An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1.
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.
Crawford
D C
DC
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA.
Zheng
N
N
Speelmon
E C
EC
Stanaway
I
I
Rieder
M J
MJ
Nickerson
D A
DA
McElrath
M J
MJ
Lingappa
J
J
D018528:ATP-Binding Cassette Transporters / Q000235:genetics* / Q000276:immunology; D001741:Black or African American / Q000235:genetics*; D005828:Genetics, Population; D015658:HIV Infections / Q000235:genetics* / Q000276:immunology; D015497:HIV-1 / Q000502:physiology*; D006801:Humans; D009549:Nigeria; D020641:Polymorphism, Single Nucleotide; D014779:Virus Replication
C501917:ABCE1 protein, human; D018528:ATP-Binding Cassette Transporters