Related Articles

Background

Podoconiosis is a neglected tropical disease (NTD) that is prevalent in red clay soil-covered highlands of tropical Africa, Central and South America, and northern India. It is estimated that up to one million cases exist in Ethiopia. This study aimed to estimate the prevalence of podoconiosis in East and West Gojam Zones of Amhara Region in northern Ethiopia.

Methodology/Principal Findings

A cross-sectional household survey was conducted in Debre Eliyas and Dembecha woredas (districts) in East and West Gojam Zones, respectively. The survey covered all 17,553 households in 20 kebeles (administrative subunits) randomly selected from the two woredas. A detailed structured interview was conducted on 1,704 cases of podoconiosis identified in the survey.

Results

The prevalence of podoconiosis in the population aged 15 years and above was found to be 3.3% (95% CI, 3.2% to 3.6%). 87% of cases were in the economically active age group (15–64 years). On average, patients sought treatment five years after the start of the leg swelling. Most subjects had second (42.7%) or third (36.1%) clinical stage disease, 97.9% had mossy lesions, and 53% had open wounds. On average, patients had five episodes of acute adenolymphangitis (ALA) per year and spent a total of 90 days per year with ALA. The median age of first use of shoes and socks were 22 and 23 years, respectively. More men than women owned more than one pair of shoes (61.1% vs. 50.5%; χ2 = 11.6 p = 0.001). At the time of interview, 23.6% of the respondents were barefoot, of whom about two-thirds were women.

Conclusions

This study showed high prevalence of podoconiosis and associated morbidities such as ALA, mossy lesions and open wounds in northern Ethiopia. Predominance of cases at early clinical stage of podoconiosis indicates the potential for reversing the swelling and calls for disease prevention interventions.

Author Summary

Podoconiosis is non-infectious elephantiasis that affects barefoot people that have prolonged exposure to red clay soil. It is common in tropical Africa, central America and northern India. Podoconiosis presents as bilateral below knee swelling. Podoconiosis can be both prevented and controlled by consistently washing feet, wearing shoes, and using antiseptics and emollients. This survey is the biggest conducted to date in Ethiopia: 17,553 households in East and West Gojam Zones of northern Ethiopia were included, and 1,704 patients were identified. We interviewed patients in detail about manifestations of acute attacks (painful inflammation of the foot and leg with swollen lymph nodes and fever), clinical disease stage, treatment seeking, foot washing and shoe wearing practices. We found the prevalence of podoconiosis to be 3.3%. Most patients were farmers, uneducated and within the economically active age group. There was no gender difference in occurrence of podoconiosis and in foot washing practices. The onset of leg swelling and the age of first shoe wearing were similar. We also found delayed treatment seeking and many days confined to bed during acute inflammatory episodes. We conclude that podoconiosis imposes a huge burden in northern Ethiopia.

Background

Podoconiosis is an environmental lymphoedema affecting people living and working barefoot on irritant red clay soil. Podoconiosis is relatively well described in southern Ethiopia, but remains neglected in other parts of the Ethiopian highlands. This study aimed to assess the burden of podoconiosis in rural communities in western Ethiopia.

Methodology/Principal Findings

A cross-sectional study was conducted in Gulliso woreda (district), west Ethiopia. A household survey in the 26 rural kebeles (villages) of this district was conducted to identify podoconiosis patients and to measure disease prevalence. A more detailed study was done in six randomly selected kebeles to describe clinical features of the disease, patients' experiences of foot hygiene, and shoe wearing practice. 1,935 cases of podoconiosis were registered, giving a prevalence of 2.8%. The prevalence was higher in those aged 15–64 years (5.2%) and in females than males (prevalence ratio 2.6∶1). 90.3% of patients were in the 15–64 year age group. In the detailed study, 335 cases were interviewed and their feet assessed. The majority of patients were farmers, uneducated, and poor. Two-third of patients developed the disease before the age of thirty. Almost all patients (97.0%) had experienced adenolymphangitis (ALA - red, hot legs, swollen and painful groin) at least once during the previous year. Patients experienced an average of 5.5 ALA episodes annually, each of average 4.4 days, thus 24 working days were lost annually. The incidence of ALA in podoconiosis patients was higher than that reported for filariasis in other countries. Shoe wearing was limited mainly due to financial problems.

Conclusions

We have documented high podoconiosis prevalence, frequent adenolymphangitis and high disease-related morbidity in west Ethiopia. Interventions must be developed to prevent, treat and control podoconiosis, one of the core neglected tropical diseases in Ethiopia.

Author Summary

Podoconiosis is a chronic non-infectious disease resulting in below-knee swelling of the legs in bare-footed people living in red clay soil areas. It is an important and yet neglected problem in tropical Africa, central and south America, and north India. Podoconiosis can be prevented by consistently wearing shoes and washing feet. We aimed to assess the burden of the disease, to characterize features of the disease, and to describe foot hygiene and shoe wearing practice of patients in west Ethiopia. First, we did a survey of the 26 rural villages. We identified 1,935 podoconiosis patients, giving a prevalence of 2.8%. Podoconiosis was twice as prevalent in females as males. Second, we did a more detailed study among 335 patients in six randomly selected villages. We found that the majority of patients were farmers, uneducated, and poor. The disease developed before the fourth decade of life and the majority of patients became bed-ridden because of frequent attacks of red, hot legs and swollen and painful groin. Shoe wearing was limited mainly due to lack of money. We conclude that podoconiosis imposes a huge burden in west Ethiopia, and recommend that interventions be developed to prevent, treat and control the disease.

