ fundamental rights. According to the Uganda Bureau of Statistics (2018), 61 percent of employed persons in the country were classified as engaged in vulnerable employment with the share being higher for female Ugandans (71 percent). Similarly, 68 percent of employed persons living in Uganda’s rural areas are more likely to engage in vulnerable employment compared to 48 percent living in the country’s urban areas.

While agriculture employs nearly 77 percent of the rural population, recorded growth in the sector was low at 2.8 percent in 2016/17 (UBOS 2018). However, sectors providing more productive and better-paying jobs, like agro-processing and high value-added agro-industry have clear linkages to agriculture sector’s overall performance in the country. Weak economic growth in agriculture, therefore, affects agro-industrialization, which, in turn, has implications for the employment viability in the dominant agro-industry. Sector-level performance is also deterred by irregularities and erratic decisions in the business and policy environment. Consequently, the vast majority of Uganda’s labor force remains employed in labor intensive and less productive sectors. Even within agriculture, only a very small proportion of agricultural workers are engaged in the cultivation of high-value, commercialized crops.

The above narrative is also exacerbated by the small and not expanding number of formal jobs, especially in Uganda’s public sector. This lack of available “white collar jobs” is met by a significant number of youth graduating annually either with a certificate, diploma, or degree who aspire to find such employment. While the private sector is coming in to fill the gap in creating jobs for this segment of the population, current efforts are not sufficient, and more opportunities for jobs to be created for this segment of the labor force need to be identified and supported.

In order to create jobs, especially for the youth, there is need to raise private investment in labor-intensive industries. Besides providing jobs, labor-intensive industries—historically manufacturing— can pave the way for continuous upgrading to higher value-added economic activities. However, the average share of manufacturing in Uganda’s GDP keeps declining, from 11 percent between 2000 and 2010 to 9 percent between 2011 and 2018. Therefore, manufacturing will not be able to absorb the 600,000 young Ugandans entering the jobs market each year (AfDB, 2019).

In light of the slow growth of the manufacturing sector, Uganda needs to find alternatives for the creation of productive jobs if the country is to achieve its Vision 2040. Service-oriented industries that share key firm characteristics with manufacturing firms have the potential to enhance growth and create decent employment opportunities. Such industries are called “industries without smokestacks” (IWOSS). Newfarmer et al. (2018) classify these as agro-industry, horticulture, tourism, business services, transit trade, and some information and communication technology (ICT) based services. This study contributes to the evidence base around this topic by analyzing the role of IWOSS in generating large-scale employment opportunities for (young) workers in Uganda, especially in the formal parts of the economy. The paper pays particular attention to three sectors: agro-processing, horticulture, and tourism, as the earlier literature indicates that these sectors have considerable potential to create large-scale formal employment opportunities for young people. 5

Specifically, this study:

Assesses the current employment creation potential along the value chains of IWOSS industries under their respective current sectoral growth trajectories;
Aims to identify the key constraints to growth in IWOSS sectors;
Estimates future labor demand in IWOSS sectors when identified constraints are removed;
Analyzes the occupation and labor skills requirements and gaps in IWOSS sectors; and
Pays particular attention to the need for soft and digital skills among youth (employed and unemployed) to ensure that suggested policy interventions can bridge them.

The remainder of the paper is organized as follows: Section 2 presents the approaches adopted as well as data sources and their limitations. Section 3 presents the country context and background with emphasis on the performance of selected IWOSS sectors in Uganda. The section further delves into employment patterns and other salient features of employment in the country. Section 4 analyzes growth patterns in terms of output, productivity, and exports with emphasis on the role of IWOSS in structural transformation. Section 5 analyzes the specific characteristics regarding sectoral employment and comparisons are made between IWOSS and non-IWOSS sectors as well as manufacturing. Section 6 presents the growth constraints that IWOSS sectors face. Section 7 provides projections for the size of labor force by 2029/30 according to skill groups, projections that inform discussion on the skills gaps that need to be filled to solve current employment gaps. Section 8 presents firm-level surveys that provide insights into future employment requirements and the need for digital skills along the IWOSS value chains selected for this study (horticulture, agro-industry, and tourism). Section 9 concludes with policy recommendations to leverage IWOSS sectors for employment generation, especially for youth.

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Uganda Case Study

This report is part of Cost of Capital Observatory

About this report

The Cost of Capital Observatory is an initiative from the IEA, the World Economic Forum, ETH Zurich and Imperial College London. The aim of the Observatory is to increase transparency in the energy sector and inspire investor confidence, especially in emerging and developing countries where data on financing costs is scarcer.

Case Studies include lessons learnt of how policymakers, together with the private sector, development finance institutions and other entities managed to mitigate risks and mobilise capital for clean energy sectors across the emerging and developing world.

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Equator Initiative - Case Studies Local sustainable development solutions for people, nature, and resilient communities; Kibale Association for Rural and Environmental Development (KAFRED), Uganda

November 19, 2015.

Local and indigenous communities across the world are advancing innovative sustainable development solutions that work for people and for nature. Few publications or case studies tell the full story of how such initiatives evolve, the breadth of their impacts, or how they change over time. Fewer still have undertaken to tell these stories with community practitioners themselves guiding the narrative. To mark its 10-year anniversary, the Equator Initiative aims to fill this gap.

The following case study is one in a growing series that details the work of Equator Prize winners – vetted and peer-reviewed best practices in community-based environmental conservation and sustainable livelihoods. These cases are intended to inspire the policy dialogue needed to take local success to scale, to improve the global knowledge base on local environment and development solutions, and to serve as models for replication. Case studies are best viewed and understood with reference to ‘ The Power of Local Action: Lessons from 10 Years of the Equator Prize ’, a compendium of lessons learned and policy guidance that draws from the case material.

This particular case study is about the Bigodi village community, near Fort Portal, Western Uganda. It straddles an eight kilometre stretch of papyrus wetland that is home to an abundance of wildlife. Eight primate species and more than 200 bird species draw tourists from neighbouring Kibale Forest National Park, for which the Bigodi swamp forms an important wildlife corridor.

Through the work of Kibale Association for Rural and Environmental Development (KAFRED), the community benefitted substantially from this ecotourism trade by establishing guided tours along a boardwalk through the wetlands, supplemented by the sale of handicrafts by the village women’s group. This study tells its conservation story.

Report Highlights

KAFRED's key activities in the conserving the Bigodi swamp area
The impacts of their initiatives in the area and region as a whole
How their work is being sustained and replicated by others

Document Type

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Content Search

Uganda case study- upscaling community resilience through ecosystem-based disaster risk reduction, 2022, attachments.

EXECUTIVE SUMMARY

Since 2019, the United Nations Environment Programme (UNEP) in-collaboration with Partners for Resilience (PfR) have developed and implemented scalable Ecosystem-based Disaster Risk Reduction (Eco-DRR) models working alongside various governments and their respective communities in strengthening their capacity and shaping Eco-DRR policy interventions.

This case study highlights Eco-DRR interventions in Uganda focused on ecosystem restoration and protection in the Aswa river Catchment, specifcally in Middle Moroto secondary sub catchment (Otuke and Alebtong districts), Upper Agago secondary sub catchment (Abim and Agago districts), and Upper Pager Matidi secondary sub catchment (Kotido district). The key risk being addressed within this context is frequent and prolonged droughts in upstream areas and fooding in midstream areas. To address this, the project aims to strengthen resilience to drought and fooding of 160,000 vulnerable women and men in 5 districts of Eastern Aswa Catchment in northern Uganda. Specifcally, the project seeks to scale up Integrated Risk Management (IRM) and inclusive risk governance through improved catchment-based water resources management that is risk-informed, gender- and ecosystem-sensitive.

A model for upscaling community resilience has been developed through three core components of Eco-DRR: Ecosystem Restoration/Protection, Disaster Risk Reduction, and Climate Smart Livelihoods. In Uganda, there is a greater emphasis on Ecosystem Restoration and Protection through the micro-catchment restoration and establishment of guidelines for improved drought and food management. The project further focuses on the establishment of micro-water catchment committees and national guidelines for improved drought and food management. For capacity building, Community-based Organisations (CBOs) were trained on Integrated Risk Management (IRM). Other groups trained includes Village Saving Loan Association (VSLA) groups, district governments, and Aswa Catchment management committee members. 81 CBOs trained on IRM and 109,388 benefciaries reached of which 50% are women. A Cost-beneft Analysis (CBA) performed by the University of Massachusetts Amherst demonstrated that the benefts of Eco-DRR and resilience enhancement interventions outweigh the value of their initial costs.

This case study lays the foundation for demonstrating the need for large-scale implementation of Eco-DRR in advancing the implementation of the Sendai Framework for Disaster Risk Reduction and the Sustainable Development Agenda. The content for this case study has been developed by the United Nations Environment Programme (UNEP) in collaboration with Partners for Resilience (PfR) – a global alliance between the Netherlands Red Cross, the Red Cross/Red Crescent Climate Center, Cordaid, Wetlands International and CARE along with partner civil society and Communitybased Organisations in the countries where they work.

Uganda: 2023 IFRC network annual report, Jan-Dec (27 August 2024)

Uganda strengthens emergency response with avohc-surge training, together for localised humanitarian action in uganda.

Knowledge & Resources

Case Study: Breaking down AMR barriers in Uganda

The Fleming Fund is working with Uganda’s health care system to break down the barriers to disease surveillance by strengthening laboratory and diagnostic capacity in antimicrobial resistance (AMR) - leveraging in-country infrastructure and sustainability - for global health security.

By supporting the integration of bacteriology services in regional laboratories to study bacteria and form a national surveillance system in Uganda, the Fleming Fund injects sustainability into efforts to combat AMR.

Strengthening Uganda’s AMR surveillance system will involve the production of high quality, robust data to influence government policy and trigger action.

The East and Southern Africa (ESA) Fleming Fund hub, managed by Mott MacDonald , is working with the Infectious Diseases Institute to ensure the provision of required training, equipment, reagents, and consumables to enhance Uganda’s bacterial diagnostic capacity.

This support is aligned with Uganda’s Health Sector Strategic Development Plan (HSSDP), which outlines public health priorities, including the country’s AMR National Action Plan (NAP).

The NAP was developed, costed, and is being implemented by the One Health Secretariat to ensure that AMR surveillance is prioritised by the diagnostic departments within different One Health sectors.

Jinja Regional Referral Hospital. Credit: Mott MacDonald.

Barriers to investment

Facing several barriers to investment in AMR infrastructure, Uganda’s laboratories are largely dependent on donor support.

The bulk of government spending is directed toward building low-level health centres (under district hospitals) to improve primary health care. These investments could be undermined if AMR is not considered as a major health problem.

In Uganda, the financing of capital investments for AMR surveillance has come from a combination of donor support for improving global health security preparedness and the Government’s own investments.

For example, Uganda’s Central Public Health Laboratory was recently elevated to the National Health and Laboratory Services Department within the Ministry of Health, allowing access to more domestic funding, and heightened public awareness.

The department has also benefitted from external funding, including the Global Fund to fight AIDs , Tuberculosis and Malaria, the President's Emergency Plan for AIDS Relief (PEPFAR) and the US Centers for Disease Control and Prevention (CDC).

These partners have supported the recruitment of staff, the procurement and servicing of equipment, and the supply of reagents and consumables. The East Africa Public Health Laboratory Networking Project (EAPHLNP), funded by the World Bank, has also provided improvements to several regional referral hospitals.

Sector vulnerability

Despite these developments, laboratories were under-resourced and required support from the Fleming Fund to improve AMR diagnostics and surveillance.

The Fund has contributed to skills and equipment to establish and support laboratory services at 12 sites across the ESA region, including the national reference laboratories.

To help improve sustainability, the Fleming Fund is working within the structures of the wider governmental plans and providing support while the Government finds alternative, more permanent funding streams. Long-term support is important to continue to provide diagnostic services and surveillance data.

“Sustainability is a key principle of the Fleming Fund’s investments.

“Commitment to contribute funding is an important first step, and to make that commitment, governments need the right data to help with decision-making and prioritisation; that’s what the Fleming Fund hopes to support.”

Dr Toby Leslie, Global Technical Lead for the Fleming Fund at Mott MacDonald.

Lab tech recording results of bacterial growth at the Jinja Referral Hospital. Credit: Mott MacDonald.

In the animal health sector, the National Animal Disease Diagnostics and Epidemiology Centre (NADDEC) sits under the Chief Veterinary Officer but is challenged by a lack of resources and skills.

In addition to the Fleming Fund’s input, infrastructure investments have been supported by the Food and Agriculture Organisation (FAO) and the Danish International Development Agency (DANIDA).

