Inherited disorders are an important cause of physical handicap, deafness, mental retardation and blindness. There is considerable variation in the geographic and ethnic distribution of genetic disease due to biological pressures and historical accidents. In this context the relative prevalence of common inherited disorders and the recognition of rare conditions in isolated communities is of great academic importance. Oceanic islands are of special significance in the study of inherited disease. Virtually nothing has been documented concerning genetic disorders on the Island of Mauritius with a population of one million people. This study was undertaken to document the impact of inherited disorders on handicapping conditions in this community. As genetic disease concentrates in institutions, formal screening of all the schools for the deaf and blind, and the associations for the physically and mentally handicapped on Mauritius was undertaken. This involved a careful history, clinical examination and genealogical study, with radiographic, biochemical and ancillary testing performed where appropriate. Referral clinics were also established for the assessment of individuals and families known, or thought to be afflicted with abnormalities or handicap of a genetic origin. To ensure completeness, a similar survey was performed on Rodrigues, a neighbouring island, as this community is included under the responsibilities of the Mauritian Ministry of Health. Accumulated data concerning 681 patients were analysed. Genetic disorders accounted for disability in 265 individuals representing 38,6% of the causes of handicap. Of these persons 54 were deaf, 30 were blind, 99 were mentally retarded and 80 were physically handicapped. Several new entities, considered unique to the area and a consequence of either consanguinity or the founder effect, were documented. Karyotyping on selected individuals was undertaken in the laboratories of the Department of Human Genetics, University of Cape Town. A molecular genetic study of a large family with X-linked deafness of Nance, conducted by the same laboratory, revealed tight linkage with the probe pDP34; linkage analysis was performed on patients with Duchenne muscular dystrophy. The collation of these original data, the delineation of the new genetic conditions and an analysis of the results form the subject of this thesis and provide a basis for the future development of genetic services on Mauritius.

Mendelian Randomization (MR) is a powerful tool for accessing causality of exposure on an outcome using genetic variants as the instrumental variables. Much of the recent developments is propelled by the increasing availability of GWAS summary data. However, the accuracy of the MR causal effect estimates could be challenged in case of the MR assumptions are violated. The source of biases could attribute to the weak effects arising because of polygenicity, the presentence of horizontal pleiotropy and other biases, e.g., selection bias. In this thesis, we proposed two works, expecting to deal with these issues.In the first part, we proposed a method named 'Bayesian Weighted Mendelian Randomization (BMWR)' for causal inference using summary statistics from GWAS. In BWMR, we not only take into account the uncertainty of weak effects owning to polygenicity of human genomics but also models the weak horizontal pleiotropic effects. Moreover, BWMR adopts a Bayesian reweighting strategy for detection of large pleiotropic outliers. An efficient algorithm based on variational inference was developed to make BWMR computationally efficient and stable. Considering the underestimated variance provided by variational inference, we further derived a closed form variance estimator inspired by a linear response method. We conducted several simulations to evaluate the performance of BWMR, demonstrating the advantage of BWMR over other methods. Then, we applied BWMR to access causality between 126 metabolites and 90 complex traits, revealing novel causal relationships. In the second part, we further developed BWMR-C: Statistical correction of selection bias for Mendelian Randomization based on a Bayesian weighted method. Based on the framework of BWMR, the probability model in BWMR-C is built conditional on the IV selection criteria. In such way, BWMR-C delicated to reduce the influence of the selection process on the causal effect estimates and also preserve the good properties of BWMR. To make the causal inference computationally stable and efficient, we developed a variational EM algorithm. We conducted several comprehensive simulations to evaluate the performance of BWMR-C for correction of selection bias. Then, we applied BWMR-C on seven body fat distribution related traits and 140 UK Biobank traits. Our results show that BWMR-C achieves satisfactory performance for correcting selection bias. Keywords: Mendelian Randomization, polygenicity, horizontal pleiotropy, selection bias, variation inference.