Background

Podoconiosis is a non-filarial elephantiasis caused by long-term barefoot exposure to volcanic soils in endemic areas. Irritant silicate particles penetrate the skin, causing a progressive, debilitating lymphoedema of the lower leg, often starting in the second decade of life. A simple patient-led treatment approach appropriate for resource poor settings has been developed, comprising (1) education on aetiology and prevention of podoconiosis, (2) foot hygiene (daily washing with soap, water and an antiseptic), (3) the regular use of emollient, (4) elevation of the limb at night, and (5) emphasis on the consistent use of shoes and socks.

Methodology/Principal Findings

We did a 12-month, non-comparative, longitudinal evaluation of 33 patients newly presenting to one clinic site of a non-government organization (the Mossy Foot Treatment & Prevention Association, MFTPA) in southern Ethiopia. Outcome measures used for the monitoring of disease progress were (1) the clinical staging system for podoconiosis, and (2) the Amharic Dermatology Life Quality Index (DLQI), both of which have been recently validated for use in this setting. Digital photographs were also taken at each visit. Twenty-seven patients completed follow up. Characteristics of patients completing follow-up were not significantly different to those not. Mean clinical stage and lower leg circumference decreased significantly (mean difference -0.67 (95% CI −0.38 to −0.96) and −2.00 (95% CI −1.26 to −2.74), respectively, p<0.001 for both changes). Mean DLQI diminished from 21 (out of a maximum of 30) to 6 (p<0.001). There was a non-significant change in proportion of patients with mossy lesions (p = 0.375).

Conclusions/Significance

This simple, resource-appropriate regimen has a considerable impact both on clinical progression and self-reported quality of life of affected individuals. The regimen appears ideal for scaling up to other endemic regions in Ethiopia and internationally. We recommend that further research in the area include analysis of cost-effectiveness of the regimen.

Author Summary

Podoconiosis is a type of leg swelling that occurs in the tropics among subsistence farmers who spend long hours in contact with irritant soil derived from volcanic parent rock. People with this disease often live in very remote areas far from health facilities, and do not realize that the condition can be treated. A patient association in southern Ethiopia has pioneered low cost treatment. We followed 27 patients with podoconiosis through their first year of treatment. The regimen emphasizes understanding the disease process and self-treatment through foot hygiene, elevation of the limb at night, use of emollients, socks and shoes. We made clinical observations, measured quality of life and took digital photographs at the start and after 12 months of self-treatment. Leg circumference decreased by an average of 2 cm, the stage of disease decreased (indicating improvement) by almost one full stage. Quality of life improved dramatically, with patients reporting levels of life quality equivalent to non-patients. Even in a very resource-scarce setting, we have shown that patients benefit physically and psychologically from understanding the disease and being shown how to look after their feet.

Background

Both podoconiosis and soil-transmitted helminth (STH) infections occur among barefoot people in areas of extreme poverty; however, their co-morbidity has not previously been investigated. We explored the overlap of STH infection and podoconiosis in Southern Ethiopia and quantified their separate and combined effects on prevalent anemia and hemoglobin levels in podoconiosis patients and health controls from the same area.

Methods and Principal Findings

A two-part comparative cross-sectional study was conducted in Wolaita zone, southern Ethiopia. Data were collected from adult patients presenting with clinically confirmed podoconiosis, and unmatched adult neighborhood controls living in the same administrative area. Information on demographic and selected lifestyle factors was collected using interviewer-administered questionnaires. Stool samples were collected and examined qualitatively using the modified formalin-ether sedimentation method. Hemoglobin level was determined using two different methods: hemoglobinometer and automated hematology analyzer. A total of 913 study subjects (677 podoconiosis patients and 236 controls) participated. The prevalence of any STH infection was 47.6% among patients and 33.1% among controls (p<0.001). The prevalence of both hookworm and Trichuris trichiura infections was significantly higher in podoconiosis patients than in controls (AOR 1.74, 95% CI 1.25 to2.42, AOR 6.53, 95% CI 2.34 to 18.22, respectively). Not wearing shoes and being a farmer remained significant independent predictors of infection with any STH. There was a significant interaction between STH infection and podoconiosis on reduction of hemoglobin level (interaction p value = 0.002).

Conclusions

Prevalence of any STH and hookworm infection was higher among podoconiosis patients than among controls. A significant reduction in hemoglobin level was observed among podoconiosis patients co-infected with hookworm and ‘non-hookworm STH’. Promotion of consistent shoe-wearing practices may have double advantages in controlling both podoconiosis and hookworm infection in the study area.

Author Summary

Podoconiosis and soil-transmitted helminth infections are neglected tropical diseases occurring among barefoot people in areas of extreme poverty, and both promote poverty through effects on education, economic productivity and disability. In Ethiopia, little research on podoconiosis has been conducted and though social, economic and psychological burdens have been described, no previous study has investigated co-morbidity with other neglected tropical diseases. We therefore aimed to explore the overlap of soil-transmitted helminth infection and podoconiosis in southern Ethiopia by comparing the prevalence of STH infections among podoconiosis patients and healthy controls. We also demonstrate the separate and combined impact of STH infection and podoconiosis on hemoglobin level. We found that the prevalence of any STH and hookworm infection was higher among podoconiosis patients than among controls. A significant reduction in hemoglobin level was observed among podoconiosis patients co-infected with hookworm and ‘non-hookworm STH’. Based on the current findings, integrated control programs that include targeted anthelminthic distribution to control STH among podoconiosis patients, and promotion of consistent shoe-wearing practices are recommended in the study area.