These investments primarily focus on animal health, which the Fleming Fund has provided essential support through their investment in laboratory development and bacteriology services.

Staff provision

The Ministry of Health and Ministry of Agriculture Animal Industry and Fisheries (MAAIF) have stretched budgets, and the majority is dedicated to standing costs such as human resources.

In the MAAIF, the government is working towards increasing staffing levels at the NADDEC, pledging to absorb all the external staff costs which are currently being paid for by donors.

This is an important recognition of the importance of animal health surveillance, and a major step towards sustainability.

Lab tech taking a blood sample at the Jinja Referral Hospital. Credit: Mott MacDonald.

10-year Roadmap

In progressing the AMR project, the Government of Uganda has worked with partners to set up a 10-Year Roadmap for Health Supply Chain Self-Reliance , promoting a sustainable supply of quality reagents and consumables.

They have also set up a biomedical engineering department and created new positions for consultants within the human health laboratory units, encouraging the retention of highly qualified staff.

In cementing these gains and turning them into a functioning and beneficial surveillance system, it’s vital advocacy is sustained. In the next phase of the Fleming Fund Country Grant for Uganda, Mott MacDonald will work with the UK Foreign & Commonwealth Office (FCDO) and the INTOSAI Development Initiative to support the use of AMR evidence in decision-making and promote such sustainability.

This will involve working with the AMR community and the Ugandan government to encourage the mobilisation of health resources nationally and integrate AMR surveillance within the financing of wider infrastructure systems. These efforts will help push AMR to the forefront of public health policy.

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Studies & Reports

From Studies & Reports, MAAP warns Africa ‘flying blind’ from stark findings of incomplete AMR data , Date: 18/11/2022

Date: 18/11/2022

A new report is calling for a drastic increase in AMR data across the continent.

From News, Demystifying AMR in Kenya: the real-life impact , Date: 08/03/2024

Date: 08/03/2024

On International Women's Day, we celebrate the Fleming Fund Policy Fellows Dr Romona Ndanyi and Dr Evelyn Wesangula, supported by the University of Edinburgh, who have produced a powerful documentary on the real-life impact of AMR, ‘The Silent Pandemic'.

Brokering Development - Summary of Uganda Case Study - IFAD

IFAD is the world’s fund for transforming agriculture, rural economies and food systems.

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From building resilience to empowering rural people and protecting the environment, explore our main areas of work.

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Things look a bit different here, right!

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Brokering Development - Summary of Uganda Case Study

A case study of the Oil Palm PPP in Kalangala, Uganda. The PPP aimed to establish oil palm production (a new cash crop in Uganda) through private sector-led agro-industrial evelopment on Bugala Island, Lake Victoria.

The study is mainly based on qualitative data collection through semi-structured key informant interviews and focus group discussions, and a document review. Researchers interviewed representatives of the main partners involved.

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Publication

Programme Brief: Agroecological Transitions for Building Resilient and Inclusive Agricultural and Food Systems

This brief describes the Agroecological Transitions programme which empowers farmers in low- and middle-income countries to make climate-informed agroecological transitions.

Project Brief: Improving Agricultural Resilience to Salinity through Development and Promotion of Pro-poor Technologies (RESADE)

RESADE is improving food security, agricultural productivity and incomes of poor smallholder farmers in salinity-affected areas in seven countries. It does so by introducing salt-tolerant crops, using suitable agronomic management practices, developing value chains for new crops, building capacity, influencing national development policies, providing good quality seeds.

Project Brief: Agricultural Transformation in Nigerian Federal States and Togolese Regions Towards Achieving Zero Hunger

Increasing food demand is a key concern in Nigeria and Togo as price increases exacerbate poverty. The project improves food security and agricultural productivity within the rice and cassava value chains by introducing resilient crop varieties, improving crop management practices and implementing enabling policies.

The World Bank in Uganda

Real GDP growth is expected to accelerate to 6.6% in FY26, mainly driven by investments in the oil sector. With the advancing preparation of the drilling fields and supportive infrastructure, oil exports are expected to commence by end of 2025. However, timing may slip if some of the financing, anticipated from external creditors, is delayed.

Economic growth has accelerated slightly despite external shocks. GDP grew by 5.3% during the first quarter of FY24, supported by an oil-related construction boom and robust growth of agriculture, despite volatile weather conditions. An uptick in private investments and employment growth reinforced domestic demand deeper into the year, with sustained increases in output, new orders, and employment. Hence GDP is expected to grow by an estimated 6.0% in FY24. While Uganda’s exports surged with increased volumes of production and improvement in terms of trade, resumption of gold trade, and recovery of tourism, imports grew stronger supported by demand from investments into the country’s oil development program, hence weakening the current account.

The Bank of Uganda (BoU) – the central bank – tightened monetary policy in March 2024 to curb possible passthrough effects of a fast-depreciating shilling. Low inflation, averaging 2.9% during the first half of FY24, benefitted both investments and poor households. During the second half of FY24, inflation increased – gradually to 3.4% in February 2024 but is forecast to accelerate towards the target of 5%, partly on account of the shilling depreciation recently driven by intensified portfolio outflows. Hence, on March 6, 2024, BoU raised its policy rate to 10% from the 9.5% maintained since August 2023.

Real GDP growth is expected to accelerate to 6.6% in FY26, mainly driven by investments in the oil sector. With the progressed preparation of the drilling fields and supportive infrastructure, oil exports are expected to commence by the end of 2025. However, timing may slip if the financing, anticipated from external creditors delays. The investments and exports of oil will support the government’s other promotion efforts for tourism, export diversification, and agro-industrialization. Lower inflation will enable BoU to ease its stance, which, combined with reduced fiscal pressures under a fiscal consolidation, augurs well for both foreign and domestic investment. Nonetheless, the slowdown of global growth and disruptions in global financial conditions remain major downward risks.

Accelerated growth may reduce poverty (measured at the $2.15/day international poverty line) from 41.3% in 2024 to 40.1% by 2026. But because households have limited adaptive capacity, the pace of poverty reduction will ultimately depend on how food access and affordability evolve, and on the incidence of weather and any environmental shocks. The trickle-down effect of oil for the poor will depend on adopting the right set of policies and strengthening existing and setting up new institutions.

Development Challenges

Increased shocks and less momentum behind policy reform create challenges for sustaining economic growth and reducing poverty in Uganda. Rapid population growth has kept a large share of the population below the poverty line, while human capital and infrastructure deficits have limited the country’s growth potential and social welfare improvement. The challenge of creating productive jobs for the almost one million working-age Ugandans entering the labor market every year is enormous. Although services constitute a large share of GDP, it has created few jobs, mainly informal and low-skilled. Most of the jobs are in the agriculture sector which is prone to natural disasters that climate change is making more frequent and severe—and adapting to which is hampered by low adaptive capacity.

To promote economic growth and reduce poverty over the medium-term, the Ugandan economy needs to structurally transform and shift labor into more productive employment, ahead of oil revenue flows. The first required reform is to shift investments towards the private sector by reducing the cost of doing business and fostering access to finance. Second, the government must invest more strongly in human capital by shifting spending into social sectors alongside measures to reduce inequality and strengthen resilience, and promote uptake of digital and other innovative technologies.

Finally, the government needs to maintain prudent macroeconomic management alongside pursuing structural policies to manage oil revenue better while also building resilience to climate shocks.

Human Capital

Uganda’s Human Capital Index is low. Children born in Uganda today are likely to be 38% as productive when they grow up as they could be if they enjoyed complete education and full health. Children who start schooling at the age of four years are only expected to complete 6.8 years of school by their 18 th birthday, compared to the Sub-Saharan average of 8.3. However, a child’s actual years of learning are 4.3, with 2.5 years considered “wasted” due to the poor quality of education.

Last Updated: Apr 03, 2024

A Country Partnership Framework (CPF) is the tool that guides the World Bank Group's (WBG) support to a member country such as Uganda. A new CPF to support Uganda’s vision of a society transformed from a peasant economy to a modern and prosperous country by 2040 will soon be prepared by the WBG in collaboration with the Government of Uganda and in consultation with civil society, private sector, academia, development partners, and the public.

The investment portfolio in Uganda is financed by the International Development Association (IDA) , which provides interest-free credits on concessional terms, attracting no interest charges and a commitment charge of up to 0.5% on the undisbursed amount and grants. The commitment charge is decided annually by the IDA Board of Directors. For the fiscal year that started July 1, 2023, the Board set the rate at 0%. Effective July 1, 2022, any new IDA loans have a duration of 50 years, including a 10-year grace period.

As of March 31, 2024, the World Bank’s portfolio of IDA-financed credits and grants stood at $4.86 billion in commitments, comprising 19 national projects and one regional. The portfolio is complemented by trust fund resources (currently standing at more than $75 million contributed by seven donors through an in-country Multi-Donor Trust Fund), knowledge products, and technical assistance and is spread across various sectors ( see pie chart below ). The urban sector dominates the portfolio with a share of 21%, followed by energy at 13%. The portfolio also includes $841 million (90% in grants) from the Window for Host Communities and Refugees focused on supporting the implementation of Uganda’s integrative refugee policies. This is development support for host communities and refugees.

Engagement by the International Finance Corporation (IFC) in Uganda focuses on investment and advisory activities that help diversify the economy, grow agribusiness, develop energy infrastructure, and improve access to finance and jobs. As of June 30, 2023, IFC’s committed investment and advisory portfolio in Uganda stood at $162.2 million across infrastructure, agribusiness, health, and financial services. Examples of IFC’s involvement include working with agribusinesses to support smallholder farmers, working with financial sector partners to boost lending to small businesses, and providing thought leadership on key sectors such as financial inclusion.

As of February 29, 2024, MIGA’s portfolio had a combined gross exposure of $457.5 million , supporting projects in the energy and finance sectors. This includes:

Coverage of The Rise Fund’s equity investment in the mobile money and digital financial services companies operating under the Airtel Money brand.
Coverage of the acquisition of the Bujagali hydropower project to support incoming investors.
Capital optimization of an international bank to provide headroom for lending operations in Uganda.
Support to the first Regional Development Bank , TDB, of which Uganda is a member.

Social Sustainability and Inclusion Under the Uganda Development Response to Displacement Impacts Project , 3,295,419 refugee-hosting community members and refugees gained access to social and economic services and infrastructure through more than 6,000 project activities. This is an addition of nearly 478,000 beneficiaries in the last several months. The project has also increased interaction and smoothed relationships between refugees and host communities; relieved pressure of refugees on host community facilities; and addressed perceptions of inequitable service provision.

Sub-national Government Capacity Uganda Intergovernmental Fiscal Transfers is a governance project with many facets, including supporting local governments in effective delivery of social services. Recent results include:

Under education, 105 seed secondary schools built and operational with minimum staffing of at least 16 out of the 32 staff required. Construction of another 150 schools is underway.
Under health, out of the 371 health centers to be upgraded/constructed, 239 are complete, with the rest under construction, in addition to two regional blood banks.
Under the water sector, 418 tap stands/public stand posts have been constructed up from an annual average of 106 taps. As such, 485,700 people now have safe, clean water, with additional service restored to serve 32,700 persons who are using the rehabilitated point sources, including extension of water to 21 health centers and 28 schools constructed under the program. More than 1,320 farmers have received microscale irrigation equipment and been trained in operation and maintenance in the 40 phase one districts.
Across the board, key management information systems have been rolled out to support decision-making and resource allocation. These are the Teacher Effectiveness and Learners Achievement System and e-Inspection to address absenteeism in schools; Water and Environment MIS; and Electronic Medical Records System.

Health Achievements of the Uganda Reproductive Maternal and Child Health Services Improvement Project include:

The government leveraged the project to scale up results-based financing (RBF – linking funding to predefined results) nationally covering 131 of the 135 districts and 1,426 health facilities using national public finance management systems. Consequently, RBF principles were mainstreamed into the government’s own primary healthcare care grant system from July 2023 with support from a sister program – Uganda Intergovernmental Fiscal Transfers.
Training of health workers in much needed but short in supply areas. Some 1,650 students were trained in various disciplines including emergency medicine, critical care nursing, imaging, anesthesiology, cold chain management, biomedical engineering, and intensive care nursing. Additionally, 4,600 health workers across 730 health facilities received clinical mentorship in maternal, neonatal and child health care disciplines.

Uganda COVID-19 Response and Emergency Preparedness Project (UCREPP) delivered the following results:

Supported the national response to the fifth outbreak of Ebola virus disease (EVD) leading to its containment in a record 69 days by early 2023, preventing further spread and minimizing the impact on public health.
Trained 411 healthcare workers in emergency care response and critical care in refugee-hosting districts and regional referral hospitals. Further trained 19,800 community health workers in 20 districts and 2 cities and 144 community health extension workers.
Purchase of 44 ambulances to support emergency medical services; and construction of three ambulance call and dispatch centers is ongoing.

