Associations of genetically determined continental ancestry with CD4+ count and plasma HIV-1 RNA beyond self-reported race and ethnicity

Journal of Acquired Immune Deficiency Syndromes

Volumn 71, Issue 5, 2016, Pages 544-550

  Brummel, Sean S ^a   Singh, Kumud K ^b,c   Maihofer, Adam X ^b   Farhad, Mona ^a   Qin, Min ^a   Fenton, Terry ^a   Nievergelt, Caroline M ^b   Spector, Stephen A ^b,c  

^a CENTER FOR BIOSTATISTICS IN AIDS RESEARCH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c RADY CHILDREN'S HOSPITAL   (United States)

Author keywords

Ancestry informative markers; CD4+ lymphocyte count; Continental ancestry; HIV; HIV RNA

Indexed keywords

VIRUS RNA; BIOLOGICAL MARKER;

ANCESTRY GROUP; ARTICLE; CD4 LYMPHOCYTE COUNT; CHILD; ETHNICITY; FEMALE; GENE FREQUENCY; GENETIC ASSOCIATION; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; NONHUMAN; PRIORITY JOURNAL; RACE; RANDOMIZED CONTROLLED TRIAL (TOPIC); REAL TIME POLYMERASE CHAIN REACTION; SELF REPORT; UNITED STATES; BLOOD; ETHNOLOGY; GENETICS; IMMUNOLOGY; INFANT; PRESCHOOL CHILD; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VIRUS LOAD;

BIOMARKERS; CD4 LYMPHOCYTE COUNT; CHILD; CHILD, PRESCHOOL; CONTINENTAL POPULATION GROUPS; FEMALE; GENE FREQUENCY; GENOTYPE; HIV INFECTIONS; HIV-1; HUMANS; INFANT; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; REGRESSION ANALYSIS; RNA, VIRAL; UNITED STATES; VIRAL LOAD;

EID: 84946422943     PISSN: 15254135     EISSN: 10779450     Source Type: Journal    
DOI: 10.1097/QAI.0000000000000883     Document Type: Article

References (33)

