Table 1. | A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

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A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

Table 1.

Affiliation details

École Polytechnique Fédérale de Lausanne, Switzerland; University Hospital and University of Lausanne, Switzerland; Eötvös Loránd University and the Hungarian Academy of Sciences, Hungary; Swiss Institute of Bioinformatics, Switzerland; Microsoft Research, United States; BC Centre for Excellence in HIV/AIDS, Canada; Simon Fraser University, Canada; Murdoch University, Australia; Vanderbilt University Medical Center, United States; Universitat Autònoma de Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Spain; Instituto de Salud Carlos III, Spain; University of Bern & Inselspital, Switzerland; University Hospital and University of Zürich, Switzerland; Regional Hospital of Lugano, Switzerland; Cantonal Hospital, Switzerland; University of Basel, Switzerland; Geneva University Hospitals, Switzerland; St. Petersburg State University, Russia; Massachusetts General Hospital, United States; University of British Columbia, Canada
Table 1.

Associations between HIV-1 amino acid variants and human polymorphisms

DOI: http://dx.doi.org/10.7554/eLife.01123.005

HIV geneHIV positionSNPCTL epitope (codons)Tagging HLA (D’/r2)SNP vs aa (p)SNP vs VL (p)aa vs VL (p)
GAG12chr6:31285512B*49:01 (1.00/1.00)2.20E-136.70E-015.60E-01
GAG26rs12524487B*15:01 (1.00/0.82)6.10E-192.10E-011.40E-01
GAG28rs1655912RLRPGGKKK (20–28)A*03:01 (1.00/0.81)2.70E-555.60E-012.00E-02
GAG79chr6:31267544LYNTVATL (78-85)C*14:02 (1.00/0.96)2.40E-123.50E-012.80E-01
GAG147rs1055821C*06:02 (0.95/0.71)3.10E-173.30E-072.90E-05
GAG242rs73392116TSTLQEQIGW (240–249)B*57:01 (1.00/0.98)2.40E-621.90E-061.70E-05
GAG248rs41557213TSTLQEQIGW (240-249)B*57:01 (1.00/0.97)4.80E-152.00E-065.30E-03
GAG264chr6:31376564KRWIILGLNK (263–272)B*27:05 (1.00/0.92)2.30E-135.50E-023.50E-01
GAG268rs2249935GEIYKRWIIL (259–268)B*08:01 (1.00/0.43)2.20E-145.10E-011.90E-01
GAG340rs11966319B*15:01 (0.94/0.42)6.70E-144.60E-017.70E-01
C*03:04 (0.99/0.59)
GAG357rs2523612GPGHKARVL (355-363)B*07:02 (0.99/0.95)2.70E-192.20E-011.20E-01
C*07:02 (0.99/0.84)
GAG397rs61754472A*31:01 (0.97/0.83)8.80E-213.50E-018.30E-01
GAG403rs288965718.90E-217.90E-018.60E-01
GAG437rs34268928RQANFLGKI (429-437)B*13:02 (1.00/0.96)8.70E-141.80E-026.80E-02
GP41206rs17881210B*15:01 (1.00/0.88)6.10E-176.10E-013.00E-01
GP41267rs9278477RLRDLLLIVTR (259–269)A*03:01 (1.00/0.01)1.00E-127.80E-012.60E-01
INT11rs2596477B*44:02 (1.00/0.64)5.10E-331.50E-011.80E-01
INT32rs1050502B*51:01 (0.97/0.92)4.80E-187.20E-014.00E-01
INT119rs9264954C*05:01 (1.00/1.00)1.30E-247.90E-011.10E-01
INT122rs9264419C*05:01 (1.00/0.95)4.50E-228.30E-017.80E-01
INT124chr6:31345421STTVKAACWW (123–132)B*57:01 (1.00/1.00)3.00E-131.10E-069.70E-03
NEF71rs2596488FPVTPQVPLR (68–77)B*07:02 (1.00/0.98)3.80E-552.50E-018.10E-02
C*07:02 (0.95/0.83)