Agriculture and Nutrition The Agriculture Cluster Development Project :

Enabled more than 450,000 farm households to access and use improved agro-inputs such as tarpaulins and fertilizer resulting in concomitant increases in on-farm yields. Yields of all five selected commodities (rice, maize, cassava, beans, coffee) increased, with rice and Robusta coffee exceeding the target.

The Uganda Multi-Sectoral Food Security and Nutrition Project results:

Enhanced knowledge on good nutrition resulting in improved household nutrition and incomes for 1.55 million direct project beneficiaries in 15 participating districts. For example, the percentage of children aged 6–23 months in households with minimum dietary diversity increased from 45.9% at baseline to 51.78% against the target of 51.63%. This work is being considered for scaling to address food and nutrition insecurity more broadly.

Urban The Uganda Support to Municipal Infrastructure Development Program - Additional Financing (USMID) results include:

A majority of infrastructure projects in tens of cities and municipalities –74.8km of urban roads tarred, lit streets, smooth pavements/walkways, improved drainage, greenings – are either completed or are expected to be finalized by June 2024 when the project closes. The program has transformed the look of urban centers and facilitated business in the entire country.

Water The Integrated Water Management and Development Project ‘s support has resulted in 5,000 households outside the capital Kampala receiving water services, a number expected to increase to about 20,000.

Last Updated: Apr 08, 2024

The World Bank Group works closely with other development partners, including the United Nations, for a more coordinated approach to development support in Uganda. The World Bank is the co-chair of the Local Development Partners Group (LDPG). The Bank also supports the LDPG secretariat and website through its Multi-Donor Trust Fund. Backed by the LDPG technical working groups, and in close consultation with Government of Uganda (GoU) counterparts, partners work together to align support with national priorities set out in the five-year Third National Development Plan of Vision 2040, whose goal is to transform Ugandan society from a peasant to a modern and prosperous country by 2040. They hold joint LDPG-GoU meetings to ensure a continuation of the partnership dialogue and to maximize support through better coordination.

The LDPG’s technical working groups are organized around sectors such as agriculture, energy, climate change, and gender. More recently, a development partners group on inclusion and non-discrimination was formed in response to changes in some areas of Uganda’s legal framework. It is co-led by the World Bank and the Office of the United Nations Resident Coordinator.

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Uganda Case Study - YOUTH AHEAD: Policy Innovations to Create Opportunities for Young People in Africa’s Agrifood Systems

This case study on Uganda highlights the country's young population, with 74% under 30 years old and 34% classified as youth. Uganda's economy relies heavily on agriculture, accounting for significant portions of GDP, employment, and foreign exchange earnings. The country has made notable progress in agricultural growth, meeting commitments under the Malabo Declaration to reduce hunger and poverty. Uganda has also achieved broader economic development, with improvements in GDP per capita, life expectancy, access to electricity, and internet usage. Efforts to reduce youth unemployment have seen success, with plans in place to create more quality jobs and improve access to education and training in STEM fields. The country's initiatives aim to foster youth employment and empowerment within Uganda's agrifood systems, contributing to sustainable development and economic growth.

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Reasons and motives for foreign aid

Generally, reasons for providing foreign aid can relate to humanitarian, political and economic motives (Lancaster, 2007). Humanitarian motive is closely associated with moral or ethical responsibilities of rich individuals and countries to help poor individuals and countries.

Humanitarian motive for providing foreign aid is also associated with the notion of altruism, which stresses the moral obligation of each individual to help other individuals (Moyo, 2009). Moreover, ulitarilism, as an extreme version of altruism dictates that the moral standards of actions are determined by the levels of their capacity to provide benefits to all parties (Lundsgaarde, 2012)

Political motive , on the other hand, can be guided by strategic interests of developed countries in a way that foreign aid is provided in exchange for a support of a particular stand or initiatives. The Marshall Plan initiative can be mentioned to illustrate the case of foreign aid guided by political motive, because this initiative has been developed in order to safeguard European countries from the influence of Communist USSR.

The relevance of political motive to the provision of foreign aid to Uganda in particular can be specified as minimal because this point is barely addressed by media and individual writers and researchers.

The provision of foreign aid as economic self-interests can be facilitated mainly in two forms. Firstly, foreign aid can be provided in order to develop new markets to sell the products of developed countries. The case study of Nestle Cerelac baby food can be mentioned to explain this point. Specifically, Nestle has been accused of inappropriate marketing practices in Uganda in a way that its Cerelac baby food products have been advertised as being more beneficial to babies compared to breastfeeding (Baby Milk Action, 1997).

Secondly, provision of foreign aid can be used as a means of disposing of surpluses. Developed countries, as well as, many developing countries maintain certain amount of food surpluses to be consumed in times of natural catastrophes, environmental disasters etc. It is a common practice to send these surpluses as foreign aid to poor countries such as Uganda upon the approach of their expiry dates.

The benefits of foreign aids and level of dependency of Uganda on foreign aid

European Recovery Program, also known as The Marshall Plan is considered to be a major force behind the evolution of foreign aid towards its present form. The Marshall Plan involved the donation of up to 3 percent of national income in the USA to restore Europe following The Second World War.

Due to the major positive impact associated with the implementation of The Marshall Plan officials in highly developed countries became convinced that the same strategy could be used to solve extreme poverty and other issues faced by countries in African continent.

The publication of ‘Assessing Aid’ by the World Bank in 1998 also marks an important event in the development of foreign aid practices. These practices mainly consist of providing food or cash or reducing the levels of debts of countries involved.

Supporters of foreign aid to Africa in general, and Uganda in particular point to the developments associated with a range of specific programs and initiatives such as UN Millennium Project, Poverty Eradication Action Plan, Live 8 concerts and others.

Moreover, World Economic Forum (2005), African Development Bank, World Food Programme and International Fund for Agriculture and Development are often credited for assisting in the development of overall infrastructure in Uganda, and promoting economic growth through various aid programmes and a series of debt relief initiatives.

Nevertheless, still Uganda is highly dependent on foreign aid “since the mid-1990s, Uganda has enjoyed an influx of foreign aid amounting to 80 percent of its development expenditures and has been the beneficiary of a number of generous donor initiatives” (Branch, 2011, p.84)

Supporters of providing foreign aid to Uganda argue that “ever increasing injections of foreign aid have been essential for the long-term rehabilitation of infrastructure, for funding new projects, and for balance of payment support” (Leggett, 2001, p.60)

The UN Millennium Project, introduced by the UN in 2000 is especially praised by various parties for its considerable progress in terms of achieving its declared goals. Specifically, the official eight goals of the UN Millennium Project consist of eradicating extreme hunger and poverty, achieving universal primary education, promoting gender equality and empowering woman, reducing child mortality, improving maternal health, combating HIV/AIDS and other diseases, ensuring environmental sustainability, and developing a global partnership for development (Sumner and Mallett, 2013).

The positive impact of the UN Millennium Project to promote growth in Uganda in particular has been linked with tens of thousands of families using combinations of fertiliser trees, phosphorus, and biomass, construction of emergency obstetric care facilities for women, achieving the coordination of Uganda AIDS Commission with 1000 partner agencies, and addressing the issue of female genital mutilation (UN Millennium Project Report, 2005).

Moreover, UN Millennium Project is credited for the development of financial instruments in order to protect farmers against price fluctuations and natural disasters.

The launch of Commission for Africa in 2005 by then Prime Minister Tony Blair in the UK has been perceived by some as indication of focused approach being adopted by highly developed countries in terms of assisting Africa with its severe problems. Comprising seventeen members in total and nine members from Africa, the Commission for Africa has aimed to propose a coherent package of initiatives to making Africa stronger and more prosperous. Importantly, recommendations proposed by Commission for Africa have been discussed and taken into account in G8 meetings in Glenagles on July 2005.

Global initiatives such as Live 8 charity concert organised by Irish pop star Sir Bob Geldof has involved more than 1000 musicians performing with the broadcasts on 182 television networks and more than 2000 radio networks worldwide. Communicating the message of making poverty a history, the concerts took place on July 2, 2005 in 10 venues in the UK, France, Germany, Italy, USA, Canada, Japan and Russian Federation.

The success of Live 8 is linked to the fact that rather than asking individuals, organisations and countries for financial contribution in a direct manner, the initiative has aimed to increase the level of awareness of people towards the issues of poverty in general.

Provision of food aid to Uganda and its advantages

Provision of food aid to Uganda is associated with a set of conflicting objectives such as the willingness of developed countries to dispose of expiring food surplus at the same time when implementing their foreign policy (Branch, 2011).

The benefits of food aid to Uganda as well as any other poor country in African continent is obvious and they are related to providing resources free of charge, saving many human lives from famine, and a potential for achieving stabilisation of food supply and price.

At the same time, disadvantages of providing food as a foreign aid include formation or increasing level of dependency of receiver to this type of foreign aid and high costs associated with supply of food for donors.

Disadvantages of foreign aid to Uganda: popular sceptical arguments

As it has been discussed above UN Millennium Project is often praised by UN member governments for making substantial contribution in terms of promoting growth in Africa. At the same time, critics of the UN Millennium Project point to the absence of specific and measurable criteria against which the success of the project could be evaluated.

Critics argue that due to the foreign aid Uganda is more indebted today than ever before. It has been assessed that “approximately USD 3,100 million is owed to the multilateral creditors with World Bank, IMF, and African Development Bank being the main creditors” (Kazimbazi and Alexander, 2011, p.29).

In other words, it can be observed that instead of promoting economic growth and providing funds for the government to deal with a range of severe issues the country is faced with, the intervention of World Bank, IMF, African Development Bank and other external organisations with the economy of Uganda have resulted in more debts being accrued.

Aid absorption, defined as “the widening of the current account deficit due to incremental aid” (Schabbel, 2007, p.277) can be mentioned as a stark example of ineffectiveness of foreign aids in Uganda in terms of contributing to economic development.

The negative impact of corruption in Uganda in distribution and utilisation of foreign aid is significant. There are convincing evidences (Barkan, 2011) that in all sectors in general, and in educational sector in particular only a small fraction of foreign aid reaches its intended destination, the major part being unlawfully consumed by corrupt officials.

This problem has escalated to an extent where the World Bank’s county director Kundavi Kadiresan has warned Ugandan President Yoweri Museveni with stopping the aids altogether unless decisive measures are taken to fight with corruption (Ford, 2010)

Interestingly, at the same time, the practice of donors channelling money to non-government organisations in a direct manner via commercial banks is often criticised by various parties, because Central Bank cannot control this money and accordingly, the real amount of aid coming to the country remains unclear.

Moreover, economists argue that substantial amount of cash entering Uganda as aids are increasing the level of demand for products and services, at the same time when the level of output of products and services are not increasing, and this situation is blamed for a very high level of inflation in Uganda (Bilur et al., 2011).

Foreign aid to Uganda has been also blamed for sustaining unfair and corrupt regime of President Yoweri Museveni from a political collapse (Ernst, 2011). In other words, there is an argument that if not for foreign aid the current corrupt regime of Yoweri Museveni would have collapsed due to public discontent in the face of major challenges facing the country and it could be replaced with more competent government.

Alternatively, at least the necessity of economic and political reforms would have been appreciated by the current government of President Yoweri Museveni if it was not subsidised by regular foreign aid.

Some critics remain pessimistic to Tony Blair’s Commission for Africa because of the choice of traditional tools to help Africa selected by the Commission. Specifically, it has been argued that Commission for Africa relies on traditional strategies of endorsing increased foreign aid and writing off debts of African countries, and these strategies have proved to be ineffective and even counter-productive in the past.

Moreover, an institutional practice of debt relief implemented towards Uganda and other countries in African continent in a regular manner can decrease the level of motivation of government officials to make the most effective use of the loans provided. In other words, government officials in Uganda may develop the habit of relying on assumptions that loans being provided are going to be written off after a certain period of time, and thus they are not going to assume due level of responsibility towards the funds being given.

Interestingly, critics argue that the majority of present day debt of Uganda was not incurred under the violent rule of Idi Amin, however disastrous his regime might have been. On the contrary, more than 90 per cent of Ugandan debts have been incurred as a result of reforms initiated by IMF and the World Bank starting from 1981 (Mwenda, 2006).