Background

Podoconiosis is a form of non-filarial elephantiasis that affects barefoot individuals in highland tropical areas. The disease presents with bilateral, asymmetric swelling of the legs, usually confined to below the knee. This study aimed to assess podoconiosis patients’ perceptions of prevention, control, causes and familial clustering of the disease, and to document physical, social and economic impairments associated with the disease, with the ultimate aim of enabling development of tailored interventions in this region.

Methods

This descriptive study is part of the largest cross-sectional community-based household survey yet conducted on podoconiosis. It was completed in November and December, 2011, in Debre Eliyas and Dembecha Woredas of East and West Gojam Zones, northern Ethiopia, and consisted of a house-to-house census by community health workers followed by interviews of identified patients using a structured questionnaire.

Results

In the 17,553 households surveyed, 1,319 patients were identified. More male as compared to female patients were married (84.6% vs. 53.6%, χ2 = 157.1, p < 0.0001) while more female as compared to male patients were divorced (22.5% vs. 3.6%, χ2 = 102.3, p < 0.0001). Less than half of the study subjects believed podoconiosis could be prevented (37.5%) or controlled (40.4%) and many (41.3%) did not know the cause of podoconiosis. Two-fifths of the study subjects had a relative affected with podoconiosis. Approximately 13% of the respondents had experienced one or more forms of social stigmatization. The coping strategies adopted by patients to mitigate the physical impairments caused by podoconiosis were: working only occasionally (44.9%), avoiding physically demanding tasks (32.4%), working fewer hours (21.9%) or completely stopping work (8%). Most study subjects (96.4%) had noticed a decline in their income following the development of podoconiosis, and 78% said they were poorer than their healthy neighbours.

Conclusion

This study shows that podoconiosis has strong psychosocial, physical and economic impacts on patients in East and West Gojam Zones of northern Ethiopia. Concerns related to familial clustering, poor understanding of the causes and prevention of podoconiosis all add to the physical burden imposed by the disease. Strategies that may ease the impact of podoconiosis include delivery of tailored health education on the causes and prevention of disease, involving patients in intervention activities, and development of alternative income-generating activities for treated patients.

Background

The consent process for a genetic study is challenging when the research is conducted in a group stigmatized because of beliefs that the disease is familial. Podoconiosis, also known as 'mossy foot', is an example of such a disease. It is a condition resulting in swelling of the lower legs among people exposed to red clay soil. It is a very stigmatizing problem in endemic areas of Ethiopia because of the widely held opinion that the disease runs in families and is untreatable. The aim of this study was to explore the impact of social stigma on the process of obtaining consent for a study on the genetics of podoconiosis in Southern Ethiopia.

Methods

We adapted a rapid assessment tool validated in The Gambia. The methodology was qualitative involving focus-group discussions (n = 4) and in-depth interviews (n = 25) with community members, fieldworkers, researchers and staff of the Mossy Foot Treatment and Prevention Association (MFTPA) working on prevention and treatment of podoconiosis.

Results

We found that patients were afraid of participation in a genetic study for fear the study might aggravate stigmatization by publicizing the familial nature of the disease. The MFTPA was also concerned that discussion about the familial nature of podoconiosis would disappoint patients and would threaten the trust they have in the organization. In addition, participants of the rapid assessment stressed that the genetic study should be approved at family level before prospective participants are approached for consent. Based on this feedback, we developed and implemented a consent process involving community consensus and education of fieldworkers, community members and health workers. In addition, we utilized the experience and established trust of the MFTPA to diminish the perceived risk.

Conclusion

The study showed that the consent process developed based on issues highlighted in the rapid assessment facilitated recruitment of participants and increased their confidence that the genetic research would not fuel stigma. Therefore, investigators must seek to assess and address risks of research from prospective participants' perspectives. This involves understanding the issues in the society, the culture, community dialogues and developing a consent process that takes all these into consideration.

Background

Despite its great public health importance, few control initiatives addressing podoconiosis (non-filarial elephantiasis, a geochemical neglected tropical disease) exist. In June 2010, the first podoconiosis program in Northern Ethiopia, consisting of prevention, awareness, and care and support activities, began in Debre Markos, Northern Ethiopia. This study aims to document and disseminate the lessons learned from a new community podoconiosis program in Debre Markos.

Methods/Principal Findings

We used a content analysis approach to examine and evaluate data from a series of sources. These sources include conducted interview transcripts, a focus group discussion transcript and secondary sources including monitoring and evaluation field reports, observation notes, and research obtained from a literature review. Themes were identified and grouped into matrix tables. Overall, sixteen program steps were identified and grouped into 6 domains: Initial preparation, training and sensitization, foundation building, treatment activity implementation, awareness, and follow-up. Emphasis is placed on the need for baseline data, effective training, local leadership, experience-sharing, mass-awareness, cross-cutting sector issues (i.e., water and waste management), and integration with government health systems. Related successes and challenges are also described, as are stakeholder roles and misconceptions and socio-cultural challenges affecting the program start-up. Many of the identified successes and challenges are relevant to the aim of the podoconiosis program to be sustainable and community-led.

Conclusions/Significance

Much of this information has already been used to improve the Debre Markos program. We also anticipate that the domains and steps identified will be useful in guiding new programs in other settings where podoconiosis is highly prevalent. We hope to encourage partnerships and collaboration among podoconiosis stakeholders in future growth and disease control expansion.