1. Witzig R. The medicalization of race: scientific legitimization of a flawed social construct. Ann Intern Med. 1996;125:675-679.
2. Burchard EG, Ziv E, Coyle N, et al. The importance of race and ethnic background in biomedical research and clinical practice. N Engl J Med. 2003;348:1170-1175.
3. Kaufman JS, Cooper RS. Commentary: considerations for use of racial/ethnic classification in etiologic research. Am J Epidemiol. 2001; 154:291-298.
4. Tang H, Quertermous T, Rodriguez B, et al. Genetic structure, selfidentified race/ethnicity, and confounding in case-control association studies. Am J Hum Genet. 2005;76:268-275.
5. Johnson J. Predictability of the effects of race or ethnicity on pharmacokinetics of drugs. Int J Clin Pharmacol Ther. 2000;38:53-60.
6. Kappelhoff BS, Huitema AD, Yalvaç Z, et al. Population pharmacokinetics of efavirenz in an unselected cohort of HIV-1-infected individuals. Clin Pharmacokinet. 2005;44:849-861.
7. Bidulescu A, Choudhry S, Musani SK, et al. Associations of adiponectin with individual European ancestry in African Americans: the Jackson Heart Study. Front Genet. 2014;5:22.
8. Daya M, van der Merwe L, van Helden PD, et al. The role of ancestry in TB susceptibility of an admixed South African population. Tuberculosis. 2014;94:413-420.
9. Winkler CA, Nelson GW, Smith MW. Admixture mapping comes of age. Annu Rev Genomics Hum Genet. 2010;11:65-89.
10. Winkler C, An P, O'Brien SJ. Patterns of ethnic diversity among the genes that influence AIDS. Hum Mol Genet. 2004;13:R9-R19.
11. Seldin MF, Price AL. Application of ancestry informative markers to association studies in European Americans. PLoS Genet. 2008;4:e5.
12. Theodorou I, Capoulade C, Combadiere C, et al. Genetic control of HIV disease. Trends Microbiol. 2003;11:392-397.
13. An P, Winkler CA. Host genes associated with HIV/AIDS: advances in gene discovery. Trends Genet. 2010;26:119-131.
14. Singh KK, Spector SA. Host genetic determinants of human immunodeficiency virus infection and disease progression in children. Pediatr Res. 2009;65:55R-63R.
15. Frasco MA, Mack WJ, Van Den Berg D, et al. Underlying genetic structure impacts the association between CYP2B6 polymorphisms and response to efavirenz and nevirapine. AIDS. 2012;26:2097-2106.
16. Nicholaou MJ, Martinson JJ, Abraham AG, et al. HAART-associated dyslipidemia varies by biogeographical ancestry in the multicenter AIDS cohort study. AIDS Res Hum Retroviruses. 2013;29:871-879.
17. Cheruvu VK, Igo RP Jr, Jurevic RJ, et al. African ancestry influences CCR5-2459G.A genotype-associated virologic success of highly active antiretroviral therapy. J Acquir Immune Defic Syndr. 2014;66:102-107.
18. Nievergelt CM, Maihofer AX, Shekhtman T, et al. Inference of human continental origin and admixture proportions using a highly discriminative ancestry informative 41-SNP panel. Invest Genet. 2013;4:13.
19. Englund JA, Baker CJ, Raskino C, et al. Zidovudine, didanosine, or both as the initial treatment for symptomatic HIV-infected children. AIDS Clinical Trials Group (ACTG) Study 152 Team. N Engl J Med. 1997; 336:1704-1712.
20. McKinney RE Jr, Johnson GM, Stanley K, et al. A randomized study of combined zidovudine-lamivudine versus didanosine monotherapy in children with symptomatic therapy-naive HIV-1 infection. The Pediatric AIDS Clinical Trials Group Protocol 300 Study Team. J Pediatr. 1998; 133:500-508.
21. Palumbo PE, Raskino C, Fiscus S, et al. Virologic and immunologic response to nucleoside reverse-transcriptase inhibitor therapy among human immunodeficiency virus-infected infants and children. J Infect Dis. 1999;179:576-583.
22. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945-959.
23. Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003;164:1567-1587.
24. White H. A heteroskedasticity-consistent covariance matrix estimator and a direct test for heteroskedasticity. Econometrica. 1980;48:817-838.
25. Qin M, Brummel S, Singh KK, et al. Associations of host genetic variants on CD4+ lymphocyte count and plasma HIV-1 RNA in antiretroviral naive children. Pediatr Infect Dis J. 2014;33:946-952.
26. Lin DY, Zeng D. Correcting for population stratification in genomewide association studies. J Am Stat Assoc. 2011;106:997-1008.
27. Nassir R, Kosoy R, Tian C, et al. An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels. BMC Genet. 2009;10:39.
28. Tian C, Plenge RM, Ransom M, et al. Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet. 2008;4:e4.
29. Menotti A, Lanti M, Puddu P, et al. Coronary heart disease incidence in northern and southern European populations: a reanalysis of the seven countries study for a European coronary risk chart. Heart. 2000;84: 238-244.
30. Miller TI, Borkowsky W, DiMeglio LA, et al. Metabolic abnormalities and viral replication are associated with biomarkers of vascular dysfunction in HIV-infected children. HIV Med. 2012;13:264-275.
31. Aldrovandi GM, Lindsey JC, Jacobson DL, et al. Morphologic and metabolic abnormalities in vertically HIV-infected children and youth. AIDS. 2009;23:661-672.
32. VanderWeele TJ, Robins JM. Four types of effect modification: a classification based on directed acyclic graphs. Epidemiology. 2007; 18:561-568.
33. Rough K, Tassiopoulos K, Kacanek D, et al. Dramatic decline in substance use by HIV-infected pregnant women in the United States from 1990 to 2012. AIDS. 2015;29:117-123.