Debt relief as foreign aid at its consequences

Uganda has been presented with debt relief on seven occasions during the period of 1982 – 2006. As a result of series of debt relief initiatives by IMF, the World Bank and MDRI “Uganda’s total debt outstanding declined form its 1992 peak of 102 per cent of GDP to about 12 per cent of GDP in 2007” (Bulir et al., 2011, p.7)

High level of ineffectiveness of the strategy involving debt relief for Uganda is best illustrated by the fact that in one particular occasion “immediately after Uganda’s debts were forgiven, the government bought a private jet for the president at a cost of USD 35 million” (Mwenda, 2006).

Unfortunately, the occasions of debt relief are generally not perceived by government officials in Uganda as opportunities to increase the standard of life through channelling the newly available funds for development purposes. On the contrary, each occasion of debt relief has been traditionally utilised by the government as an opportunity to borrow more funds only to be misused as a result of corruption.

Poverty Eradication Action Plan and its impact on Uganda’s economy

Poverty Eradication Action Plan for Uganda first initiated during the presidential elections by Meseveni and implemented by the Ministry of Finance, Planning, and Economic Development is considered to be an important event that has increased the amount of foreign aid received by the country.

Aiming to reduce the poverty to 10 percent by 2017, the Poverty Eradication Action Plan comprises five major building blocks: a) economic management; b) production, competitiveness, and incomes; c) security, conflict resolution and disaster-management; d) good governance, and e) human development (Ernst, 2011).

The initiative has been highly appraised by a range of developed countries and international organisations. For example, the World Bank and IMF have referred to the Poverty Eradication Action Plan as a sample document to be devised by other countries as well that aim to attract foreign aid in order to deal with internal challenges.

Alternatives to foreign aid for Uganda

Taking into account negative impacts in various levels foreign aid have had on the economy of Uganda and other countries in Africa, this essay points to a set of alternatives to foreign aid that need to be looked at in order to improve the situation.

Public expenditure reforms in Uganda represent a realistic opportunity of achieving economic development and increasing the standards of life. The practices of recruiting ‘ghost soldiers’ have been revealed in Uganda the salaries of whom are taken by high level army officers (Mwenda, 2006).

There is also a realistic potential for Uganda to increase the level of government revenues through taxes though reforming the country’s taxation system. Under the current system, the corporate tax in Uganda amounts to 42,9 per cent of gross profit which is very high compared to many other countries globally, and this situation can be blamed for encouraging tax evasion practices (Ernst, 2011).

Moreover, top individual income tax totals to 30 per cent which is also high by international standards. The taxation system in Uganda needs to be reformed in a way that the level of taxes need to be reduced at the same time when relevant government agencies need to ensure collection of taxes from all private and organisational entities according to the jurisdiction. In this way there would be more incentives for businesses to pay taxes with positive implications on national economy.

Increasing the level of domestic investment is considered to be one of the most obvious and most effective strategies to decrease the levels of dependency of Uganda on foreign aid. At present “agriculture accounts for about 60% of the GDP, with major export crops including coffee, tea and tobacco. Over 90% of Ugandans are either subsistence farmers or work in agriculture-related fields” (Briggs, 2010, p.27).

Taking into account the high level of popularity of coffee, tea and cotton in global markets and the possibility of harvesting the same products of a high quality in Uganda it can be stated that the standard of life in Uganda can be significantly increased through achieving better deals for its agricultural products in an international market.

The discovery of oil in the Lake Alberta can be interpreted as a signal for potential reserve of natural resources in Uganda that yet to be found and utilised. It has been found that in Lake Alberta alone “the estimated reserves are 2.3 billion barriers, with the potential production estimated to be as high as 200,000 barrels per day” (Barkan, 2011, p.14).

This is a justified reason to believe that further explorations can result in finding additional reserves of oil, gas, coal or other natural resources and this could have highly positive implications on the standard of life in Uganda.

The levels of fiscal responsibility, instead of fiscal dependency of the government of Uganda need to be increased. This can be achieved through imposing fixed conditions associated with the provision of aid. However, it has to be acknowledged that the implementation of this scenario in practice is associated with a set of specific issues. For example, it is difficult to ensure that the fixed conditions mentioned above would not serve foreign politics of developed countries at the same time.

Extremely high levels of inflation in Uganda can be specified as one of the roots of its major economic issues. Accordingly, Central Bank of Uganda and Ministry of Finance, Planning, and Economic Development should work on devising effective fiscal policies at the same time when encouraging the levels of outputs of products and services within the country.

It is important to note that the state of national economy in Uganda has been directly related to the world price for coffee for the last several decades. Specifically, the rise of coffee prices to USD 2,58 per kg in 1995 from USD 0,87 in 1992 has had positive implications on the standard of life of Ugandan people. Similarly, when international price for coffee fell to USD 0.89 in 2005, the negative implications of this change to the standard of life of Ugandan people was stark (Mwenda, 2006).

Accordingly, taking into account the fact that the government of Uganda possesses no instruments to impact the international price for coffee in a direct manner, it needs to decrease the levels of dependency of the national economy on agriculture through supporting other sectors of economy such as manufacturing and services.

It has to be noted that the amounts of foreign aid to Uganda and other countries in Africa have decreased during the last several years as a result of budget constraints in the USA and Europe due to macroeconomic issues being faced by developed countries (Lundsgaarde, 2012). This situation increases the importance of exploring alternatives to foreign aid discussed above in practical levels.

To put it simply, unless internal issues in Uganda are addressed as specified above, the economic situation within the country is most likely to deteriorate due to reductions on the volume of foreign aid the county receives.

Education as solution of problems in Uganda

Major issues today Uganda is faced with are mainly related to lack of competency of government officials and a high level of corruption in all levels of government. Therefore, instead of providing foreign aid in the forms of food, money and debt relief, donors can aim at increasing the level of professional competency of government officials so that greater positive impact can be made.

Various educational grants and work experience opportunities can be provided to Ugandan government officials at various ranks so that the knowledge and experience gained in a developed country can be applied in Uganda in order to achieve economic growth. Upon the implementation of this strategy in practice enhanced focus need to be directed to young professionals in Uganda, because investments in their training and development can provide substantial benefits in long-term perspectives.

Conclusions

International aid to Uganda and other poor countries in Africa can be both, part of the problem or part of the solution for the issues of poverty reduction and achieving economic growth. So far due to a set of specific factors international aid has proved to be part of the problem towards the issues of poverty reduction and achieving economic growth in Uganda.

Specifically, these factors include but not limited to the lack of incentives for government officials to promote economic growth and extremely high levels of corruption within various government ranks

It is evident that despite the massive part of foreign aid being stolen by local authorities, foreign aid can assist Ugandan people to a certain extent. This is because food can be provided to poor people, as well as, schools can be built from a small fraction of foreign aid that eventually reaches the people it was intended for in the first place.

However, the provision of foreign aid in the forms of food, cash and debt relief is only short-sighted approach to the issue, and the solution of problems for long-term perspectives require deep institutional changes.

Today foreign aid in Uganda is found to be subsidising a high level of corruption and incompetence of government officials and thus the provision of foreign aid in its present form needs to be subjected to immediate and comprehensive critical evaluation.

This essay has outlined a set of available opportunities that the government of Uganda can explore in order to decrease the level of dependency to foreign aid. These opportunities have been found to include reforming public expenditures, reforming the country’s taxation system, increasing the levels of domestic investment, and achieving better deals for its agricultural products in an international market. Moreover, the government of Uganda needs to engage in explorations and search for natural resources within its borders, as the discovery of large oil reserve in the Lake Alberta can be interpreted as an indication of the presence of other similar reserves.

Problems in Uganda and many other countries in African continent need to be solved internally, rather than externally. Internal solutions are directly related to modernisation of policies and a wide range of important domestic institutions. The sources of revenues for Ugandan government need to be changed from foreign aid to revenues generated from the private sector. However, in order to achieve this appropriate policy changes need to be introduced and adequate infrastructure needs to be developed for the private sector.

Baby Milk Action (1997) Available at: http://www.babymilkaction.org/boycott/boyct18.html
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Barlas, R. & Yong, J.L. (2010) “Uganda” Marshall Gavendish Benchmark
Bulir, A., Daniel, J. & Alma, R.B. (2011) “Dynamic Implications of Debt Relief for Low-Income Countries” Working Paper, IMF
Branch, A. (2011) “Displacing Human Rights: War and Intervention in Northern Uganda” Oxford University Press
Briggs, P. (2010) “Uganda” Bradt Travel Guides
Callinicos, A. (2009) “Imperialism and Global Political Economy”, Polity.
Ernst, J. (2011) “Aid Collaboration in Uganda” International Affairs Review , Vol. XX, No1, Winter 2011.
Ford, L. (2010) “Donors threaten to cut aid to Uganda over corruption” The Guardian, Available at: http://www.guardian.co.uk/katine/2010/mar/04/donor-threat-uganda-aid
Kasimbazi, E. & Alexander, K. (2011) “Environmental Law in Uganda” Kluwer Law International
Lancaster, C. (2007) “Foreign Aid: Diplomacy, Development, Domestic Politics” University of Chicago Press
Leggett, I. (2001) “Uganda: The Background, The Issues, the People” Oxfam
Lundsgaarde, E. (2012) “The Domestic Politics of Foreign Aid” Routledge
Moyo, D. (2009) “Why Foreign Aid Is Hurting Africa” Wall Street Journal , March 31, 2009
Mwenda, A. (2006) “Foreign Aid and the Weakening of Democratic Accountability in Uganda” Foreign Policy Briefing
Ravenhill, J. (2008) “Global Political Economy”, 2 nd edition, Oxford: Oxford University Press.
Sumner, A. & Mallett, R. (2013) “The Future of Foreign Aid” Palgrave Macmillan
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UN Millennium Project Report (2005) UN
Williams, D (2011) “International Development and Global Politics: History, Theory and Practice” Routledge

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Decolonizing Health Governance: A Uganda Case Study on the Influence of Political History on Community Participation

Volume 23/1, June 2021, pp. 259-271

Moses Mulumba, Ana Lorena Ruano, Katrina Perehudoff, and Gorik Ooms

This paper presents a case study of how colonial legacies in Uganda have affected the shape and breadth of community participation in health system governance. Using Habermas’s theory of deliberative democracy and the right to health, we examine the key components required for decolonizing health governance in postcolonial countries. We argue that colonization distorts community participation, which is critical for building a strong state and a responsive health system. Participation processes grounded in the principles of democracy and the right to health increase public trust in health governance. The introduction and maintenance of British laws in Uganda, and their influence over local health governance, denies citizens the opportunity to participate in key decisions that affect them, which impacts public trust in the government. Postcolonial societies must tackle how imported legal frameworks exclude and limit community participation. Without meaningful participation, health policy implementation and accountability will remain elusive.

Introduction

Community participation is a critically important component of building public trust in health governance, as well as a key feature of the right to health. [1] It refers to the free, active, meaningful, and inclusive processes through which people make decisions on issues that affect them, their families, and their communities. [2] Colonialism deeply affects a country’s social fabric and inherently changes social, cultural, political, and economic structures in a way that continues to be felt decades after independence. [3] Using elements of Jürgen Habermas’s theory of deliberative democracy and the right to health as normative frameworks, this paper examines the legacies of colonialism in Uganda and how they have affected community participation in health system governance. We propose that health system decolonization requires embedding community participation through policies that incentivize historically marginalized and excluded groups to better disperse decision-making power, which is a consequential first step in truly achieving self-determination.

Colonization disrupts people’s connection to the land and forces a new country identity on existing cultures, communities, and families, and does so through policies that seek to control, stigmatize, and intervene in their lives. [4] Decolonization calls for the dismantling of several layers of complex and entrenched colonial structures, ideologies, narratives, identities, and practices, as well a reconstruction process that focuses on reclaiming humanity, rebuilding bodily integrity, and reasserting self-determination. [5] The political, economic, social, and cultural control that was leveraged on an occupied nation breaks down local social fabrics and creates inequality and public mistrust in the governance system. As a result, some populations become more and more excluded, and these historical cycles of disempowerment lead to further exclusion. [6] Colonialism also shapes the health system and all governance processes within, with a history of colonization acting as a key determinant of health for many vulnerable population groups.