Author Summary

Podoconiosis is a chronic non-infectious disease that causes leg swelling among those living and walking bare-footed in red clay soil areas. It can be prevented and treated primarily by the use of shoes and foot hygiene. In Ethiopia, it is estimated that nearly 11 million people are at risk but few control programs exist. We aimed to assess and document the lessons learned from the first community podoconiosis program started in Northern Ethiopia in June 2010. We conducted interviews and a focus group discussion in addition to examining monitoring and evaluation field reports, observation notes, and other research articles. Overall, sixteen program steps were identified and grouped into 6 domains: Initial preparation, training and sensitization, foundation building, treatment activity implementation, awareness, and follow-up. Related successes and challenges, stakeholder roles, misconceptions and socio-cultural challenges affecting the program start-up were also identified. We hope that the results will be useful in guiding new programs in other settings where podoconiosis is highly prevalent.

Summary

Background

Podoconiosis (endemic non-filarial elephantiasis) is a geochemical disease in individuals exposed to red-clay soil. Despite the prevalence and public health importance of podoconiosis, there is as yet no accepted clinical staging system.

Objective

We aimed to develop and test a robust clinical staging system for podoconiosis.

Methods

We adapted the Dreyer system for staging filarial lymphoedema and tested it in four re-iterative field tests conducted in an area of high podoconiosis prevalence in Southern Ethiopia. The system finally arrived at has five stages according to proximal spread of disease and presence of dermal nodules, ridges and bands. We measured the one-week repeatability and the inter-observer agreement of the final staging system.

Results

We have developed a five-stage system that is readily understood by community workers with little health training. Kappa for one-week repeatability was 0.88 (95% CI 0.80 to 0.96), Kappa for agreement between health professionals was 0.71 (95% CI 0.60 to 0.82), while that between health professionals and community podoconiosis agents without formal health training averaged 0.64 (95% CI 0.52 to 0.78).

Conclusions

A simple staging system with good inter-observer agreement and repeatability has been developed to assist in the management and further study of podoconiosis.

Podoconiosis is a non-infectious tropical disease caused by exposure of bare feet to irritant alkalic clay soils. This causes an asymmetrical swelling of the feet and lower limbs due to lymphoedema. This swelling is called “elephantiasis” and may lead to severe disability of the patient. It is found in areas of tropical Africa, Central and South America and north-west India, where such soils coexist with high altitude, high seasonal rainfall and low income. Social stigmatization of people with the disease is widespread and economic losses are enormous. Podoconiosis is unique in being an entirely preventable non-communicable tropical disease. However, so far it has received little attention from health care policy makers.

Background

Neglected tropical diseases (NTDs) are a group of chronic parasitic diseases and related conditions that are the most common diseases among the 2·7 billion people globally living on less than US$2 per day. In response to the growing challenge of NTDs, Ethiopia is preparing to launch a NTD Master Plan. The purpose of this review is to underscore the burden of NTDs in Ethiopia, highlight the state of current interventions, and suggest ways forward.

Results

This review indicates that NTDs are significant public health problems in Ethiopia. From the analysis reported here, Ethiopia stands out for having the largest number of NTD cases following Nigeria and the Democratic Republic of Congo. Ethiopia is estimated to have the highest burden of trachoma, podoconiosis and cutaneous leishmaniasis in sub-Saharan Africa (SSA), the second highest burden in terms of ascariasis, leprosy and visceral leishmaniasis, and the third highest burden of hookworm. Infections such as schistosomiasis, trichuriasis, lymphatic filariasis and rabies are also common. A third of Ethiopians are infected with ascariasis, one quarter is infected with trichuriasis and one in eight Ethiopians lives with hookworm or is infected with trachoma. However, despite these high burdens of infection, the control of most NTDs in Ethiopia is in its infancy. In terms of NTD control achievements, Ethiopia reached the leprosy elimination target of 1 case/10,000 population in 1999. No cases of human African trypanosomiasis have been reported since 1984. Guinea worm eradication is in its final phase. The Onchocerciasis Control Program has been making steady progress since 2001. A national blindness survey was conducted in 2006 and the trachoma program has kicked off in some regions. Lymphatic Filariasis, podoconiosis and rabies mapping are underway.

Conclusion

Ethiopia bears a significant burden of NTDs compared to other SSA countries. To achieve success in integrated control of NTDs, integrated mapping, rapid scale up of interventions and operational research into co implementation of intervention packages will be crucial.

Background

Currently there is increasing recognition of the need for research in developing countries where disease burden is high. Understanding the role of local factors is important for undertaking ethical research in developing countries. We explored factors relating to information and communication during the process of informed consent, and the approach that should be followed for gaining consent. The study was conducted prior to a family-based genetic study among people with podoconiosis (non-filarial elephantiasis) in southern Ethiopia.

Methodology/Principal Findings

We adapted a method of rapid assessment validated in The Gambia. The methodology was entirely qualitative, involving focus-group discussions and in-depth interviews. Discussions were conducted with podoconiosis patients and non-patients in the community, fieldworkers, researchers, staff of the local non-governmental organisation (NGO) working on prevention and treatment of podoconiosis, and community leaders. We found that the extent of use of everyday language, the degree to which expectations of potential participants were addressed, and the techniques of presentation of information had considerable impact on comprehension of information provided about research. Approaching podoconiosis patients via locally trusted individuals and preceding individual consent with community sensitization were considered the optimal means of communication. Prevailing poverty among podoconiosis patients, the absence of alternative treatment facilities, and participants' trust in the local NGO were identified as potential barriers for obtaining genuine informed consent.