Alopecia Areata (AA) is a highly prevalent autoimmune disease in the US with a lifetime risk of 2.1%. In AA, autoimmunity develops against the hair follicles, which leads to infiltration of immune cells around affected follicles. Among genetic risk factors in complex autoimmune diseases, variants cluster in genes regulating the immune response, as well as the target organ. AA is believed to result from both genetic and environmental factors. To identify underlying genetic drivers in AA, we analyzed AA risk genes using various sequencing techniques and analysis methods to identify causal variants and placed them in functionally relevant contexts using innovative mapping techniques. To address the role of variants in immune function, we studied the Interleukin-2 Receptor Alpha (IL2RA), which we identified as a significant locus to study genetic factors underlying immune function from our AA GWAS studies (p=1.74*10-12)11. IL2RA plays a crucial role in regulating immune tolerance and controlling activity of regulatory T cells (Treg)13. We identified significant causal variants in the IL2RA region associated with AA using GWAS, targeted resequencing, and custom capture exome sequencing approaches. We validated the expression of these variants in immune cell cluster tissue types in silico, and specifically in CD4+ T cells. The variant rs3118740 increases AA susceptibility for carriers of the C allele. Such allele specific effects could lead to a perturbation of Treg function, for example, one study in T1D where patients with the rs3118470 risk variant have Treg with IL-2 signaling defects14. These studies demonstrated that identifying causal variants may lead to an improved understating of Treg function and risk of autoimmunity in AA. Next, to study genetic susceptibility in the target organ in AA, the hair follicle (HF), the second candidate GWAS susceptibility gene we studied was peroxiredoxin 5 (PRDX5) (p= of 8.7*10-14), which is also a GWAS gene in Crohn’s disease, sarcoidosis, and psoriasis15,16. PRDX5 is a member of the family of antioxidant enzymes that are crucial for regulating oxidative stress. Our lab performed whole exome sequencing in 849 AA patients, together with selected custom capture regions of genomic sequencing. Using a test of variant enrichment, we identified variants in PRDX5 that were significant in both our GWAS and exome studies, and thus represented likely candidate causal variants. Using Bayesian fine mapping, we identified a GWAS and exome sequencing variant, rs574087, that was significantly enriched in both, and is predicted to be a causal variant in keratinocytes and melanocytes. To functionally validate PRDX5, we immunostained healthy human HF and AA affected HF, and found that PRDX5 is upregulated AA human HF. PRDX5 is expressed in cultured melanocytes by immunostaining, which is consistent with melanocytes exhibiting high levels of oxidative stress. We postulated that PRDX5 may be involved in protection from oxidative stress, and that its dysregulation may contribute to autoimmunity. Finally, along with genetic predisposition, environmental triggers such as the microbiome have emerged as potential factors contributing to pathologic immune responses in autoimmune diseases. To determine the role of the microbiome in AA pathobiology, we performed 16S rRNA sequencing of skin swabs, hair follicles, and stool samples from a cohort of 34 AA patients and 12 healthy controls (HCs). Unexpectedly, we found evidence of striking gut dysbiosis, consisting of over-representation of Firmicutes and under-representation of Bacteroides in the gut microbiome of AA patients compared with healthy subjects, but no significant differences in skin or hair follicle (HF) microbiome composition. To investigate the role of the gut microbiome in AA development in vivo, we depleted the gut microbiome in C3H/HeJ mice and found that the mice were largely protected from AA developing. These data revealed a requirement for gut microbiota in the onset of murine AA. Taken together with recent reports in the literature of reversal of AA in several patients following fecal microbiota transplant (FMT)17,18, our findings suggest that restoring homeostasis of the gut microbiome may represent an effective new treatment modality in the management of AA.

This document only includes an excerpt of the corresponding thesis or dissertation. To request a digital scan of the full text, please contact the Ruth Lilly Medical Library's Interlibrary Loan Department (rlmlill@iu.edu).

