Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population.
Slavé Petrovski,Slavé Petrovski,Jacques Fellay,Kevin V. Shianna,Nicole Carpenetti,Johnstone Kumwenda,Gift Kamanga,Deborah Kamwendo,Norman L. Letvin,Andrew J. McMichael,Barton F. Haynes,Myron S. Cohen,David Goldstein +12 more
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This is the first genome-wide association study of host determinants of HIV-1 susceptibility, performed in an African population, and investigates whether common genetic variants associate with HIV- 1 susceptibility in Africans.Abstract:
To date, CCR5 variants remain the only human genetic factors to be confirmed to impact HIV-1 acquisition. However, protective CCR5 variants are largely absent in African populations, in which sporadic resistance to HIV-1 infection is still unexplained. We investigated whether common genetic variants associate with HIV-1 susceptibility in Africans.read more
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Journal ArticleDOI
Human genetic susceptibility to infectious disease
TL;DR: Insight is provided into the genetic architecture of infectious disease susceptibility and immune molecules and pathways that are directly relevant to the human host defence are identified.
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Natural selection and infectious disease in human populations.
TL;DR: The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics.
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Transethnic meta-analysis of genomewide association studies.
TL;DR: A novel transethnic meta‐analysis methodology that takes account of the expected similarity in allelic effects between the most closely related populations, while allowing for heterogeneity between more diverse ethnic groups is proposed.
Journal ArticleDOI
Diversity and inclusion in genomic research: why the uneven progress?
TL;DR: The rationale for conducting genomic research in diverse populations is described by reviewing examples of advances facilitated by their inclusion and some of the factors that perpetuate the disproportionate attention on well-represented populations are explored.
Journal ArticleDOI
Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls
Paul J. McLaren,Paul J. McLaren,Paul J. McLaren,Cédric Coulonges,Stephan Ripke,Stephan Ripke,Leonard H. van den Berg,Susan Buchbinder,Mary Carrington,Mary Carrington,Andrea Cossarizza,Judith Dalmau,Steven G. Deeks,Olivier Delaneau,Andrea De Luca,James J. Goedert,David W. Haas,Joshua T. Herbeck,Sekar Kathiresan,Sekar Kathiresan,Gregory D. Kirk,Olivier Lambotte,Olivier Lambotte,Ma Luo,Ma Luo,Simon Mallal,Daniëlle van Manen,Daniëlle van Manen,Javier Martinez-Picado,Laurence Meyer,José M. Miró,James I. Mullins,Niels Obel,Stephen J. O'Brien,Florencia Pereyra,Florencia Pereyra,Francis A. Plummer,Francis A. Plummer,Guido Poli,Ying Qi,Pierre Rucart,M. S. Sandhu,M. S. Sandhu,Patrick R. Shea,Hanneke Schuitemaker,Hanneke Schuitemaker,Ioannis Theodorou,Fredrik O. Vannberg,Jan H. Veldink,Bruce D. Walker,Bruce D. Walker,Amy C. Weintrob,Cheryl A. Winkler,Steven M. Wolinsky,Amalio Telenti,David Goldstein,Paul I.W. de Bakker,Paul I.W. de Bakker,Paul I.W. de Bakker,Jean-François Zagury,Jacques Fellay,Jacques Fellay +61 more
TL;DR: Analysis of genome-wide single nucleotide polymorphism data collected by 25 cohorts, studies, or institutions on HIV-1 infected individuals and compared them to carefully matched population-level data sets suggest that genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size.
References
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Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
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Alkes L. Price,Alkes L. Price,Nick Patterson,Robert M. Plenge,Robert M. Plenge,Michael E. Weinblatt,Nancy A. Shadick,David Reich,David Reich +8 more
TL;DR: This work describes a method that enables explicit detection and correction of population stratification on a genome-wide scale and uses principal components analysis to explicitly model ancestry differences between cases and controls.
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Mark I. McCarthy,Mark I. McCarthy,Gonçalo R. Abecasis,Lon R. Cardon,Lon R. Cardon,David Goldstein,Julian Little,John P. A. Ioannidis,John P. A. Ioannidis,Joel N. Hirschhorn,Joel N. Hirschhorn,Joel N. Hirschhorn +11 more
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Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene.
Michel Samson,Frédérick Libert,Benjamin J. Doranz,Joseph Rucker,Corinne Liesnard,Claire-Michèle Farber,Sentob Saragosti,Claudine Lapoumeroulie,Jacqueline Cognaux,Christine Forceille,Gaëtan Muyldermans,Chris Verhofstede,Guy Burtonboy,Michel Georges,Tsuneo Imai,Shalini Rana,Yanji Yi,Robert J. Smyth,Ronald G. Collman,Robert W. Doms,Gilbert Vassart,Marc Parmentier +21 more
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Genetic Restriction of HIV-1 Infection and Progression to AIDS by a Deletion Allele of the CKR5 Structural Gene
Michael Dean,Mary Carrington,Cheryl A. Winkler,Gavin A. Huttley,Michael W. Smith,Rando Allikmets,James J. Goedert,Susan Buchbinder,Eric Vittinghoff,Edward D. Gomperts,Sharyne Donfield,David Vlahov,Richard A. Kaslow,Alfred J. Saah,Charles R. Rinaldo,Roger Detels,Stephen J. O'Brien +16 more
TL;DR: The CKR5Δ32 deletion may act as a recessive restriction gene against HIV-1 infection and may exert a dominant phenotype of delaying progression to AIDS among infected individuals.
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