{"id":165798,"date":"2013-10-29T00:00:00","date_gmt":"2013-10-29T00:00:00","guid":{"rendered":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/msr-research-item\/a-genome-to-genome-analysis-of-associations-between-human-genetic-variation-hiv-1-sequence-diversity-and-viral-control\/"},"modified":"2018-10-16T20:15:51","modified_gmt":"2018-10-17T03:15:51","slug":"a-genome-to-genome-analysis-of-associations-between-human-genetic-variation-hiv-1-sequence-diversity-and-viral-control","status":"publish","type":"msr-research-item","link":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/publication\/a-genome-to-genome-analysis-of-associations-between-human-genetic-variation-hiv-1-sequence-diversity-and-viral-control\/","title":{"rendered":"A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control"},"content":{"rendered":"<div class=\"asset-content\">\n<p>HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations to a total of 48 HIV-1 amino acid variants (p<2.4 \u00d7 10\u221212). All associated SNPs mapped to the HLA class I region. Clinical relevance of host and pathogen variation was assessed using VL results. We identified two critical advantages to the use of viral variation for identifying host factors: (1) association signals are much stronger for HIV-1 sequence variants than VL, reflecting the \u2018intermediate phenotype\u2019 nature of viral variation; (2) association testing can be run without any clinical data. The proposed genome-to-genome approach highlights sites of genomic conflict and is a strategy generally applicable to studies of host\u2013pathogen interaction.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>HIV-1 sequence diversity is affected by selection pressures arising from host genomic factors. Using paired human and viral data from 1071 individuals, we ran >3000 genome-wide scans, testing for associations between host DNA polymorphisms, HIV-1 sequence variation and plasma viral load (VL), while considering human and viral population structure. We observed significant human SNP associations 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