{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T06:30:13Z","timestamp":1769754613589,"version":"3.49.0"},"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2015,3,18]],"date-time":"2015-03-18T00:00:00Z","timestamp":1426636800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0118149","type":"journal-article","created":{"date-parts":[[2015,3,18]],"date-time":"2015-03-18T20:24:42Z","timestamp":1426710282000},"page":"e0118149","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["Novel Genetic Locus Implicated for HIV-1 Acquisition with Putative Regulatory Links to HIV Replication and Infectivity: A Genome-Wide Association Study"],"prefix":"10.1371","volume":"10","author":[{"given":"Eric O.","family":"Johnson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dana B.","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan C.","family":"Gaddis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua L.","family":"Levy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Grier","family":"Page","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott P.","family":"Novak","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristie","family":"Glasheen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy L.","family":"Saccone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John P.","family":"Rice","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael P.","family":"Moreau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kimberly F.","family":"Doheny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jane M.","family":"Romm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew I.","family":"Brooks","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bradley E.","family":"Aouizerat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura J.","family":"Bierut","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex H.","family":"Kral","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,3,18]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"a007203","DOI":"10.1101\/cshperspect.a007203","article-title":"Host genes important to HIV replication and evolution","volume":"2","author":"A Telenti","year":"2012","journal-title":"Cold Spring Harb Perspect Med"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.1371\/journal.pbio.0060032","article-title":"In vitro whole-genome analysis identifies a susceptibility locus for HIV-1","volume":"6","author":"C Loeuillet","year":"2008","journal-title":"PLoS Biol"},{"key":"ref3","first-page":"1116","article-title":"A model-based estimate of HIV infectivity via needle sharing","volume":"5","author":"EH Kaplan","year":"1992","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1136\/bmj.304.6830.809","article-title":"Comparison of female to male and male to female transmission of HIV in 563 stable couples. European Study Group on Heterosexual Transmission of HIV","volume":"304","year":"1992","journal-title":"BMJ"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1097\/00007435-200201000-00007","article-title":"Reducing the risk of sexual HIV transmission: quantifying the per-act risk for HIV on the basis of choice of partner, sex act, and condom use","volume":"29","author":"B Varghese","year":"2002","journal-title":"Sex Transm Dis"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/gm138","article-title":"A whole genome association study of mother-to-child transmission of HIV in Malawi","volume":"2","author":"BR Joubert","year":"2010","journal-title":"Genome Med"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"e28632","DOI":"10.1371\/journal.pone.0028632","article-title":"Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure","volume":"6","author":"JR Lingappa","year":"2011","journal-title":"PLoS One"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1097\/QAD.0b013e328343817b","article-title":"Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population","volume":"25","author":"S Petrovski","year":"2011","journal-title":"AIDS"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"11899","DOI":"10.1128\/JVI.01499-12","article-title":"A genetic polymorphism of FREM1 is associated with resistance against HIV infection in the Pumwani sex worker cohort","volume":"86","author":"M Luo","year":"2012","journal-title":"J Virol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1903","DOI":"10.1093\/hmg\/ddt033","article-title":"A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A","volume":"22","author":"J Lane","year":"2013","journal-title":"Hum Mol Genet"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1093\/infdis\/jis028","article-title":"Multicohort genomewide association study reveals a new signal of protection against HIV-1 acquisition","volume":"205","author":"S Limou","year":"2012","journal-title":"J Infect Dis"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e1003515","DOI":"10.1371\/journal.ppat.1003515","article-title":"Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls","volume":"9","author":"PJ McLaren","year":"2013","journal-title":"PLoS Pathog"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1038\/382722a0","article-title":"Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene","volume":"382","author":"M Samson","year":"1996","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1093\/hmg\/8.10.1939","article-title":"Genetics of HIV-1 infection: chemokine receptor CCR5 polymorphism and its consequences","volume":"8","author":"M Carrington","year":"1999","journal-title":"Hum Mol Genet"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e1001033","DOI":"10.1371\/journal.ppat.1001033","article-title":"Host genetics and HIV-1: the final phase?","volume":"6","author":"J Fellay","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/S0140-6736(00)04562-1","article-title":"Sexual transmission of HIV-1 among injection drug users in San Francisco, USA: risk-factor analysis","volume":"357","author":"AH Kral","year":"2001","journal-title":"Lancet"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1093\/aje\/kwg070","article-title":"Trends in human immunodeficiency virus seroincidence among street-recruited injection drug users in San Francisco, 1987\u20131998","volume":"157","author":"AH Kral","year":"2003","journal-title":"Am J Epidemiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1534\/g3.111.001198","article-title":"Genotype imputation with thousands of genomes","volume":"1","author":"B Howie","year":"2011","journal-title":"G3 (Bethesda)"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","year":"2010","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e12600","DOI":"10.1371\/journal.pone.0012600","article-title":"Multiethnic genetic association studies improve power for locus discovery","volume":"5","author":"SL Pulit","year":"2010","journal-title":"PLoS One"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1002\/gepi.20630","article-title":"Transethnic meta-analysis of genomewide association studies","volume":"35","author":"AP Morris","year":"2011","journal-title":"Genet Epidemiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.ajhg.2010.11.007","article-title":"Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height","volume":"88","author":"MB Lanktree","year":"2011","journal-title":"Am J Hum Genet"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1093\/hmg\/dds396","article-title":"Gene-centric meta-analyses of 108 912 individuals confirm known body mass index loci and reveal three novel signals","volume":"22","author":"Y Guo","year":"2013","journal-title":"Hum