RGD Reference Report - An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1. - Rat Genome Database

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

Authors: Crawford, DC  Zheng, N  Speelmon, EC  Stanaway, I  Rieder, MJ  Nickerson, DA  McElrath, MJ  Lingappa, J 
Citation: Crawford DC, etal., Genes Immun. 2009 Dec;10(8):715-21. doi: 10.1038/gene.2009.57. Epub 2009 Aug 6.
RGD ID: 11041871
Pubmed: PMID:19657357   (View Abstract at PubMed)
PMCID: PMC2829431   (View Article at PubMed Central)
DOI: DOI:10.1038/gene.2009.57   (Journal Full-text)

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.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
human immunodeficiency virus infectious disease  IAGP 11041871DNA:mutations:multiple (human)RGD 
human immunodeficiency virus infectious disease  ISOABCE1 (Homo sapiens)11041871; 11041871DNA:mutations:multiple (human)RGD 

Objects Annotated

Genes (Rattus norvegicus)
Abce1  (ATP binding cassette subfamily E member 1)

Genes (Mus musculus)
Abce1  (ATP-binding cassette, sub-family E member 1)

Genes (Homo sapiens)
ABCE1  (ATP binding cassette subfamily E member 1)


Additional Information