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Thesis (MScMedSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Please see fulltext for abstract / AFRIKAANSE OPSOMMING: Parkinson se siekte ( PD ) is 'n toenemend algemene neurodegeneratiewe siekte wat die progressiewe verlies van dopaminergiese neurone in die substantia nigra pars compacta behels, wat lei tot die ontwrigting van die motororiese senuweestelsel. ’n Neuronale verlies van meer as 50% van die normale vlakke is nodig vir die ontwikkeling van die kliniese simptome, insluitende bewing, spier rigiditeit, bradykinesia, en posturale onstabiliteit. Alhoewel beskikbare medikasies vir PD wel simptome onderdruk, is dit nie in staat om die siekte te voorkom of vordering daarvan te verhoed nie. Een van die mees bedeidende risikofaktore vir PD is toenemende ouderdom. Huidige epidemiologiese studies voorspel ‘n toename in populasie ouderdom wat belangrike implikasies vir die voorkoms van PD kan inhou. Die molekulere meganismes onderliggend aan die neurale agteruitgang in PD is steeds onbekend, maar dit blyk dat ‘n aantal genetiese faktore (in kombinasie met omgewingsfaktore) bydra tot die komplekse patogeniese agteruitgang van die siekte. Agt bevestigde gene is gevind om direk betrokke te wees by die etiologie van PD, naamlik: parkin, PINK1, DJ-1, ATP13A2, SNCA, LRRK2, VPS35, en EIF4G1. Hierdie gene is oorwegend geïdentifiseer en bestudeer in die Europese, Noord-Amerikaanse en Asiatiese bevolkings; terwyl die bestudering van Sub -Sahara- Afrika (SSA) bevolkings, veral dié van Swart Afrika afkoms, onderverteenwoordig bly in genetiese studies. Siende dat resultate verkry vanaf ander bevolkings nie verwant is aan die SSA bevolking nie, en ook nie ‘n voorspelling van wereldwye toename van die siekte kan verteenwoordig nie, is dit van belang dat omvattende genetiese studies uitgevoer word op hierdie onderbestudeerde bevolkings van SSA. Desnieteenstaande, die doel van die studie was om die molekulere etiologie van PD in ‘n groep Swart Suid-Afrikaanse (SA) PD pasiente te ondersoek. ‘n Totaal van 47 pasiente is gewerf vir die studie waarvan 26% ‘n famielie geskiedenis het vir die afwyking. Die gemiddelde ouderdom van aanvang vir die pasiente was 55.3 ± 11.2 jaar. Mutasie volgorderbepaling vir alle bekende PD gene is uitgevoer. Addisionele mutasie volgorderbepaling vir die GBA is ook uitgevoer siende dat heterosigotiese mutasies in die geen dien as ‘n sterk risikofaktor vir die ontwikkeling van PD. ‘n Verskeidenheid mutasie volgordebepalingstegnieke is geinkorporeer vir die studie, naamlik: Sanger volgordebepaling en hoë resolusie smelt tegniek (vir die identifisering van missense mutasies asook kleinskaalse invoegings of weglatings), en multiplex-afbinding afhanklike ondersoek versterkingstoets (vir die opsporing van veranderinge in kopiegetal). Verder is volgende generasie volgordebepaling gebruik vir die sistematiese ondersoek van die bekende PD gene, asook vir 160 kandidaat gene wat vooraf bepaal is. Fluoreserend-geetiketeerde polymerase ketting reaksie primers is gebruik vir genotipering van CAG herhalings uitbreidings in die ataxin-2 (SCA2) en die ataxin-7 (SCA7) gene, gevolg deur elektroforese met behulp van die “ABI 3130x1 Genetic Analyzer”. Mutasie volgordebepaling het voor die lig gebring dat die bekende PD gene klaarblyklik nie ‘n beduidende oorsaaklike rol speel in die patogenese van die siekte in die huidige groep Swart SA pasiente nie, want slegs 2 uit die 47 (43%) pasiente koester mutasies in parkin. Een van die pasiente besit ‘n heterosigotiese duplikasie van ekson 2 en ‘n heterosigotiese weglating van ekson 9; in die ander pasient is ‘n heterosigotiese ekson 4 weglating en ‘n heterosigotiese G430D mutasie geïdentifiseer. Verder is ‘n Q311K verandering in parkin gevind asook vier nuwe variante (I610T, H1758P, N2133S en T2423S) in die LRRK2 geen. Die patogenisiteit van hierdie variante moet egter nog bepaal word. Geen patogeniese herhaalings uitbreidings is gevind in die SCA2 en SCA7 lokusse nie, en die moontlikheid van die twee spinocerebellar ataksie subtipes as genetiese bepalers vir PD is uitgekanselleer. Geen patogeniese mutasies is gevind in enige van die oorblywende bekende PD gene nie, dit is dus waarskeinlik dat die pasiente wel mutasies in nuwe PD-geassosieerde gene besit. Hierdie is die eerste molekulere genetiese studie uitgevoer op uitsluitlik Swart SA PD pasiente, en ook die eerste omvattende ondersoek van al die bekende PD gene in ‘n SSA bevolking. Die algemene patogeniese mutasies in gene, wat voorheen bewys is as siekte veroorsakend in ‘n aantal Europese bevolkings, is nie bespeur in die huidige studie nie en kan dus nie verantwoordelik gehou word vir die voorkoms van PD in hierdie pasiente nie. Maar, siende dat die steekproefgrootte in hierdie studie relatief klein was, kan addisionele volgordebepaling van ‘n groter pasient groep voordelig wees in die bepaal van nuwe siekte-veroorsakende gene wat die potensiaal het om huidige hipoteses, dat die genetiese etiologie van PD duidelik verskil oor verskeie etniese groepe wereldwyd, te weerlê of bevestig. Die voortsetting van genetiese ondersoeke onder hierdie groep pasiente kan bydra tot insig met betrekking tot bevolking-spesifieke genetiese bepalers, en uiteindelik tot die identifisering van nuwe teikens vir medikasies teen die siekte.

