An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1.

Crawford DC, Zheng N, Speelmon EC, Stanaway I, Rieder MJ, Nickerson DA, McElrath MJ, Lingappa J
Genes Immun. 2009 10 (8): 715-21

PMID: 19657357 · PMCID: PMC2829431 · DOI:10.1038/gene.2009.57

Signatures of natural selection occur throughout the human genome and can be detected at the sequence level. We have re-sequenced ABCE1, a host candidate gene essential for HIV-1 capsid assembly, in European- (n=23) and African-descent (Yoruban; n=24) reference populations for genetic variation discovery. We identified an excess of rare genetic variation in Yoruban samples, and the resulting Tajima's D was low (-2.27). The trend of excess rare variation persisted in flanking candidate genes ANAPC10 and OTUD4, suggesting that this pattern of positive selection can be detected across the 184.5 kb examined on chromosome 4. Owing to ABCE1's role in HIV-1 replication, we re-sequenced the candidate gene in three small cohorts of HIV-1-infected or resistant individuals. We were able to confirm the excess of rare genetic variation among HIV-1-positive African-American individuals (n=53; Tajima's D=-2.34). These results highlight the potential importance of ABCE1's role in infectious diseases such as HIV-1.

MeSH Terms (9)

African Americans ATP-Binding Cassette Transporters Genetics, Population HIV-1 HIV Infections Humans Nigeria Polymorphism, Single Nucleotide Virus Replication

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