Decolonizing health systems allows for a return of community participation that establishes true partnerships between communities and decision makers through empowerment cycles. Getting rid of the lasting impact of colonization calls for raising citizen awareness of rights and obligations and building collective action that promotes self-determination through dedicated policy frameworks and incentives that help ensure the dispersion of decision-making power in health policy. [7] This diffuses decision-making power among more stakeholders and ensures that health services reflect local needs, which increases communities’ control over maintaining and improving their health. [8] However, establishing these processes in contexts of exclusion and marginalization requires time and sustained support that allows for the reconfiguration of societal-level power dynamics. [9] This is crucial for strengthening public trust in health governance, which is a central building block of health systems’ ability to provide services efficiently, effectively, and equitably. [10]

Like many countries in Sub-Saharan Africa and around the world, Uganda struggles with a recent colonial past and its legacy. In many former colonies, the effects of often brutal and forced colonization influence all aspects related to governance well into postcolonial self-rule. [11] Table 1 shows how many sub-Saharan countries were under colonial rule from as early as the late 1890s and began achieving independence only in the 1960s. For South Sudan, this came as late 2011. Today, almost all low-income countries in Sub-Saharan Africa have serious health governance challenges, and most still struggle with their colonial legacies.

We argue that achieving the highest attainable standard of health is intrinsically linked to Habermas’s theory of deliberative democracy. Communicative action, the power of speech, legitimacy, and the principles of legitimacy and the public sphere shape community participation and affect the way that communities engage with the health system and enjoy their right to health. Many postcolonial societies with weak deliberative democracy values continue to struggle with democracy because colonization impacted self-determination, which limits popular sovereignty, especially in context of extreme poverty and resource constraints. [12] This exclusion delegitimizes the public space, which is coopted by officials who were not elected by the people. This weakens democracy and increases authoritarian leadership, hence impacting public trust in the health system’s governance. [13] Democracy and human rights are co-original and can act in virtuous cycles of empowerment when they integrate previously excluded groups and lead to the type of systemic change that dismantles colonial structures at the ideological and practical level. Finally, community participation is central to the realization of the right to health, as stated in the United Nations Committee on Economic, Social and Cultural Rights’ General Comment 14. [14] By framing participation disparities as rights violations, public health advocates can draw on international legal standards to frame responsibilities and evaluate policies, shifting the analysis of health reform from a focus on the quality of care to one on social justice. [15]

Colonial governments’ dominance of their colonies required achieving control over the territory, which in turn involved the erosion of self-determination and the imposition of a rule rooted in the colonizer’s beliefs and practices. [16] Oftentimes, this translated into the enforcement of a foreign culture, religion, and social mores and customs through the slave trade, misappropriated natural resources, exploitative trade relations, and unfavorable means of producing wealth. [17] Such foreign systems of rule of law limited local peoples’ self-determination and sovereignty, for subjected communities were beholden to laws that they had not participated in making. The repressive systems that crushed Indigenous legal and health systems also disregarded local traditional values, which were then replaced by those of the colonial rules. These systems include the health system, which was organized by the colonizers based on their own ideas and beliefs around the type and number of services that should be provided to the local population.

As the Ugandan case study demonstrates, postcolonial countries continue to grapple with the impacts of colonial values on their legal and health systems. Laws criminalizing abortion and same-sex unions are just some examples. The missionary hospitals and schools introduced during colonial rule continue to account for almost 20% of Uganda’s health and education systems. [18] The values that guide these systems, instituted through colonial rule, disregard current scientific knowledge and human rights and represent key challenges to the delivery of empowering and liberating health and education systems. Uganda provides a good case study on the influence of political history on community participation.

This paper uses a qualitative, historical case-study methodology and is guided by an analysis of the political history of community participation in Uganda from the precolonial, colonial, and postcolonial periods. [19] The literature review included publicly available documents located through online searches for academic articles, government documents, nongovernmental organization (NGO) reports, and other gray literature. The publications considered were published in English and used rights-based approaches to health system strengthening. Additionally, publications that described or contextualized the historical events that shaped Uganda’s political setup and a health system were included in the study.

We analyzed data through a content analysis using two normative frameworks: (1) Habermas’s concept of deliberative democracy and (2) the right to health framework. Both frameworks center around the concept of community participation whereby people and communities are at the center of decision-making processes in health. These frameworks emphasize the tenets of the power of speech, legitimacy, and the public sphere, and they advance the argument that the decolonization of health systems is important for allowing community participation in health systems to thrive.

Our analysis focused on understanding the colonial period’s subrogation of community participation and public trust in health governance. By applying the normative guidance provided by Habermas’s deliberative democracy framework and the right to health framework, we uncovered the need for decolonization that emphasizes community participation as part of building public trust in the health system.

The Uganda case study

Uganda provides an opportunity for studying the historical and political influences of colonialism on community participation as an integral part of the right to health and health governance generally. Uganda has transitioned through the precolonial, colonial, and present-day periods of developing a democracy and a health system. The formation of its national development agenda in the post-colonial period and the rolling out of its decentralized health system also offers an opportunity to examine the colonial influences on the structures for community participation through the lens of constitutional provisions, local government legislation, and other policy frameworks that provide the foundation for operationalizing community participation. Through periodization into precolonial, colonial, and postcolonial, the history of the country allows us to critically assess the extent to which community participation was lost during the colonial period. This then provides a basis for examining the decolonization steps needed to bring back community participation as part of good health governance. As we argue, it is difficult to separate Uganda’s current health system from its colonial and political history, as the latter continues to influence the architecture of the health system today.

Precolonial community participation

During the precolonial period, communities organized around kingdoms, in which community participation was a key social tenet. [20] For example, in the Buganda Kingdom, kingship was made into a kind of state lottery in which all clans could participate. [21] The community consolidated its efforts behind a centralized kingship, and this provided the community an opportunity to expand. Everyday life was organized around communal efforts. Social capital was critical for mobilization, which included rotating groups for labor sharing in the clearing, planting, weeding, and harvesting stages of agriculture, as well as emergency-oriented arrangements, such as local burial assistance groups that provided material and psychosocial support to bereaved families. [22] Community participation evolved around self-help projects, which enhanced communities’ economic and social welfare through a scheme called bulungi bwansi (“for the good of the community”). [23] Community participation was therefore interwoven into the fabric of precolonial Ugandan society. It also included some features of deliberative democracy and the right to health.

The practice of traditional medicine was the only health system that existed in Uganda during the precolonial period. [24] Traditional medicine practitioners included herbalists, bonesetters, psychic healers, birth attendants, faith healers, diviners, and spiritualists who used Indigenous knowledge to develop materials and procedures. [25] Despite the colonial government’s suppression of traditional medicine practitioners, traditional medicine survived colonization and continues to play a role in Uganda’s present-day health system. The question of regulating these practices remains a major health governance issue for Uganda’s health system. Communities have continued to demonstrate trust in traditional healers, despite the documented public health hazards that they have caused.

The key lesson from this period is that in the quest for a normative community participation structure that decolonizes health governance, Indigenous ideas and innovation should be taken into account. This is especially important when trying to understand the public sphere and how culture, attributes, beliefs, and norms can inform the normative structure of community participation. [26] In applying the human rights framework, validating and empowering these Indigenous spaces is important for advancing the right to participation as enshrined in international human rights law.

Community participation during Uganda’s colonial period

Uganda was a protectorate of the British Empire from 1894 to 1962, and although the economic, social, and political landscape changed dramatically, the country retained a degree of self-government that was uncommon. [27] Different Indigenous communities now inhabiting the country were brought together during the colonial period following the declaration of a British protectorate over Uganda in 1894. [28] Political dispensations unified traditional kingdoms that had enjoyed sovereign powers until then. New lawmaking processes were developed in Britain and enforced first in Buganda and quickly expanded to other kingdoms. The period saw many developments that would later shape the discussion on community participation in health governance amid British rule and the continued influence of the kingdoms.

The colonial administration imposed its own system of administration through indirect rule, whereby the British administered the protectorate through local chiefs and kings, who surrendered sovereignty in return for British protection. Because the colonialists obliged certain communities to merge, the uniformity of former autonomous chiefdoms was lost along with traditional practices of community participation. [29] The traditional discursive spaces were dismantled as the British enforced their rules and introduced forced labor and exploitative tax systems.

During this period, Britain signed a number of agreements with both Buganda as a kingdom and later Uganda as a protectorate that spelled out governance issues between the colonizers and the colony. [30] Through these agreements, Britain shaped the structure of government, including provisional administrative decisions and the administration of justice and maintenance of order. [31] However, the structures introduced were devoid of key elements of deliberative democracy, such as a public sphere. Local communities were excluded from formal decision-making, which was now the exclusive competence of the colonial rulers. At the signing of the 1900 Buganda Agreement, for instance, the Buganda signatories were allowed only to append signatures, and there is no evidence of them being included in the development of the agreement itself. [32] Therefore, the Buganda Agreement was not a legitimate instrument when seen through the lens of deliberative democracy.

The agreement then became part of Uganda’s modern legal system. Interestingly, it also introduced the concept of public interest, which was not discussed but mentions cursorily that government was to be the custodian of resources on behalf of the people. Today, the families and communities affiliated with those who benefited from the Buganda Agreement continue to dominate land ownership. Given the centrality of land as a resource, a large amount of decision-making power is now concentrated among a few families, and critical processes such as the allocation of land for health facilities and leadership in community participation structures are still separated from the people who would benefit the most from them. [33] These families act as power centers and exert control in many governance processes, including those related to the health system.

The next significant step that the British government took to solidify its rule in the Protectorate of Uganda after the Buganda Agreement was the establishment of the 1902 Orders in Council. [34] The Orders in Council dealt with matters of constitutional significance and were the benchmark against which many laws in colonial and postcolonial Uganda were built, as they provided the first legal instrument for establishing a legal framework of government for the entire protectorate. [35] Their major limitation was that they brought in UK legal frameworks without any adaptation to the local context. This was in complete disregard of the importance of community participation in legal decision-making for a country. Lord Denning, in the case of Nyali Ltd. v. Attorney General , challenged this practice when he used an analogy of an oak tree and concluded that one cannot transplant an oak tree from English soil and plant it on Kenyan soil and expect it to flourish well like it did before. [36]

Article 15(1) of the 1902 Orders in Council established the judicial system, including the High Court, which was to have full civil and criminal jurisdiction over all persons and matters in Uganda. The court system is critical for health governance given the important role of litigation in health issues, as witnessed in present-day Uganda. The relevance of courts in health governance is visible in the important court decisions and pronouncements in relation to accessing health care. The Constitutional Court, for instance, has ruled that the government’s failure to provide adequate maternal health services violates human rights protected in international treaties and the Ugandan Constitution, including the right to health, the right to life, the rights of women, and the prohibition of inhuman and degrading treatment. [37] The courts have also declared the criminal legislation concerning mental health as violating rights and have called for provisions that better enhance the rights of persons with disabilities. [38] The colonial procedural challenges in the usage of courts to advance health have seen some of these cases take as long as nine years to be decided.

Although the 1902 Orders in Council put in place the basic elements and structures of government, they did not further democracy in the protectorate. Uganda remained under direct control of the British, and there was no Indigenous representation within the government. The concept of democracy calls for the representation of people in government, and their exclusion signals an absence of it. The subjugation of community participation and the direct importation of British laws denied Ugandans the opportunity to participate in key decisions that affected them. As Kwanele Asante has argued, a non-rights-based approach absolves state parties of their duty to ensure that patients (communities) are substantively involved in the development of key health policies. [39] We agree with Asante that diluted community inclusion not only absolves states of their human rights duties with respect to the right to health and right to participate, but also renders communities unable to hold policy makers and governments accountable for inadequately discharging their right to health duties.

The control of sleeping sickness—the focal medical policy between 1900–1908—is an example of the implications of the aforementioned colonial governance structures for health. Sleeping sickness is caused by the tsetse fly, commonly found in tropical climates, including the region around Lake Victoria in Uganda. Kirk Arden Hoppe recounts how from 1906 onward local ordinances devoid of community participation were imposed by British rulers under the guise of disease control. For example, the Entebbe Township Ordinance of 1906 permitted the inspection and punishment of Ugandan canoe owners and crew who were found to have a tsetse fly on board. Punishment was in the form of a fine or one month’s imprisonment. The 1907 Uganda Fishing Ordinance made it illegal to fish on Lake Victoria and to possess or sell lake fish, which was an important source of nutrition and income for local Ugandans. In 1908 and 1909, health regulations were issued to consolidate and later evict 33 island communities in Lake Victoria to the mainland. Although framed as a disease control initiative, these regulations were a covert method of strategically depopulating people from an area (the Lake Victoria region) rich in hunting, fishing, and charcoal. [40]

These laws and regulations further marginalized Ugandans by depriving them of interdependent civil, economic, and social rights, including autonomy and the social determinants of health. Ugandans affected by these rules had no avenue for recourse to hold colonial decision-makers accountable, which is an essential component of the right to health. However, by the time of independence, Uganda had begun to witness some form of democracy that would see citizens participate in decision-making on issues affecting them.