Thesis (MSc)--Stellenbosch University, 2000. / ENGLISH ABSTRACT: Hereditary haemochromatosis (HH) is an autosomal recessive iron storage disease where the accumulation of iron in parenchymal organs may lead to diabetes, heart failure, liver cirrhosis, arthropathy, weakness and a variety of other ailments if preventive measures are not taken. HH is often not considered as a cause of these conditions, particularly not in the elderly where the background frequencies of type II diabetes, osteoarthritis and heart failure are generally high. Heterozygosity for C282Y, the HFE-mutation causing HH in approximately 80% of affected individuals worldwide, has been linked to a raised incidence of malignancies of the colon and rectum, stomach and the haematological system. One of the highest carrier-frequencies (116) in the world for this mutation has been reported in the South-African Afrikaner population, resulting in C282Y-homozygosity in approximately 1 in every 115 people in this group. A sample of 197 elderly Afrikaner volunteers was recruited for genotype/phenotype association studies. Their clinical presentation was denoted, biochemical iron-status determined and HFE genotyping performed. Either an increase or decrease in survival, or both, were proposed, depending on possible gender effects. HH has been positively associated with various cancer types, but may also protect against iron-deficiency anaemia which is by far the most frequent cause of anaemia in the older person. This study has led to the following findings: 1. The carrier frequency of mutation C282Y was found to be 1/8 in the elderly population (similar in males and females), which is slightly lower than the 1/6 reported in younger adults from the same population. Only one C282Y homozygote and two C282YIH63D compound heterozygotes were detected, all of them female. 2. The prevalence of diabetes, heart disease, arthropathy or a combination of these conditions did not differ significantly in C282Y heterozygotes and the mutationnegative group. 3. Among 24 C282Y heterozygotes only one individual with rectal carcmoma was detected compared with two cases with rectal- and seven with colonic malignancies in 153 mutation-negative individuals. The single female C282Y homozygote identified suffered from both rectal and colon carcinoma and died approximately 6 months ago as a consequence of her colon malignancy. 4. Serum ferritin appears to be a highly unreliable parameter of iron status, particularly in the elderly where a variety of factors that may influence the levels are often present in elderly individuals. This may be due to ageing alone or as a result of multiple comorbidities. 5. Serum ferritin levels were lower than expected in elderly subjects with mutation C282Y and compound heterozygotes with both C282Y and H63D, which may be related to a variable penetrance of the HFE gene mutations. It is possible that variation in other genes exist that confer protection against iron-loading by gene-gene interaction. The probability that environmental factors (e.g. a low iron diet) are more important in this respect cannot be excluded, although this is considered less likely in the light of the fact that the same trend was observed in all mutation-positive elderly individuals. It is therefore highly likely that C282Y -positive subjects with significant iron loading have died before reaching their seventies, particularly since none of the males included in this study were homozygous or compound heterozygous for the mutations analysed. In conclusion, possession of a mutant HFE gene does not appear to confer a survival advantage in old age, neither does it seem that mutation carriers with significant ironloading are overlooked by the medical fraternity. Further investigations are warranted to shed more light on the contributions of gene-gene and gene-environment interaction in the clinical manifestation of Hll, and how these processes can be manipulated to prevent the symptoms of this largely underdiagnosed disease. / AFRIKAANSE OPSOMMING: Oorerflike hemochromatose (OH) is 'n outosomaal resessiewe yster-oorladingssiekte waar akkumulasie van