Mol Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1093\/bioinformatics\/btq340","article-title":"METAL: fast and efficient meta-analysis of genomewide association scans","volume":"26","author":"CJ Willer","year":"2010","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1002\/gepi.20303","article-title":"Estimation of the multiple testing burden for genomewide association studies of nearly all common variants","volume":"32","author":"I Pe'er","year":"2008","journal-title":"Genet Epidemiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1128\/CDLI.12.9.1013-1019.2005","article-title":"The Women's Interagency HIV Study: an observational cohort brings clinical sciences to the bench","volume":"12","author":"MC Bacon","year":"2005","journal-title":"Clin Diagn Lab Immunol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1038\/ng.888","article-title":"Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations","volume":"43","author":"DG Torgerson","year":"2011","journal-title":"Nat Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1016\/j.jaci.2012.07.054","article-title":"Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans","volume":"130","author":"RA Myers","year":"2012","journal-title":"J Allergy Clin Immunol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e1000294","DOI":"10.1371\/journal.pbio.1000294","article-title":"Rare variants create synthetic genome-wide associations","volume":"8","author":"SP Dickson","year":"2010","journal-title":"PLoS Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e1001008","DOI":"10.1371\/journal.pbio.1001008","article-title":"The importance of synthetic associations will only be resolved empirically","volume":"9","author":"DB Goldstein","year":"2011","journal-title":"PLoS Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/sj.hdy.6800717","article-title":"Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix","volume":"95","author":"J Li","year":"2005","journal-title":"Heredity (Edinb)"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1086\/383251","article-title":"A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other","volume":"74","author":"DR Nyholt","year":"2004","journal-title":"Am J Hum Genet"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"D930","DOI":"10.1093\/nar\/gkr917","article-title":"HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants","volume":"40","author":"LD Ward","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature08903","article-title":"Transcriptome genetics using second generation sequencing in a Caucasian population","volume":"464","author":"SB Montgomery","year":"2010","journal-title":"Nature"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2474","DOI":"10.1093\/bioinformatics\/btq452","article-title":"Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies","volume":"26","author":"TP Yang","year":"2010","journal-title":"Bioinformatics"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1038\/ng.2394","article-title":"Mapping cis- and trans-regulatory effects across multiple tissues in twins","volume":"44","author":"E Grundberg","year":"2012","journal-title":"Nat Genet"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e1002639","DOI":"10.1371\/journal.pgen.1002639","article-title":"Patterns of cis regulatory variation in diverse human populations","volume":"8","author":"BE Stranger","year":"2012","journal-title":"PLoS Genet"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.tig.2010.01.002","article-title":"Host genes associated with HIV\/AIDS: advances in gene discovery","volume":"26","author":"P An","year":"2010","journal-title":"Trends Genet"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1375\/twin.8.2.87","article-title":"Allele frequencies and the r2 measure of linkage disequilibrium: impact on design and interpretation of association studies","volume":"8","author":"NR Wray","year":"2005","journal-title":"Twin Res Hum Genet"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3943","DOI":"10.1073\/pnas.1217271110","article-title":"Related F-box proteins control cell death in Caenorhabditis elegans and human lymphoma","volume":"110","author":"M Chiorazzi","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/sj.cdd.4400822","article-title":"Biochemical mechanisms of HIV induced T cell apoptosis","volume":"8","author":"N Selliah","year":"2001","journal-title":"Cell Death Differ"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"9698","DOI":"10.1128\/JVI.72.12.9698-9705.1998","article-title":"Human immunodeficiency virus induces a dual regulation of Bcl-2, resulting in persistent infection of CD4(+) T- or monocytic cell lines","volume":"72","author":"F Aillet","year":"1998","journal-title":"J Virol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e1002636","DOI":"10.1371\/journal.ppat.1002636","article-title":"Treatment with IL-7 prevents the decline of circulating CD4+ T cells during the acute phase of SIV infection in rhesus macaques","volume":"8","author":"L Vassena","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"24718","DOI":"10.1074\/jbc.M803497200","article-title":"The PDZ and band 4.1 containing protein Frmpd1 regulates the subcellular location of activator of G-protein signaling 3 and its interaction with G-proteins","volume":"283","author":"N An","year":"2008","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/j.jmb.2013.01.003","article-title":"Structural and biochemical characterization of the interaction between LGN and Frmpd1","volume":"425","author":"Z Pan","year":"2013","journal-title":"J Mol Biol"},{"key":"ref46","article-title":"Human MCS5A1 candidate breast cancer susceptibility gene FBXO10 is induced by cellular stress and correlated with lens epithelium-derived growth factor (LEDGF)","author":"X Xu","year":"2012","journal-title":"Mol Carcinog"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"a006890","DOI":"10.1101\/cshperspect.a006890","article-title":"HIV DNA Integration","volume":"2","author":"R Craigie","year":"2012","journal-title":"Cold Spring Harb Perspect Med"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/1742-4690-10-31","article-title":"Molecular signatures of T-cell inhibition in HIV-1 infection","volume":"10","author":"M Larsson","year":"2013","journal-title":"Retrovirology"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1016\/j.cell.2006.03.028","article-title":"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases","volume":"125","author":"JR Whetstine","year":"2006","journal-title":"Cell"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e1000554","DOI":"10.1371\/journal.ppat.1000554","article-title":"CpG methylation controls reactivation of HIV from latency","volume":"5","author":"J Blazkova","year":"2009","journal-title":"PLoS Pathog"}],"updated-by":[{"DOI":"10.1371\/journal.pone.0129671","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2015,5,29]],"date-time":"2015-05-29T00:00:00Z","timestamp":1432857600000}}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0118149","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T00:30:57Z","timestamp":1598833857000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0118149"}},"subtitle":[],"editor":[{"given":"Weijing","family":"He","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,3,18]]},"references-count":50,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2015,3,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0118149","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pone.0129671","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,18]]}}}