NEF81rs9295987RPMTYKAAL (77–85)B*07:02 (1.00/0.01)4.80E-362.50E-019.50E-02
C*04:01 (0.90/0.63)
NEF83rs34768512B*15:01 (1.00/0.47)2.20E-172.80E-011.50E-02
C*03:04 (0.96/0.54)
NEF85rs2395475RPMTYKAAL (77–85)B*07:02 (1.00/0.29)1.90E-248.10E-011.30E-03
B*08:01 (1.00/0.22)
C*07:02 (0.97/0.30)
NEF92rs16896166AVDLSHFLK (84–92)A*11:01 (1.00/0.99)1.00E-275.30E-011.50E-01
NEF94rs9265972FLKEKGGL (90–97)B*08:01 (1.00/0.97)9.60E-359.80E-011.20E-01
NEF102rs2524277B*44:03 (0.98/0.96)1.10E-134.40E-012.40E-01
NEF105rs1049709C*07:01 (1.00/0.98)1.10E-359.00E-012.70E-01
NEF116chr6:31402358HTQGYFPDW (116–124)B*57:01 (1.00/1.00)3.00E-221.90E-063.30E-01
NEF120chr6:31236168-C*14:02 (1.00/1.00)4.40E-163.60E-011.20E-02
NEF126chr6:31102273B*51:01 (1.00/0.18)1.10E-121.80E-014.90E-02
NEF133chr6:31397689B*35:01 (0.95/0.89)2.80E-192.50E-013.40E-01
NEF135rs72845950RYPLTFGW (134–141)A*24:02 (1.00/0.88)2.70E-669.10E-025.50E-03
PR35rs2523577EEMNLPGRW (34-42)B*44:02 (1.00/0.64)1.70E-181.60E-015.70E-01
PR93rs2263323B*15:01 (0.98/0.92)5.60E-304.70E-019.50E-01
RNASE28rs2428481B*08:01 (1.00/1.00)1.80E-128.10E-016.20E-01
RT135rs1050502TAFTIPSI (128–135)B*51:01 (0.97/0.92)6.70E-457.20E-013.00E-01
RT245chr6:31411714IVLPEKDSW (244–252)B*57:01 (1.00/0.98)2.90E-211.20E-065.40E-02
RT277rs3128902QIYPGIKVR (269–277)A*03:01 (1.00/0.99)1.20E-658.20E-012.70E-01
RT369rs17190134B*13:02 (0.93/0.86)3.50E-206.40E-021.40E-01
RT395rs17194293-1.50E-121.20E-017.70E-02
TAT29rs9260615A*32:01 (0.98/0.95)4.40E-143.90E-011.40E-01
TAT32rs16899214CCFHCQVC (30–37)C*12:03 (0.98/0.96)6.40E-213.40E-014.90E-01
VIF33chr6:31430060ISKKAKGWF (31–39)B*57:01 (1.00/0.98)1.50E-139.90E-079.30E-03
VIF51rs7767850B*49:01 (1.00/1.00)1.40E-125.20E-012.10E-01
VIF74rs2395029B*57:01 (1.00/0.98)5.40E-139.70E-072.80E-01
VPR32chr6:31362941VRHFPRIWL (31–39)B*27:05 (1.00/0.94)3.10E-135.40E-026.50E-01
  • Significant associations (p < 2.4 × 10-12) were observed for 48 HIV-1 amino acid variants. The table shows the major amino acid variants present at each specific HIV-1 position, the strongest associated SNP and its linked HLA class I allele(s), if applicable. The column ‘CTL Epitope (codons)’ lists published, optimally described CTL epitopes (available at http://www.hiv.lanl.gov/content/immunology/tables/optimal_ctl_summary.html and in [Carlson et al., 2012]) restricted by the tagged HLA class I allele(s) specified, and their positions within the protein. Where multiple overlapping epitopes restricted by the same HLA class I allele have been described, only one is shown. Associations where no relevant CTL epitope has been described are indicated with a dash. The last three columns give association p-values for comparisons between human SNPs and viral amino acids, human SNPs and plasma VL and viral amino acids and plasma VL, respectively. For tests involving viral amino acids accommodating more than 1 alternate allele, the smallest association p-value observed at that position is reported.