Conclusions

Researchers should evaluate the effectiveness of consent processes in providing appropriate information in a comprehensible manner and in supporting voluntary decision-making on a study-by-study basis.

Author Summary

Informed consent to biomedical research in developing countries is a highly topical issue. When consent forms and processes are simply borrowed from developed countries, obtaining genuine informed consent becomes extremely challenging. This paper examines how a quick and relatively simple intervention (Rapid Assessment) can influence the design and implementation of informed consent processes in the context of biomedical research involving poor, socially stigmatized and illiterate communities in a developing country. The paper goes on to discuss the effect of social, cultural, and economic factors identified by the intervention in a particular context and demonstrates how knowledge of these influences helped to develop a socially relevant and practical consent process prior to conducting a programme of community-based genetic research. The paper concludes that this intervention is an effective and economical means by which to ensure the efficacy and ethical integrity of consent processes when recruiting participants to new research sites, even within countries with which researchers are already acquainted.

Background

Podoconiosis is a lymphoedema of non-infectious cause which results in long-term ill health in affected individuals. Simple, effective treatment is available in certain parts of Ethiopia, but evidence indicates that not all patients continue collecting treatment supplies from clinic sites once started. We used qualitative techniques to explore factors related to discontinued attendance at outreach clinics of a non-government organization in southern Ethiopia.

Methods

A cross-sectional qualitative study was conducted in four clinic sites through unstructured in-depth interviews, key informant interviews and focus group discussions with the involvement of 88 study subjects.

Results

Discontinuation of clinic visits is common among podoconiosis patients. The reasons were: remoteness from the clinic sites, unrealistic expectation of ‘special’ aid, worry about increasing stigma, illness and misconceptions about treatment.

Conclusions

Several of these factors are remediable through community and individual information and education. Appropriate routes to deliver this information must be identified. Certain factors (such as distance to clinic sites and stigma) require substantial expansion of services or liaison with village-level government health services.

OBJECTIVE

Both podoconiosis (a geochemical non-filarial disease) and chronic filarial disease result in lower limb elephantiasis. The aims of the present study were to determine whether the elephantiasis in Midakegn district, central Ethiopia is filarial or non-filarial (podoconiosis) using serological, parasitological, and clinical examinations, and to estimate its prevalence.

METHODS

House-to-house visits were made in 330 randomly selected households. All household members that had elephantiasis were interviewed and clinically examined at the nearby health center to confirm presence of elephantiasis, check presence of scrotal swelling, and rule out other causes of lymphoedema. Midnight blood sample was obtained from each participant with elephantiasis for microscopic examination of W. bancrofti microfilaria. Day time blood sample was obtained from half of the participants for serological confirmation using the immuno-chromatographic test card.

RESULTS

Consistent with features of podoconiosis (non-filarial elephantiasis), none of the elephantiasis cases had consistently worn shoes since childhood; 94.3% had bilateral swelling limited below the level of the knees; no individual had thigh or scrotal elephantiasis; parasitological test for microfilariae and serological tests for W. bancrofti antigen turned negative in all samples. The prevalence of the disease was 7.4%. Prevalence peaked in the third decade of life, which also includes the most economically active age groups.

CONCLUSIONS

This study has shown high prevalence of podoconiosis (endemic non-filarial elephantiasis) and absence of filarial elephantiasis in Midakegn district. Prevention, treatment, and control of podoconiosis must be among the top priorities of public health programs in the district.

OBJECTIVE

This study aimed to investigate whether the presence of autoantibodies specific for type 1 diabetes (T1D) is determined by the major genetic susceptibility locus for the disease at the HLA genes, using the T1D Genetics Consortium data.

METHODS

We analyzed anti-IA-2 and anti-GAD 65 autoantibody data from 2,282 T1D patients from 1117 multiplex families. HLA genotyping was available for all cases and their parents and association with autoantibody positivity was tested by the transmission disequilibrium test.

RESULTS

Association of anti-IA-2 with the HLA genes was detected at high statistical signficance. HLA-DRB1*0401 confers both the strongest type 1 diabetes risk, and positive association of anti-IA-2, whereas the DRB1*03- DQA1*0501-DQB1*0201 haplotype, associated less strongly with T1D, showed a significant negative association with anti-IA-2 positivity. Interestingly, HLA-A*24 is also negatively associated with anti-IA-2, independently of the DRB1*03- DQA1*0501-DQB1*0201 haplotype. No statistically significant association was identified between anti-GAD65 and HLA.

CONCLUSIONS

This study highlights that IA-2 as an autoantigen depends on HLA genotype and suggests new insights into the mechanism of loss of immune tolerance.

Background

Given moderately strong genetic contributions to variation in alcoholism and heaviness of drinking (50–60% heritability), with high correlation of genetic influences, we have conducted a quantitative trait genomewide association study for phenotypes related to alcohol use and dependence.

Methods

Diagnostic interview and blood/buccal samples were obtained from sibships ascertained through the Australian Twin Registry. Genomewide SNP genotyping was performed with 8754 individuals [2062 alcohol dependent cases] selected for informativeness for alcohol use disorder and associated quantitative traits. Family-based association tests were performed for alcohol dependence, dependence factor score and heaviness of drinking factor score, with confirmatory case-population control comparisons using an unassessed population control series of 3393 Australians with genomewide SNP data.