yster in parenkimale organe kan lei tot suikersiekte, hartversaking, lewer sirrose, artropatie, moegheid en 'n verskeidenheid van ander probleme indien voorkomende maatreëls nie getref word nie. OH word gewoonlik nie oorweeg as moontlike oorsaak vir hierdie toestande nie, veral nie in ouer mense nie waar die agtergrond-frekwensie van tipe II diabetes, osteoartritis en hartversaking in elk geval hoog is. Heterosigositeit vir die HFE mutasie C282Y, wat OH veroorsaak in ongeveer 80% van geaffekteerde gevalle wêreldwyd, is geassosieer met 'n verhoogde voorkoms van kanker van die kolon, rektum, maag en ook die hematologiese sisteem. Van die hoogste draer frekwensies ter wêreld vir hierdie mutasie (1/6) is gevind in die Afrikaner populasie van Suid-Afrika, wat daarop dui dat 1 uit elke 115 mense in die groep homosigoties vir die C282Y mutasie kan wees. Eenhonderd sewe-en-negentig bejaarde Afrikaner vrywilligers het aan die studie deelgeneem wat daarop gemik was om genotipe/fenotipe korrelasies uit te voer. Die kliniese beeld van elke individu is gedokumenteer, die yster status biochemies bepaal en HFE genotipering uitgevoer. Die a priori veronderstelling was dat oorlewing sou toeneem of afneem, of beide, afhangende van die geslag van die individu. Daar is voorheen 'n verband gevind tussen OH en die ontwikkeling van bogenoemde maligniteite, maar aan die ander kant kan dit moontlik ook beskerm teen anemie as gevolg van yster gebrek, wat juis die mees algemene oorsaak van anemie in die ouer persoon is. Hierdie studie het tot die volgende bevindings gelei: 1. Die draer frekwensie van mutasie C282Y was 1/8 in die bejaardes (dieselfde in mans en vrouens), wat effens laer is as die 1/6 wat gerappoteer is in jonger volwassenes. Slegs een C282Y homosigoot en twee C282YIH63D saamgestelde heterosigote is opgespoor, en al drie was vroulik. 2. Die voorkoms van suikersiekte, hartsiekte, gewrigspyne of 'n kombinasie van hierdie aandoenings het nie betekenisvol verskil tussen die C282Y heterosigote en die mutasienegatiewe groep nie. 3. Daar was slegs een persoon met rektum karsinoom in die groep van 24 bejaarde C282Y heterosigote, terwyl daar twee gevalle met rektum kanker en sewe gevalle met kolon kanker gevind is onder die 153 mutasie-negatiewe individue. Die enkele vroulike C282Y homosigoot wat opgespoor is het beide rektum- en kolonkanker gehad en is ongeveer 6 maande vóór voltooing van die tesis oorlede aan haar kolon karsinoom. 4. Dit wil voorkom asof serum ferritien veral in bejaardes 'n hoogs onbetroubare maatstaf is vir yster status, aangesien dit deur 'n verskeidenheid faktore beïnvloed word wat dikwels in bejaardes aanwesig is as gevolg van veroudering of veelvuldige komorbiditeite. 5. Die serum ferritien vlakke was laer as verwag in sowel die bejaarde C282Y-homosigoot as in die twee saamgestelde heterosigote met mutasies C282Y en H63D, wat moonlik die gevolg is van die wisselende graad van penetrasie van HFE mutasies. Dit is moontlik dat variasie in ander gene beskerming bied teen yster-oorlading deur middel van geen-geen interaksie. Die moontlikheid dat omgewingsfaktore (soos 'n lae-yster dieet) 'n belangrike rol speel in hierdie verband kan nie uitgesluit word nie, hoewel dit minder waarskynlik lyk te wees in die lig van die feit dat dieselfde neiging waargeneem is in alle mutasie-positiewe bejaardes. Die kans is dus redelik groot dat individue met die C282Y mutasie en betekenisvolle yster oorlading oorlede is voordat hulle die sewentiger jare kon bereik, veral omdat geeneen van die mans wat ingesluit is in die studie homosigoot of 'n saamgestelde heterosigoot was vir die mutasies wat geanaliseer is nie. Opsommend wil dit voorkom asof die teenwoordigheid van 'n mutante HFE geen nie 'n beter oorlewingskans bied op ouer leeftyd nie, en dit blyk ook dat mutasie draers met betekenisvolle ysteroorlading nie deur dokters misgekyk word nie. Verdere navorsing is nodig om meer lig te werp op die bydrae van geen-geen- en geen-omgewing interaksie in die kliniese manifestasie van OH, en ook hoe hierdie prosesse gemanipuleer kan word om die simptome van hierdie onder -gediagnoseerde siekte te voorkom.