Health governance in the colonial period

The colonial period saw the introduction of the formal health system through the establishment of mission hospitals. By 1909, three health centers in Mulago, Mengo, and Masaka were established for the treatment of venereal diseases, a new epidemic that affected mostly Europeans doing the postcolonial work and Indians who had been brought in to develop the infrastructure. Controlling venereal disease was a core medical policy of the colonial government from 1908 until the 1920s. [41] The Mulago health center was later developed into a general national referral hospital for venereal diseases. More hospitals and dispensaries were established in provincial and district headquarters throughout Uganda. These institutions were planned from the central level and without any community participation. Moreover, the epidemic of venereal disease was an opportunity for the colonial government to exert social control and to impose notions about sexuality and Christian values brought by missionaries. [42] These ideas, differing from local conceptions of venereal disease, were later enshrined in the Venereal Diseases Act of 1977. [43] One example of how the Venereal Disease Act violates the right to health is the requirement that a person with a sexually transmitted disease identify the person who infected him or her. Such forced disclosure tears at the social fabric of a community.

However, it was also during the colonial period that Uganda first witnessed a form of decentralization, when the British secretary for colonial administration made it colonial policy to promote the creation of local governments. This decentralization influenced Uganda’s health system through the introduction of health subdistricts.

The colonial control systems equated the practice of traditional medicine with witchcraft. As a result, the colonial government introduced the Witchcraft Act in 1957, which had provisions for the prevention of witchcraft and punishments for persons practicing witchcraft. In this way, the law attempted to strip Ugandans of the informal health system offered by traditional medicine. In 1997, the Supreme Court of Uganda, in the case of Salvatori Abuki and Richard Abuga v. Attorney General , held section 7 of this legislation unconstitutional for permitting the banishment of persons convicted of practicing witchcraft from their homes. [44] This judgment is a good example of some of the efforts to decolonize legislation introduced during colonial times. The judgment emphasized the importance of measuring the colonial laws against Uganda’s constitutional values.

Much of the health-related legislation that remains on the books today was imposed through the doctrine of legal reception, in which the British legal culture was transferred to Uganda. Laws such as the Public Health Act (1935), the Mental Treatment Act (1938), the Venereal Diseases Act (1977), the Penal Code Act (1950), and many others still affect health governance in Uganda. Starting in the 1930s, the colonial government shifted its medical focus to public health policy. [45] During this time, many laws relating to public health were adopted and have not been comprehensively reviewed since. Changing socioeconomic conditions call for legal frameworks to be updated, and often strengthened. [46] Some of these laws have been criticized for being restrictive in the area of reproductive rights, such as with regard to sexual orientation and access to safe and legal abortion. [47] In such cases, as part of decolonization, it is important to open a participatory dialogue around legal review to address gaps between policy, law, and practice.

It is also important to note that while colonial laws have stayed on the books, a number of areas that these laws targeted—such as harmful practices by traditional healers—continue today. For example, the recent wave of ritual murders, including child sacrifice, have prompted Ugandan parliamentarians to call for a law regulating the activities and practices of traditional healers and herbalists. [48] Abortion practices criminalized in the colonial Penal Code Act continue to contribute 1,200 deaths out of the total 6,500 maternal deaths each year. [49] There are also shared positive experiences and preferences by the population to use traditional healers because of their easy access, the ability to pay in installments or in kind for services rendered, and the kindness of traditional birth attendants. [50] These are important indications of the need to ensure community participation in the development of new regulatory frameworks that could address the country’s current health governance needs.

Postcolonial Uganda and community participation

Uganda gained independence on October 9, 1962, with signs of constitutionalism. [51] A constitution had been worked out as a result of negotiation among the major political actors. [52] Direct universal suffrage was put in place except for Buganda, where representatives to Parliament were indirectly elected through the Council of Buganda. On the first anniversary of independence, the Constitution was amended by Parliament to provide for a ceremonial president to replace the governor-general. [53] Overall, postcolonial Uganda had a mix of struggles to establish democratic structures and an early turbulent time with civil wars and coups that saw the obliteration of the earlier democratic structures that would have facilitated community participation in the health system. The post-colonial Uganda descended into dictatorial regimes in the tenures of Milton Obote, Idi Amin, Yusuf Lule, and Godfrey Binaisa, a period that did not feature community participation in decision-making for the country. In 1971, for instance, President Idi Amin Dada contradicted most of the constitutional provisions of 1962 and 1966. He denied Ugandan citizens democracy and ruled by decree.

Developments in the health system included the creation of the Ministry of Health, which had been formed just before independence to replace the colonial medical department responsible for medical services. [54] In addition, missionary health organizations provided health services in rural and urban areas through cost sharing. [55] The most important factors affecting the provision of socialized health services were the prevailing economic and political conditions in the country.

The government and its Ministry of Health had an ambitious program to build 22 100-bed hospitals, which was feasible due to the country’s economic prosperity between 1962 and 1971, during the first tenure of President Obote. [56] The country had four recognized health care service types and levels: (1) primary health care, consisting of centers and clinics; (2) secondary health care, consisting of district hospitals; (3) tertiary health care, consisting of general referral hospitals; and (4) quaternary health care, consisting of two national referral hospitals. [57] There were regional referral hospitals throughout the country. The role of health in Uganda’s development was one of high priority. The country’s planning strategies had health services and education as one of three important development goals. [58]

Uganda’s health system was going through some important reforms, but there is no evidence of community participation in the making of the policies or the implementation of health reforms during this period. The challenges that resulted from this nonparticipation were the adoption of reforms based on technical considerations without the integration of community perspectives. As a result, some of the health governance structures (such as health unit management committees) do not respond to community needs, and communities do not view them as “theirs.” This approach advances a colonial legacy of focusing on communities as passive beneficiaries.

The political and economic turmoil of the 1970s and 1980s also severely curtailed community engagement in the health systems. Social services, including health, broke down. [59] The working environment in the health sector became hostile, and many physicians migrated to other countries for security and economic reasons. Medicines, equipment, and hospital facilities were in limited supply, and the quality of health care fell drastically. At the same time, an unregulated private sector mushroomed rapidly to fill the services gap created by the poorly functioning government facilities that dominated the colonial health system architecture. This situation dashed any hopes of building a health system grounded in community participation.

After independence in 1962, efforts to strengthen national and cultural identities began to reemerge. For instance, it is now clear that the government is interested in providing support to the practice of traditional medicine. The repeal of the 1968 Medical and Dental Practitioners Act in 1996 created a situation in which traditional practitioners are tolerated as long as they do not claim to be registered medical practitioners. [60]

During this postcolonial period, a number of colonial laws have been successfully challenged before Ugandan courts as unconstitutional and in violation of human rights standards. For instance, section 130 of the Penal Code Act has been held unconstitutional insofar as it refers to persons with mental disabilities as idiots and imbeciles. [61] In this case, the petitioners successfully argued that the Penal Code subjected persons with mental disabilities to inhuman and degrading treatment, contrary to articles 24 and 35 of Uganda’s Constitution.

This paper has demonstrated that understanding a country’s historical context is key for decolonizing its health governance. Through the Ugandan case study, we have identified key events that are central in defining a basis for decolonizing governance in health systems. The colonial legacy in Uganda imposed values and systems that undermined self-determination and sovereignty, which eroded even the most cherished precolonial systems that would provide a base for community participation as part of health governance.

While there was no defined formal space for participation in the delivery of health services in precolonial Uganda, the few existing informal spaces for community participation demonstrate the importance of community participation in decision-making on issues that affect them. However, during colonial times, there was clear subjugation of community participation in Uganda’s governance, which left a legacy that problematized precolonial arrangements; failed to appreciate and uphold the strength of Indigenous systems; created a conflicting situation within Ugandan society; and diminished public trust in health governance. There are still some practices of community joint work through bulungi bwansi that are still visible even in other postcolonial countries such as Rwanda, which takes the form of Umuganda . [62]

The precolonial systems that brought communities together were particularly important for vulnerable groups such as women, who had spaces for addressing their social issues, including health. The introduction of laws such as the Buganda Agreement took away key land resources from the communities, severing their means of welfare and access to the social determinants of health. This agreement also made them subject to royal rule, eroding their autonomy, community systems of health governance, and voice in health decision-making. This marginalized many Ugandans, made them vulnerable to ill-health, and imposed barriers to forming, contributing to, and accessing health care. These challenges continue to exist among landless communities.

The direct importation of British laws and the continued influence of Britain in Uganda’s governance denied Ugandans the opportunity to participate in key decisions that affected their health. Laws were devoid of the legitimacy envisioned by Habermas, and the previous spaces of community participation in precolonial Uganda were eroded. The imposition of a judicial system through the Orders in Council not only undermined the Indigenous justice system but also introduced a judicial system that still adjudicates on right to health cases with procedural complexities. The current legal technicalities that undermine the enforcement of the right to health and limit judicial interpretation of justice issues in the health system at the national level can be traced from the colonial legacy.

A number of colonial laws are still being applied, and while some laws have been amended, a number of them have not been subjected to the discursive test as advanced by Habermas. The most contested aspects of sexual and reproductive health and rights—such as access to safe and legal abortion, sexual orientation, comprehensive sexuality education, access to family planning, and control of venereal diseases—are still regulated through colonial legislation such as the Penal Code Act of 1950 and the Public Health Act of 1935. These laws perpetuate colonial attempts at social control and the degradation of Indigenous community fabrics.

The decolonization process requires that Uganda undertake a legal audit of all its laws and policies to assess them through the lens of human rights and current scientific evidence. The Uganda Law Reform Commission should create public spheres as spaces for discussing the areas of weakness in these laws. The parliamentary lawmaking process should equally have opportunities for people to speak and deliver opinions on aspects that the laws should address. The outcome should be laws that meet the test of legitimacy as guided by Habermas’s views of deliberative democracy.

The current model of delivery of health services is still built largely on the colonial model. Missionary hospitals dominate the provision of health care, delivering care aligned with religious values, which permeate training schools organized by religious groups that were introduced by colonizers.

The colonial period also introduced missionary NGOs that deliver health care through a cost-sharing mechanism that has persisted as part of Uganda’s health system. These NGOs remain a major force in promoting religious-values-based health care delivery and have in many cases openly opposed the implementation of progressive sexual and reproductive health and rights policies. Such efforts have impeded the implementation of a human rights-based approach as part of Uganda’s health governance. Part of the decolonization process would require that Uganda, as a postcolonial country, revisit its NGO policies and ensure a regulatory framework that insulates NGO mission work from a biased model of delivery of health services based solely on religious values. This process could include a deliberate effort to build, support, and include the work of Indigenous NGOs that advance a science- and rights-based approach to health services delivery and advocacy as part of government programming. Such Indigenous NGOs can provide a forum for community participation in the delivery of health services and in decision-making around priorities for the health system.

The current structure of Ugandan health facilities is still rooted in the architecture of the colonial masters, and the upgrading of hospitals and other health facilities has been slow. The division between the delivery of physical health and the delivery of mental health introduced during colonial times continues to be the model today. This separation has led to mental health being undermined and overlooked in mainstream programming. The decolonization process requires that the design and capacities of national referral hospitals, regional referral hospitals, and other health facilities be upgraded from the colonial estimations that were based on Uganda’s population and public health needs then. In undertaking this process, the government should end the practice of making plans and decisions in technical offices without engaging local communities. The design of such health facilities should be infused with ideas of the context-specific needs of the communities where such health facilities are being proposed. This will in many ways help ensure that health facilities are designed for and embraced by the communities they serve.

The colonial training models for health professionals have continued to guide medical training in Uganda. Colonial high schools and post-high school institutions continue to dominate Uganda’s education system. In many of these schools, future health professionals receive training based on religious values that were imposed by colonial governments. The danger of such an approach has been the churning out of health professionals and policy makers who base their decisions on religious values as opposed to science and human rights. The decolonization process requires that the education system be scrutinized through a comprehensive stakeholder consultation process to ensure the maximum participation of all those affected. Impacts of the colonial legacy should be expunged and replaced with the present needs. The various training curricula should be revised and upgraded to address current training needs that result in professionals who base their decisions on evidence- and rights-based approaches. Training of trainers’ modules and workshops should be undertaken to examine the best postcolonial methodologies for training health professionals. Such methodologies should be grounded in contextual needs to ensure relevancy.

In conclusion, for the decolonization of health governance in postcolonial countries, a conceptual framework combining deliberative democracy and the right to health is needed. Decolonization calls for arrangements that strive for community participation, Indigenous ideas, and national sovereignty. This process should also take into account Habermas’s concept of deliberative democracy, which emphasizes the importance of focusing on the tenets of power of speech, legitimacy, and the public sphere.