Results

No findings reached genomewide significance (p=8.4×10−8 for this study), with lowest p-value for primary phenotypes of 1.2×10−7. Convergent findings for quantitative consumption and diagnostic and quantitative dependence measures suggest possible roles for a transmembrane protein gene (TMEM108) and for ANKS1A. The major finding, however, was small effect sizes estimated for individual SNPs, suggesting that hundreds of genetic variants make modest contributions (1/4% of variance or less) to alcohol dependence risk.

Conclusions

We conclude that (i) meta-analyses of consumption data may contribute usefully to gene-discovery; (ii) translation of human alcoholism GWAS results to drug discovery or clinically useful prediction of risk will be challenging; (iii) through accumulation across studies, GWAS data may become valuable for improved genetic risk differentiation in research in biological psychiatry (e.g. prospective high-risk or resilience studies).

Introduction

The gene MICA encodes the protein major histocompatibility complex class I polypeptide-related sequence A. It is expressed in synovium of patients with rheumatoid arthritis (RA) and its implication in autoimmunity is discussed. We analyzed the association of genetic variants of MICA with susceptibility to RA.

Methods

Initially, 300 French Caucasian individuals belonging to 100 RA trio families were studied. An additional 100 independent RA trio families and a German Caucasian case-control cohort (90/182 individuals) were available for replication. As MICA is situated in proximity to known risk alleles of the HLA-DRB1 locus, our analysis accounted for linkage disequilibrium either by analyzing the subgroup consisting of parents not carrying HLA-DRB1 risk alleles with transmission disequilibrium test (TDT) or by implementing a regression model including all available data. Analysis included a microsatellite polymorphism (GCT)n and single-nucleotide polymorphisms (SNPs) rs3763288 and rs1051794.

Results

In contrast to the other investigated polymorphisms, the non-synonymously coding SNP MICA-250 (rs1051794, Lys196Glu) was strongly associated in the first family cohort (TDT: P = 0.014; regression model: odds ratio [OR] 0.46, 95% confidence interval [CI] 0.25 to 0.82, P = 0.007). Although the replication family sample showed only a trend, combined family data remained consistent with the hypothesis of MICA-250 association independent from shared epitope (SE) alleles (TDT: P = 0.027; regression model: OR 0.56, 95% CI 0.38 to 0.83, P = 0.003). We also replicated the protective association of MICA-250A within a German Caucasian cohort (OR 0.31, 95% CI 0.1 to 0.7, P = 0.005; regression model: OR 0.6, 95% CI 0.37 to 0.96, P = 0.032). We showed complete linkage disequilibrium of MICA-250 (D' = 1, r2= 1) with the functional MICA variant rs1051792 (D' = 1, r2= 1). As rs1051792 confers differential allelic affinity of MICA to the receptor NKG2D, this provides a possible functional explanation for the observed association.

Conclusions

We present evidence for linkage and association of MICA-250 (rs1051794) with RA independent of known HLA-DRB1 risk alleles, suggesting MICA as an RA susceptibility gene. However, more studies within other populations are necessary to prove the general relevance of this polymorphism for RA.

The human leukocyte antigen (HLA) class II genes HLA-DRB1, -DQA1 and -DQB1 are the strongest genetic factors for type 1 diabetes (T1D). Additional loci in the major histocompatibility complex (MHC) are difficult to identify due to the region’s high gene density and complex linkage disequilibrium (LD). To facilitate the association analysis, two novel algorithms were implemented in this study: one for phasing the multi-allelic HLA genotypes in trio families, and one for partitioning the HLA strata in conditional testing. Screening and replication were performed on two large and independent datasets: the Wellcome Trust Case–Control Consortium (WTCCC) dataset of 2,000 cases and 1,504 controls, and the T1D Genetics Consortium (T1DGC) dataset of 2,300 nuclear families. After imputation, the two datasets have 1,941 common SNPs in the MHC, of which 22 were successfully tested and replicated based on the statistical testing stratifying on the detailed DRB1 and DQB1 genotypes. Further conditional tests using the combined dataset confirmed eight novel SNP associations around 31.3 Mb on chromosome 6 (rs3094663, p = 1.66 × 10−11 and rs2523619, p = 2.77 × 10−10 conditional on the DR/DQ genotypes). A subsequent LD analysis established TCF19, POU5F1, CCHCR1 and PSORS1C1 as potential causal genes for the observed association.

Electronic supplementary material

The online version of this article (doi:10.1007/s00439-010-0908-2) contains supplementary material, which is available to authorized users.

Background

Chronic inflammation and autoimmunity likely contribute to the pathogenesis of abdominal aortic aneurysms (AAAs). The aim of this study was to investigate the role of autoimmunity in the etiology of AAAs using a genetic association study approach with HLA polymorphisms.

Methods

HLA-DQA1, -DQB1, -DRB1 and -DRB3-5 alleles were determined in 387 AAA cases (180 Belgian and 207 Canadian) and 426 controls (269 Belgian and 157 Canadian) by a PCR and single-strand oligonucleotide probe hybridization assay.

Results

We observed a potential association with the HLA-DQA1 locus among Belgian males (empirical p = 0.027, asymptotic p = 0.071). Specifically, there was a significant difference in the HLA-DQA1*0102 allele frequencies between AAA cases (67/322 alleles, 20.8%) and controls (44/356 alleles, 12.4%) in Belgian males (empirical p = 0.019, asymptotic p = 0.003). In haplotype analyses, marginally significant association was found between AAA and haplotype HLA-DQA1-DRB1 (p = 0.049 with global score statistics and p = 0.002 with haplotype-specific score statistics).

