HLA class I, KIR, and genome-wide SNP diversity in the RV144 Thai phase 3 HIV vaccine clinical trial

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• 作者：Heather A. Prentice (1) (2) r> Philip K. Ehrenberg (1) r> Karen M. Baldwin (1) (2) r> Aviva Geretz (1) (2) r> Charla Andrews (1) (2) r> Sorachai Nitayaphan (3) r> Supachai Rerks-Ngarm (4) r> Jaranit Kaewkungwal (5) r> Punnee Pitisuttithum (6) r> Robert J. O’Connell (3) r> Merlin L. Robb (1) (2) r> Jerome H. Kim (1) r> Nelson L. Michael (1) r> Rasmi Thomas (1) (2) r>
• 关键词：Ancestry informative markers (AIMs) ; Human leukocyte antigen (HLA) ; Killer cell immunoglobulin ; like receptors (KIR) ; Population stratification ; Thailand ; RV144
• 刊名：Immunogenetics
• 出版年：2014
• 出版时间：May 2014
• 年：2014
• 卷：66
• 期：5
• 页码：299-310
• 全文大小：944 KB
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• 作者单位：Heather A. Prentice (1) (2) r> Philip K. Ehrenberg (1) r> Karen M. Baldwin (1) (2) r> Aviva Geretz (1) (2) r> Charla Andrews (1) (2) r> Sorachai Nitayaphan (3) r> Supachai Rerks-Ngarm (4) r> Jaranit Kaewkungwal (5) r> Punnee Pitisuttithum (6) r> Robert J. O’Connell (3) r> Merlin L. Robb (1) (2) r> Jerome H. Kim (1) r> Nelson L. Michael (1) r> Rasmi Thomas (1) (2) r>r>1. U.S. Military HIV Research Program (MHRP), Walter Reed Army Institute of Research, Silver Spring, MD, USA r> 2. Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA r> 3. Department of Retrovirology, US Army Medical Component, AFRIMS, Bangkok, Thailand r> 4. Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand r> 5. Center of Excellence for Biomedical and Public Health Informatics BIOPHICS, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand r> 6. Vaccine Trials Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand r>
• ISSN：1432-1211

文摘

RV144 is the first phase 3 HIV vaccine clinical trial to demonstrate efficacy. This study consisted of more than 8,000 individuals in each arm of the trial, representing the four major regions of Thailand. Human leukocyte antigen (HLA) class I and killer cell immunoglobulin-like receptor (KIR) genes, as well as 96 genome-wide ancestry informative markers (AIMs) were genotyped in 450 placebo HIV-1-uninfected individuals to identify the immunogenetic diversity and population structure of this cohort. High-resolution genotyping identified the common HLA alleles as A*02:03, A*02:07, A*11:01, A*24:02, A*24:07, A*33:03, B*13:01, B*15:02, B*18:01, B*40:01, B*44:03, B*46:01, B*58:01, C*01:02, C*03:02, C*03:04, C*07:01, C*07:02, C*07:04, and C*08:01. The most frequent three-loci haplotype was B*46:01-C*01:02-A*02:07. Framework genes KIR2DL4, 3DL2, and 3DL3 were present in all samples, and KIR2DL1, 2DL3, 3DL1, 2DS4, and 2DP1 occurred at frequencies greater than 90?%. The combined HLA and KIR profile suggests admixture with neighboring Asian populations. Principal component and correspondence analyses comparing the RV144 samples to the phase 3 International HapMap Project (HapMap3) populations using AIMs corroborated these findings. Structure analyses identified a distinct profile in the Thai population that did not match the Asian or other HapMap3 samples. This shows genetic variability unique to Thais in RV144, making it essential to take into account population stratification while performing genetic association studies. The overall analyses from all three genetic markers indicate that the RV144 samples are representative of the Thai population. This will inform subsequent host genetic analyses in the RV144 cohort and provide insight for future genetic association studies in the Thai population.