A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Conrad, Donald F.; Jakobsson, Mattias; Coop, Graham; Wen, Xiaoquan; Wall, Jeffrey D.; Rosenberg, Noah A.; Pritchard, Jonathan K.

doi:10.1038/ng1911

Cited by 475 publications

(513 citation statements)

References 44 publications

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“…3) is interesting. Not unexpectedly (Conrad et al, 2006), the African Yoruba (YRI) forms a separate cluster. What is, however, striking is that the Muslim and Hindu communities of this study form a cluster that is distinct from the remaining HapMap populations.…”

Section: Discussionmentioning

confidence: 99%

Genetic variation and haplotype structures of innate immunity genes in eastern India

Bairagya

Bhattacharya

et al. 2008

Infection, Genetics and Evolution

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This study reports results of an extensive and comprehensive study of genetic diversity in 12 genes of the innate immune system in a population of eastern India. Genomic variation was assayed in 171 individuals by resequencing ~75 kb of DNA comprising these genes in each individual. Almost half of the 548 DNA variants discovered was novel. DNA sequence comparisons with human and chimpanzee reference sequences revealed evolutionary features indicative of natural selection operating among individuals, who are residents of an area with a high load of microbial and other pathogens. Significant differences in allele and haplotype frequencies of the study population were observed with the HapMap populations. Gene and haplotype diversities were observed to be high. The genetic positioning of the study population among the HapMap populations based on data of the innate immunity genes substantially differed from what has been observed for Indian populations based on data of other genes. The reported range of variation in SNP density in the human genome is one SNP per 1.19 kb (chromosome 22) to one SNP per 2.18 kb (chromosome 19). The SNP density in innate immunity genes observed in this study (>3 SNPs kb −1 ) exceeds the highest density observed for any autosomal chromosome in the human genome. The extensive genomic variation and the distinct haplotype structure of innate immunity genes observed among individuals have possibly resulted from the impact of natural selection.

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Section: Discussionmentioning

confidence: 99%

Genetic variation and haplotype structures of innate immunity genes in eastern India

Bairagya

Bhattacharya

et al. 2008

Infection, Genetics and Evolution

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“…African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium among loci compared to non-African populations [1–8]. Nonetheless, most of our knowledge of the human genome is based on studies from populations of European ancestry, due to lack of investment in exploring genomics in Africa.…”

Section: Introductionmentioning

confidence: 99%

Implementation of genomics research in Africa: challenges and recommendations

Adebamowo

Francis

Tambo

et al. 2018

Global Health Action

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Background: There is exponential growth in the interest and implementation of genomics research in Africa. This growth has been facilitated by the Human Hereditary and Health in Africa (H3Africa) initiative, which aims to promote a contemporary research approach to the study of genomics and environmental determinants of common diseases in African populations. Objective: The purpose of this article is to describe important challenges affecting genomics research implementation in Africa. Methods: The observations, challenges and recommendations presented in this article were obtained through discussions by African scientists at teleconferences and face-to-face meetings, seminars at consortium conferences and in-depth individual discussions. Results: Challenges affecting genomics research implementation in Africa, which are related to limited resources include ill-equipped facilities, poor accessibility to research centers, lack of expertise and an enabling environment for research activities in local hospitals. Challenges related to the research study include delayed funding, extensive procedures and interventions requiring multiple visits, delays setting up research teams and insufficient staff training, language barriers and an underappreciation of cultural norms. While many African countries are struggling to initiate genomics projects, others have set up genomics research facilities that meet international standards. Conclusions: The lessons learned in implementing successful genomics projects in Africa are recommended as strategies to overcome these challenges. These recommendations may guide the development and application of new research programs in low-resource settings.

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“…23 Minor allele frequencies of many SNPs differ substantially between populations, allowing alleles, when expanded in frequency within one group, more chances to confer greater genetic susceptibility in that one particular population. 24 Examples of ethnic-specific differences in SLE genetic association studies include an association of the p53 gene in Koreans 25 that did not replicate in a Spanish Caucasian population, 26 an association of the heat-shock-protein-encoding gene, HSP70, in Spaniards and Africans but not in Mexicans 27 and the varying levels of significance of CTLA4 associated with SLE in Asians and Europeans.…”

Section: Introductionmentioning

confidence: 99%

Interferon regulatory factor-5 is genetically associated with systemic lupus erythematosus in African Americans

et al. 2008

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Increased expression of interferon (IFN)-inducible genes is implicated in the pathogenesis of systemic lupus erythematosus (SLE). One transcription factor responsible for regulating IFN, interferon regulatory factor-5 (IRF5), has been associated with SLE in genetic studies of Asian, Caucasian and Hispanic populations. We genotyped up to seven polymorphic loci in or near IRF5 in a total of 4870 African-American and Caucasian subjects (1829 SLE sporadic cases and 3041 controls) from two independent studies. Population-based case-control comparisons were performed using the Pearson's w 2 -test statistics and haplotypes were inferred using HaploView. We observed significant novel associations with the IRF5 variants rs2004640 and rs3807306 in African Americans and replicated previously reported associations in Caucasians. While we identified risk haplotypes, the majority of haplotypic effects were accounted for by one SNP (rs3807306) in conditional analyses. We conclude that genetic variants of IRF5 associate with SLE in multiple populations, providing evidence that IRF5 is likely to be a crucial component in SLE pathogenesis among multiple ethnic groups.

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A worldwide survey of haplotype variation and linkage disequilibrium in the human genome

Cited by 475 publications

References 44 publications

Genetic variation and haplotype structures of innate immunity genes in eastern India

Genetic variation and haplotype structures of innate immunity genes in eastern India

Implementation of genomics research in Africa: challenges and recommendations

Interferon regulatory factor-5 is genetically associated with systemic lupus erythematosus in African Americans

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