As part of the conceptual framework grounded in the right to health and deliberative democracy, decolonizing community participation must be premised on the recognition of each person as a valid speaking partner with a unique and valuable knowledge to contribute. Thus, respect for the inherent dignity of persons and self-determination must inform all participatory processes and strategies, and each person’s expertise, experience, and input must be valued. Local ownership and community context should inform decision-making in the health sector. This calls for efforts to examine the history and diversity of the community as important elements for shaping effective and efficient community participation as part of the right to health. Respecting local knowledge, the ability of communities, and their potential is key for decolonizing health systems that are participatory. Overall, participation should go beyond mere consultation and should build community capacity and foster public mobilization and awareness.

This paper has illustrated how Uganda’s history and political context has shaped the nation’s current system of health governance. We have argued that when decolonizing a postcolonial country’s health governance, its health system cannot be divorced from its political setup. It is thus important that the political history is mapped to identify opportunities for operationalizing decolonization in health governance.

This paper has also demonstrated that a combination of deliberative democracy and right to health principles provides both structural and procedural parameters for community participation as part of decolonization in health governance. The application of these standards, however, is highly dependent on the context of each country and community. It is therefore important to indigenize this theoretical framework. We recommend that countries undertaking decolonization strive to embed the principles of the rule of law—including respect for the right to community participation and self-determination—in order to dismantle colonial legacies.

Moses Mulumba, LLB, LLM, MPhil, is the Executive Director of the Center for Health, Human Rights and Development, Kampala, Uganda, and a doctoral researcher at the Faculty of Medicine and Health Sciences, Ghent University, Belgium.

Ana Lorena Ruano, PhD, is an Associate Professor at the Center for International Health, Department of Global Public Health and Primary Care, University of Bergen, Norway, and a researcher at the Center for the Study of Equity and Governance in Health Systems, Guatemala City, Guatemala.

Katrina Perehudoff, PhD, LLM, MSc, is Senior Research Fellow and Co-Director of the Law Centre for Health and Life at the University of Amsterdam, Netherlands; a Post-Doctoral Assistant at the International Centre for Reproductive Health at Ghent University, Belgium; and a Fellow at the Amsterdam Institute for Global Health and Development, Netherlands.

Gorik Ooms, LicJur, PhD, is a Professor in the Department of Public Health and Primary Care, Ghent University, Belgium.

Please address correspondence to Moses Mulumba. Email: [email protected].

Competing interests: None declared.

Copyright © 2021 Mulumba, Ruano, Perehudoff, and Ooms. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits unrestricted noncommercial use, distribution, and reproduction.

Acknowledgment

This research benefited from funding from the Flemish Interuniversity Council (VLIR-UOS) and the Belgian Directorate-General for Development Cooperation.

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[43] Ibid; Republic of Uganda, The Venereal Diseases Act (2000).

[44] Salvatori Abuki and Richard Abuga v. Attorney General , Constitutional Case No. 2 of 1997.

[45] Hoppe (see note 40), p. 247.

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The influence of transportation limitations on spatial development (a case study of fezzan region), ahmed mohamed alhodairi.

Mohamed Wali Abdulgader Al-Shareif

Transportation plays a fundamental and important role in the progress and development of nations, and it contributes significantly to all other human activities, influencing them and being influenced by them. The existence of an integrated transport and mobility system encourages investors to invest in areas that were previously inaccessible, giving them the opportunity to invest resources in those areas directly or through accompanying investment activities that benefit them and provide employment opportunities for individuals and groups, thus achieving comprehensive local development: economic, social and environmental. This paper examines and analyzes the transportation system in the region of Fezzan in order to identify the main factors that hinder the spread and growth of the network in the region, and thus its impact on spatial development. This system suffers from many shortcomings, both technical and operational, and in its current state it cannot meet the requirements of the region for development and progress. The remoteness of some parts of Fezzan, as well as the difficulty of the desert environment that characterizes the region, require serious consideration of alternative methods and support. Therefore, the paper reviews a set of principles that, if implemented, will contribute to achieving sustainability in all its aspects. It would be beneficial to achieve this within a framework of balanced regional and urban development for Fezzan with its cities and villages.

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Published: 25 September 2024

Development of a method for the imputation of the multi-allelic serotonin-transporter-linked polymorphic region (5-HTTLPR) in the Japanese population

Yutaro Yanagida 1 ,
Izumi Naka 2 ,
Yutaka Nakachi 1 ,
Tempei Ikegame 3 ,
Kiyoto Kasai ORCID: orcid.org/0000-0002-4443-4535 3 , 4 , 5 ,
Naoto Kajitani 6 , 7 ,
Minoru Takebayashi 6 ,
Miki Bundo 1 ,
Jun Ohashi 2 &
Kazuya Iwamoto ORCID: orcid.org/0000-0002-1780-692X 1

Journal of Human Genetics ( 2024 ) Cite this article

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Genetics research

Serotonin-transporter-linked polymorphic region (5-HTTLPR), a variable number of tandem repeats in the promoter region of serotonin transporter gene, is classified into short (S) and long (L) alleles. Initial case-control association studies claiming the risks of the S allele in depression and anxiety were not completely supported by recent studies. However, most studies, especially those on East Asian populations, have overlooked the complexity of 5-HTTLPR, which involves multiple different alleles with distinct functional properties. To address this issue, distinguishing multiple 5-HTTLPR alleles is essential. Here, using the 5-HTTLPR genotypes previously determined by exhaustive Sanger sequencing of approximately 1,500 Japanese subjects and their comprehensive SNP data, we constructed a method for 5-HTTLPR genotype imputation. We identified 28 tag SNPs for the imputation of four major 5-HTTLPR alleles, which collectively account for 97.6% of 5-HTTLPR alleles in the Japanese population. Our imputation method, achieved an accuracy of 0.872 in cross-validation, will contribute to association analysis of 5-HTTLPR in the Japanese subjects.

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Identification and functional characterization of the extremely long allele of the serotonin transporter-linked polymorphic region

Serotonin transporter functional polymorphisms potentially increase risk of schizophrenia separately and as a haplotype

A summary-statistics-based approach to examine the role of serotonin transporter promoter tandem repeat polymorphism in psychiatric phenotypes

Introduction.

Serotonin (5-hydroxytryptamine, 5-HT) is a neurotransmitter that has a wide range of physiological functions, such as blood coagulation, intestinal peristalsis, bone formation, sleep, feeding, sexual behavior, and mood [ 1 , 2 , 3 ]. In the brain, 5-HT is released from presynaptic vesicles into the synaptic cleft and binds to 5-HT receptors [ 4 , 5 ]. Some of 5-HT in the synaptic cleft is retrieved by a transporter called the 5-HT transporter (5-HTT) for reuse. It is widely believed that one of mechanisms of action of antidepressants is to inhibit this reuptake process.

5-HTT is encoded by SLC6A4 (solute carrier family 6, member 4) on chromosome 17q11.2. The transcriptional activity of this gene is influenced by a variable number of tandem repeats (VNTR) called 5-HTT-linked polymorphic region (5-HTTLPR). The 5-HTTLPR mainly consists of short (S) and long (L) alleles, each of which contains 14 and 16 repeat units, respectively. Each repeat unit is composed of 20–23 bp of highly homologous sequences [ 6 ]. It has been shown that the S allele exhibits weaker transcriptional activity than the L allele [ 7 , 8 , 9 ].

Numerous case-control association studies between 5-HTTLPR and psychiatric traits have been conducted. Most studies have reported an association between increased vulnerability to anxiety or depression in response to environmental stress and the S allele [ 10 , 11 ]. However, recent meta-analyses and case-control studies have failed to support the association [ 12 , 13 ].

On the other hand, the importance of considering the complexity of 5-HTTLPR has been increasingly recognized. At least 22 alleles, including eight different S and eight L variants, and six atypical alleles have been identified thus far [ 14 ]. Importantly, transcriptional activities differ even among the L alleles. The L 16a (L A ) showed the strongest activity among alleles, whereas, L 16d (L G ) and L 16c , the latter of which has been found mainly in Japanese populations, showed low activity, similar to S 14a [ 15 ]. These complexities have been underestimated because the major allele of Caucasian populations is L 16a (51%), followed by S 14a (40%) and L 16d (9%). In Japanese populations, the major allele is S 14a (78.8%), followed by L 16c (4.7%), L 16d (6.8%), and L 16a (7.3%) at roughly equal allele frequencies (AF), as well as atypical alleles (2.4%) [ 14 , 15 , 16 ]. Our recent case-control association studies accounting for these complexities found a significant association between low-activity 5-HTTLPR alleles and increased DNA methylation in male patients with bipolar disorder or schizophrenia [ 17 ].

To determine the 5-HTTLPR, separation of PCR products around the 5-HTTLPR was typically used. Additionally, genotyping of a SNP, rs25531, which can discriminate between L 16a and L 16d, was used for further classification [ 15 ]. In addition, imputation procedures that use comprehensive SNP information have also been developed [ 18 , 19 , 20 ]. One analysis achieved over 90% accuracy of dichotomous S or L genotyping in a Caucasian population [ 21 ]. However, given the intrinsic complexity of the 5-HTTLPR, it is necessary to reconsider the imputation method.

We previously determined the 5-HTTLPR genotypes in a Japanese population from approximately 1500 individuals via exhaustive Sanger sequencing [ 14 ]. By utilizing comprehensive SNP genotyping information obtained from the same cohort, we here developed a novel 5-HTTLPR imputation method for estimating four major alleles (L 16a , L 16c , L 16d , and S 14a ), which account for 97.6% of 5-HTTLPR alleles in the Japanese population [ 14 ]. Our imputation method enables high-throughput determination of 5-HTTLPR and will contribute to the association analysis of 5-HTTLPR in Japanese subjects.

Materials and methods

The subjects used in this study were included in the Arao cohort study, which consists of community-dwelling elderly Japanese individuals in Arao city, Kumamoto prefecture, Japan. The cohort study is a part of The Japan Prospective Studies Collaboration for Aging and Dementia (JPSC-AD) [ 22 ]. We analyzed comprehensive SNP genotyping data and previously genotyped 5-HTTLPR information [ 14 ] of subjects who consented to genetic analysis and had no missing values ( N = 1456, 39.3% male). All subjects were 65 years of age or older, with a mean and standard deviation (SD) of 74.3 and 6.6 years, respectively. The current study was approved by the ethics committee of Kumamoto University.

Genotyping with SNP microarray

Genotyping and imputation of this cohort were conducted as a part of the JPSC-AD study [ 22 ] and were described elsewhere (Furuta et. al., in revision). In brief, an Illumina Japanese Screening Array (Illumina, San Diego, CA, USA), which allowed genotyping of approximately 730,000 SNPs, was used for genotyping. Quality controls were performed at the sample level (e.g., gender discrepancy, sample call rate, close relatives, and outliers) and at the SNP level (e.g., Hardy-Weinberg equilibrium (HWE), call rate, monomorphic SNPs, minor allele count, and frequency difference with reference panels). The imputation was performed using Minimac4 v1.0.0 ( https://github.com/statgen/Minimac4 ). The reference panels included 1037 whole genome sequences from BioBank Japan and 2504 publicly available whole genome sequences from the 1000 Genomes Project (Phase 3v5) [ 23 ].

Tag SNPs for the four major 5-HTTLPR alleles

All SNPs on the long arm of chromosome 17, where the SLC6A4 locus is located, were extracted from the SNP array data of 1456 subjects. SNPs used for the 5-HTTLPR genotype imputation were further selected as follows: (1) biallelic, (2) minor allele frequency (MAF) > 0.01, (3) P -value of the test for HWE > 0.001. Next, linkage disequilibrium (LD) pruning was conducted for the SNPs selected above under the following conditions: LD threshold, 0.8; window size, 500; and window increment, 50. After LD pruning, 30,242 SNPs remained. Linear regression analysis was conducted to select tag SNPs for the four major 5-HTTLPR alleles (i.e., S 14a , L 16a , L 16c , and L 16d ) from the 30,242 SNPs using SNP & VARIATION SUITE Version 8.9.1. ( https://www.goldenhelix.com/products/SNP_Variation/ ). To perform linear regression analysis, the genotype of each SNP, the explanatory variable in the model, was coded as the number of minor alleles (i.e., 0, 1, or 2). The dependent variable was the number of focal 5-HTTLPR alleles (0, 1, or 2) possessed by each subject. Although the use of more SNPs can tag each 5-HTTLPR allele more precisely, this method is not practical for genotype imputation using PHASE software [ 24 , 25 ]. Therefore, in this study, we attempted to select 30 or fewer tag SNPs. For each 5-HTTLPR allele, we first selected the single SNP with the lowest P -value from the F -test in the simple regression analysis. The F -test indicates whether the linear regression model provides a better fit to the data than a model without explanatory variables. Incidentally, in simple regression analysis, the P -value of the F -test is equal to the P -value of the t -test used to examine if the slope is significantly different from zero. Then, after adding that SNP to the explanatory variables, the second SNP with the smallest P -value obtained from the F -test was selected. In this way, all SNPs identified up to that point were added to the explanatory variables, and the process of selecting the next SNP was repeated. When the P -value for the F -statistic exceeded 10 −10 , all SNPs selected up to that point, excluding the current SNP, were considered the tag SNPs for the focal 5-HTTLPR allele. Finally, 28 tag SNPs were selected for the four 5-HTTLPR alleles.