Conclusion

This study showed potential evidence that the HLA-DQA1 locus harbors a genetic risk factor for AAAs suggesting that autoimmunity plays a role in the pathogenesis of AAAs.

Celiac disease (CD) is a chronic inflammatory disorder triggered after gluten ingestion in genetically susceptible individuals. The major genetic determinants are HLA-DQA1*05 and HLA-DQB1*02, which encode the DQ2 heterodimer. These alleles are commonly inherited in cis with DRB1*03∶01, which is associated with numerous immune-related disorders, in some cases contributing with a different amount of risk depending on the haplotype context. We aimed at investigating those possible differences involving DRB1*03∶01-carrying haplotypes in CD susceptibility. A family (274 trios) and a case-control sample (369 CD cases/461 controls) were analyzed. DRB1*03∶01-carrying individuals were classified according to the haplotype present (ancestral haplotype (AH) 8.1, AH 18.2 or non-conserved haplotype) after genotyping of HLA-DRB1, -DQA1, -DQB1, -B8, TNF -308, TNF -376 and the TNFa and TNFb microsatellites. We observe that the AH 8.1 confers higher risk than the remaining DRB1*03∶01-carrying haplotypes, and this effect only involves individuals possessing a single copy of DQB1*02. CD risk for these individuals is similar to the one conferred by inherit DQA1*05 and DQB1*02 in trans. It seems that an additional CD susceptibility factor is present in the AH 8.1 but not in other DRB1*03∶01-carrying haplotypes. This factor could be shared with individuals possessing DQ2.5 trans, according to the similar risk observed in those two groups of individuals.

Background

Age at onset in Parkinson disease (PD) is a highly heritable quantitative trait for which a significant genetic influence is supported by multiple segregation analyses. Because genes associated with onset age may represent invaluable therapeutic targets to delay the disease, we sought to identify such genetic modifiers using a genomewide association study in familial PD. There have been previous genomewide association studies (GWAS) to identify genes influencing PD susceptibility, but this is the first to identify genes contributing to the variation in onset age.

Methods

Initial analyses were performed using genotypes generated with the Illumina HumanCNV370Duo array in a sample of 857 unrelated, familial PD cases. Subsequently, a meta-analysis of imputed SNPs was performed combining the familial PD data with that from a previous GWAS of 440 idiopathic PD cases. The SNPs from the meta-analysis with the lowest p-values and consistency in the direction of effect for onset age were then genotyped in a replication sample of 747 idiopathic PD cases from the Parkinson Institute Biobank of Milan, Italy.

Results

Meta-analysis across the three studies detected consistent association (p < 1 × 10-5) with five SNPs, none of which reached genomewide significance. On chromosome 11, the SNP with the lowest p-value (rs10767971; p = 5.4 × 10-7) lies between the genes QSER1 and PRRG4. Near the PARK3 linkage region on chromosome 2p13, association was observed with a SNP (rs7577851; p = 8.7 × 10-6) which lies in an intron of the AAK1 gene. This gene is closely related to GAK, identified as a possible PD susceptibility gene in the GWAS of the familial PD cases.

Conclusion

Taken together, these results suggest an influence of genes involved in endocytosis and lysosomal sorting in PD pathogenesis.

Leprosy is an infectious disease caused by the obligate intracellular pathogen Mycobacterium leprae and remains endemic in many parts of the world. Despite several major studies on susceptibility to leprosy, few genomic loci have been replicated independently. We have conducted an association analysis of more than 1,500 individuals from different case-control and family studies, and observed consistent associations between genetic variants in both TLR1 and the HLA-DRB1/DQA1 regions with susceptibility to leprosy (TLR1 I602S, case-control P = 5.7×10−8, OR = 0.31, 95% CI = 0.20–0.48, and HLA-DQA1 rs1071630, case-control P = 4.9×10−14, OR = 0.43, 95% CI = 0.35–0.54). The effect sizes of these associations suggest that TLR1 and HLA-DRB1/DQA1 are major susceptibility genes in susceptibility to leprosy. Further population differentiation analysis shows that the TLR1 locus is extremely differentiated. The protective dysfunctional 602S allele is rare in Africa but expands to become the dominant allele among individuals of European descent. This supports the hypothesis that this locus may be under selection from mycobacteria or other pathogens that are recognized by TLR1 and its co-receptors. These observations provide insight into the long standing host-pathogen relationship between human and mycobacteria and highlight the key role of the TLR pathway in infectious diseases.

Author Summary

Mycobacterium leprae is an obligate intracellular pathogen that causes leprosy, a disease that shares a long history with the human population but which remains endemic in many parts of the world. Despite the fact that the genome of M. leprae has been sequenced, our understanding of its pathogenesis and interaction with the human host is limited, in part due to the inability to culture the bacterium in vitro. In this gene-centric microarray study, we have genotyped SNPs in over 2,000 genes and identified TLR1 and HLA-DRB1/DQA1 as major leprosy susceptibility genes. Studying the geographical distribution of this hypo-functional TLR1 variant demonstrated extreme population differentiation at this locus. These results suggest that leprosy may have contributed to the evolution of this genomic region, and provide insight into the long history of the host-pathogen relationship between humans and M. leprae.

The aim of this study was to investigate HLA class II associations in polymyositis (PM) and dermatomyositis (DM), and to determine how these associations influence clinical and serological differences. DNA samples were obtained from 225 UK Caucasian idiopathic inflammatory myopathy patients (PM = 117, DM = 108) and compared with 537 randomly selected UK Caucasian controls. All cases had also been assessed for the presence of related malignancy and interstitial lung disease (ILD), and a number of myositis-specific/myositis-associated antibodies (MSAs/MAAs). Subjects were genotyped for HLA-DRB1, DQA1 and DQB1. HLA-DRB1*03, DQA1*05 and DQB1*02 were associated with an increased risk for both PM and DM. The HLA-DRB1*03-DQA1*05-DQB1*02 haplotype demonstrated strong association with ILD, irrespective of myositis subtype or presence of anti-aminoacyl-transfer RNA synthetase antibodies. The HLA-DRB1*07-DQA1*02-DQB1*02 haplotype was associated with risk for anti-Mi-2 antibodies, and discriminated PM from DM (odds ratio 0.3, 95% confidence interval 0.1–0.6), even in anti-Mi-2 negative patients. Other MSA/MAAs showed specific associations with other HLA class II haplotypes, irrespective of myositis subtype. There were no genotype, haplotype or serological associations with malignancy. The HLA-DRB1*03-DQA1*05-DQB1*02 haplotype associations appear to not only govern disease susceptibility in Caucasian PM/DM patients, but also phenotypic features common to PM/DM. Though strongly associated with anti-Mi-2 antibodies, the HLA-DRB1*07-DQA1*02-DQB1*02 haplotype shows differential associations with PM/DM disease susceptibility. In conclusion, these findings support the notion that myositis patients with differing myositis serology have different immunogenetic profiles, and that these profiles may define specific myositis subtypes.

OBJECTIVE

We report here genotyping data and type 1 diabetes association analyses for HLA class I loci (A, B, and C) on 1,753 multiplex pedigrees from the Type 1 Diabetes Genetics Consortium (T1DGC), a large international collaborative study.

RESEARCH DESIGN AND METHODS

Complete eight-locus HLA genotyping data were generated. Expected patient class I (HLA-A, -B, and -C) allele frequencies were calculated, based on linkage disequilibrium (LD) patterns with observed HLA class II DRB1-DQA1-DQB1 haplotype frequencies. Expected frequencies were compared to observed allele frequencies in patients.

RESULTS

Significant type 1 diabetes associations were observed at all class I HLA loci. After accounting for LD with HLA class II, the most significantly type 1 diabetes–associated alleles were B*5701 (odds ratio 0.19; P = 4 × 10−11) and B*3906 (10.31; P = 4 × 10−10). Other significantly type 1 diabetes–associated alleles included A*2402, A*0201, B*1801, and C*0501 (predisposing) and A*1101, A*3201, A*6601, B*0702, B*4403, B*3502, C*1601, and C*0401 (protective). Some alleles, notably B*3906, appear to modulate the risk of all DRB1-DQA1-DQB1 haplotypes on which they reside, suggesting a class I effect that is independent of class II. Other class I type 1 diabetes associations appear to be specific to individual class II haplotypes. Some apparent associations (e.g., C*1601) could be attributed to strong LD to another class I susceptibility locus (B*4403).

CONCLUSIONS

These data indicate that HLA class I alleles, in addition to and independently from HLA class II alleles, are associated with type 1 diabetes.

The question of what significance threshold is appropriate for genomewide association studies is somewhat unresolved. Previous theoretical suggestions have yet to be validated in practice, whereas permutation testing does not resolve a discrepancy between the genomewide multiplicity of the experiment and the subset of markers actually tested. We used genotypes from the Wellcome Trust Case-Control Consortium to estimate a genomewide significance threshold for the UK Caucasian population. We subsampled the genotypes at increasing densities, using permutation to estimate the nominal P-value for 5% family-wise error. By extrapolating to infinite density, we estimated the genomewide significance threshold to be about 7.2 × 10−8. To reduce the computation time, we considered Patterson's eigenvalue estimator of the effective number of tests, but found it to be an order of magnitude too low for multiplicity correction. However, by fitting a Beta distribution to the minimum P-value from permutation replicates, we showed that the effective number is a useful heuristic and suggest that its estimation in this context is an open problem. We conclude that permutation is still needed to obtain genomewide significance thresholds, but with subsampling, extrapolation and estimation of an effective number of tests, the threshold can be standardized for all studies of the same population.

The question of what significance threshold is appropriate for genomewide association studies is somewhat unresolved. Previous theoretical suggestions have yet to be validated in practice, whereas permutation testing does not resolve a discrepancy between the genomewide multiplicity of the experiment and the subset of markers actually tested. We used genotypes from the Wellcome Trust Case-Control Consortium to estimate a genomewide significance threshold for the UK Caucasian population. We subsampled the genotypes at increasing densities, using permutation to estimate the nominal P-value for 5% family-wise error. By extrapolating to infinite density, we estimated the genomewide significance threshold to be about 7.2×10−8. To reduce the computation time, we considered Patterson’s eigenvalue estimator of the effective number of tests, but found it to be an order of magnitude too low for multiplicity correction. However, by fitting a Beta distribution to the minimum P-value from permutation replicates, we showed that the effective number is a useful heuristic and suggest that its estimation in this context is an open problem. We conclude that permutation is still needed to obtain genomewide significance thresholds, but with subsampling, extrapolation and estimation of an effective number of tests, the threshold can be standardized for all studies of the same population.