5-HTTLPR imputation method in a multi-allelic manner

Using 28 tag SNPs, genotype imputation of 5-HTTLPR was conducted using PHASE software version 2.1 ( https://stephenslab.uchicago.edu/phase/download.html ) [ 24 , 25 ]. Because 16 5-HTTLPR alleles were found in our dataset, they were encoded as integer numbers in the input file of the PHASE software. The prediction performance of genotype imputation for the four major 5-HTTLPR alleles was evaluated by four-fold cross-validation. Specifically, data from 1456 subjects were divided into four subsets, each comprising 364 subjects. Each subset was regarded as the test dataset ( N = 364 without 5-HTTLPR genotype information), and the remaining three subsets were regarded as the training dataset ( N = 1092 with 5-HTTLPR genotype information). Genotype imputation for 5-HTTLPR on the test dataset was then performed by alternating the training and test datasets four times. After genotype imputation, the 5-HTTLPR alleles other than S 14a , L 16a L 16c , and L 16d were regarded as X. Results from four cross-validations were aggregated, and overall accuracy, recall, and precision were calculated for the aggregated data ( N = 1456).

Imputation using a previously reported method

The 5-HTTLPR imputation method for estimating the S or L allele was reported using the Family Transitions Project (FTP) and the Center for Antisocial Drug Dependence (CADD)/the Genetics of Antisocial Drug Dependence (GADD) datasets, which primarily comprise individuals of European descent [ 21 ]. In this method, 5-HTTLPR was treated as a single biallelic SNP in hg19 coordinates chr17: 28,564,497. We replicated this method using subjects only with the four major alleles ( N = 1387) based on SNPs after imputation in the same region as the previous paper (hg19 coordinates chr17: 27,064,497 to 30,064,497). To manipulate the Variant Call Format (VCF) file containing the imputed SNP information of the analyzed subjects, we used BCFtools version 1.18 ( https://github.com/samtools/bcftools ). To convert our reference VCF file to a fixed M3VCF file for use with Minimac4, we used Minimac3 version 2.0.1 ( https://github.com/Santy-8128/Minimac3 ). To convert the M3VCF file to an MVCF file and perform imputation, we used Minimac4 version 4.1.6 ( https://github.com/statgen/Minimac4 ). We classified the 5-HTTLPR into three groups (i.e., S/S, S/L, and L/L genotypes) and examined its accuracy in each cross-validation trial using Minimac4. Results of each cross-validation were aggregated to calculate the overall accuracy ( N = 1387).

Data processing and statistical analysis

General data processing was performed using R packages and in-house scripts (R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ ) or in a CentOS Linux release 7.5.1804 environment. Scripts are available upon request.

The 5-HTTLPR alleles and genotypes in the analyzed cohort

The promoter and gene structure of SLC6A4 are shown in Fig. 1a . We previously determined the 5-HTTLPR genotype using Sanger sequencing in a cohort study ( N = 1528) [ 14 ]. Among them, 1456 subjects with available SNP array information were included in this study (Fig. 1b ). The frequencies of the 5-HTTLPR genotypes observed in the 1456 subjects are presented in Supplementary Table 1 . Of the 16 5-HTTLPR alleles detected, the four most frequent alleles were S 14a ( N = 2296, 78.8%), L 16a ( N = 210, 7.2%), L 16c ( N = 138, 4.7%), and L 16d ( N = 198, 6.8%). The combined AF of these alleles was 97.5%.

SLC6A4 structure and work flow of construction of 5-HTTLPR imputation method. a The structure of SLC6A4 . The exon-intron structure, as well as 5-HTTLPR in the promoter region, is shown. 5-HTTLPR information was obtained in a previous study [ 14 ]. b Work flow of tag SNP selection and validation of genotype imputation (see details in Materials and Methods). The shown tag SNPs and 5-HTTLPR were expanded and colored by each associated allele using the UCSC genome browser [ 26 ]

Selection of tag SNPs

To identify tag SNPs for the four major 5-HTTLPR alleles, we extracted all SNPs on the long arm of chromosome 17, where the SLC6A4 locus is located, from the SNP array data. Since none of the extracted SNPs were in perfect LD (i.e., r 2 = 1) with any of the four major 5-HTTLPR alleles, we attempted to identify multiple SNPs to tag each of the four major 5-HTTLPR alleles using linear regression analysis (Fig. 1b ). We identified 28 tag SNPs including eight, seven, four, and nine SNPs for S 14a , L 16a , L 16c , and, L 16d , respectively (Supplementary Table 2 ). The details of the SNP selection procedure are described in the Materials and Methods section.

Validation of imputation using tag SNPs

In this study, genotype imputation was performed using PHASE software 2.1 [ 24 , 25 ]. Genotype imputation performance for the four major 5-HTTLPR alleles was evaluated using four-fold cross-validation. This process consisted of haplotype inference for 28 tag SNPs and 5-HTTLPR alleles followed by 5-HTTLPR genotype imputation for subjects in the test dataset (Fig. 1b ). In cross-validation, the 5-HTTLPR genotype of each of the 1456 subjects was independently estimated. Therefore, the results (i.e., genotypes imputed for four test datasets) from the four-fold cross-validation were merged. The confusion matrix for the 1456 subjects is shown in Fig. 2 . The diagonal elements represent the number of subjects whose predicted genotype matched the true genotype, whereas the off-diagonal elements represent those that were misclassified. The AF of each 5-HTTLPR allele was estimated using the confusion matrix. The major S allele, S 14a , was estimated at 82.3%, and the three major L alleles, L 16a , L 16c , and L 16d , showed frequencies ranging from 3.2% to 6.1%. These estimates were similar to the true AFs (Table 1 ).

Confusion matrix for 5-HTTLPR genotypes. The results from four cross-validations are shown in a single confusion matrix. 5-HTTLPR alleles other than the four major ones are represented as X. The diagonal elements of the confusion matrix indicate the number of cases in which the predicted genotype matched the true genotype

At the genotype level (Fig. 2 ), the accuracy was 0.872 (Supplementary Table 3 ). The recall and precision for the most frequent genotype, S 14a /S 14a were 0.982 and 0.879, respectively. Among the four major genotypes, S 14a /S 14a , S 14a /L 16a , S 14a /L 16c , and S 14a /L 16d , the only genotype with a recall or precision less than 0.7 was S 14a /L 16c (recall: 0.670). Although rare genotypes with 5-HTTLPR alleles other than S 14a , L 16a , L 16c , and L 16d could not be predicted well, the imputation method developed in this study was satisfactory.

We also tested a previously reported imputation method for dichotomous S or L alleles used in the Caucasian population [ 21 ]. For simplicity, we excluded 69 subjects harboring other alleles from the analysis. This method, using 119,207 SNPs extracted from the Japanese population, estimated the 5-HTTLPR genotypes S/S, S/L, and L/L with an accuracy of 0.574 in four-fold cross-validation (Fig. 3 and Supplementary Table 4 ).

Confusion matrix for 5-HTTLPR genotypes by the previous method. The results from four cross-validations are shown in a single confusion matrix. 5-HTTLPR alleles of subjects with the four major ones were classified into S or L types and estimated. The diagonal elements of the confusion matrix indicate the number of cases in which the predicted genotype matched the true genotype

We reported a novel imputation method using 28 tag SNPs for the 5-HTTLPR genotype, which achieved an accuracy of 0.872. This method was made possible using the PHASE software [ 24 , 25 ]. A notable feature of the PHASE software is its ability to perform genotype imputation, even for loci containing three or more alleles such as 5-HTTLPR. We acknowledge that the current accuracy suggests the potential failure to estimate the individual genotypes of approximately 13%, particularly in subjects with alleles other than S 14a , as indicated by the confusion matrix. However, we believe that this accuracy is sufficiently high for estimating multi-allelic VNTR compared to biallelic SNPs. Increasing the number of tag SNPs by including additional rare alleles in the tag SNP selection process could potentially improve accuracy. However, it is important to note that including rare alleles may lead to overfitting of the models. Additionally, while the roles of rare alleles should not be ignored, imputing them is not the focus of this study, as they may not be relevant for typical case-control association studies. If genome-wide SNP data are available for subjects, this method can be applied to large-scale cohorts or case-control studies to examine 5-HTTLPR without direct genotyping experiments and is particularly suitable for Japanese populations.

A previously developed imputation method, which demonstrated remarkable accuracy of over 90% for the FTP and CADD/GADD datasets [ 21 ], exhibited lower accuracy for the Japanese subjects. The FTP and CADD/GADD datasets primarily consist of individuals of European descent. In European populations, L 16a , with 51% AF, accounts for a dominant proportion of L type alleles, comparing with the second most common, L 16d with a mere 9% AF [ 15 ]. Therefore, distinguishing the 5-HTTLPR allele corresponds to classification of S or L type to some extent. However, in the Japanese population, L 16a (7.3%) did not show an obviously high AF, and other L types, L 16c (4.7%) and L 16d (6.8%), showed similar AFs [ 14 ]. Additionally, the structure of LD differs between European and Japanese populations, leading to lower estimation accuracy in the Japanese population.

The rs25531 variant, located within the repeated unit of 5-HTTLPR and used to distinguish between L 16a (L A ) and L 16d (L G ), was not included in the analyzed VCF file after SNP imputation. This exclusion was due to the low allele frequencies of both alleles in the Japanese population and the complexity of flanking repeated units in other alleles. As a result, rs25531 was not selected as one of the tag SNPs in this study.

This study has several limitations. The first is the possibility of overfitting in the present subjects. We estimated 5-HTTLPR using tag SNPs identified in the analysis using the same subjects. Validation of the imputation accuracy by independent Japanese subjects is needed. Second, the method used to select tag SNPs may not be the best practice. Changing the threshold of the P -value in the tag SNP selection procedure would yield different results. However, the accuracy of genotype imputation seems unlikely to be dramatically improved. Finally, although it remains unclear whether the tag SNPs selected in the present study can effectively impute the 5-HTTLPR genotype in other populations, by employing similar approaches as in this study, it appears feasible to develop optimal imputation methods customized for each population.

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This work was supported by JSPS KAKENHI grant numbers JP23H02840, JP23H03838, and JP22K07583, and by AMED grant number JP19dm0207074, JP23dk0207053, JP24wm0625302, and JP24wm0625001, and by JST Moonshot R&D Grant Number JPMJMS2021.

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Yutaro Yanagida, Yutaka Nakachi, Miki Bundo & Kazuya Iwamoto

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Yanagida, Y., Naka, I., Nakachi, Y. et al. Development of a method for the imputation of the multi-allelic serotonin-transporter-linked polymorphic region (5-HTTLPR) in the Japanese population. J Hum Genet (2024). https://doi.org/10.1038/s10038-024-01296-9

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DOI : https://doi.org/10.1038/s10038-024-01296-9

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Article Details

Main Article Content

Mohamed Wali Abdulgader Al-Shareif

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Development of a method for the imputation of the multi-allelic serotonin-transporter-linked polymorphic region (5-HTTLPR) in the Japanese population

Similar content being viewed by others

Identification and functional characterization of the extremely long allele of the serotonin transporter-linked polymorphic region

Serotonin transporter functional polymorphisms potentially increase risk of schizophrenia separately and as a haplotype

A summary-statistics-based approach to examine the role of serotonin transporter promoter tandem repeat polymorphism in psychiatric phenotypes

Materials and methods

Genotyping with SNP microarray

Tag SNPs for the four major 5-HTTLPR alleles

5-HTTLPR imputation method in a multi-allelic manner

Imputation using a previously reported method

Data processing and statistical analysis

The 5-HTTLPR alleles and genotypes in the analyzed cohort

Selection of tag SNPs

Validation of imputation using tag SNPs

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Corresponding authors

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Additional information

Supplementary information

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