TY - JOUR
T1 - Full-length next-generation sequencing of HLA class I and II genes in a cohort from Thailand
AU - Geretz, Aviva
AU - Ehrenberg, Philip K.
AU - Bouckenooghe, Alain
AU - Fernández Viña, Marcelo A.
AU - Michael, Nelson L.
AU - Chansinghakule, Danaya
AU - Limkittikul, Kriengsak
AU - Thomas, Rasmi
N1 - Funding Information:
We would like to acknowledge Kelly May and Lauryn Cofer, MHRP, HJF for laboratory assistance. We thank Dr. Richard Apps, NIH, Bethesda for critical comments. The authors would like to thank participation of the parents and their children in Ratchaburi, Thailand. Authors also acknowledge the investigational staff at Department of Tropical Pediatrics, Mahidol University in Bangkok, Thailand who conducted the study. We would also like to thank the following Sanofi Pasteur (SP) employees for their contribution to the organization of the CYD59 study activities: Sanjay Gurunathan for WRAIR and SP partnership liaison, Julien Bertrand for clinical program management, Chalit Kosolsak for study monitoring and logistics, Fabrice Bailleux as biostatistician, Elena Puente for her support in writing the study report, and Anne Dagot for data management. Authors also acknowledge Louis Macareo and his team from Armed Forces Research Institute of Medical Sciences in Bangkok, Thailand for saliva samples shipment from Bangkok to WRAIR. This research was supported by a cooperative agreement (W81XWH-07-2-0067) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense (DOD). This research was funded, in part, by the U.S. National Institute of Allergy and Infectious Disease. The views expressed are those of the authors and should not be construed to represent the positions of the U.S. Army or the DOD.
Funding Information:
We would like to acknowledge Kelly May and Lauryn Cofer, MHRP, HJF for laboratory assistance. We thank Dr. Richard Apps, NIH, Bethesda for critical comments. The authors would like to thank participation of the parents and their children in Ratchaburi, Thailand. Authors also acknowledge the investigational staff at Department of Tropical Pediatrics, Mahidol University in Bangkok, Thailand who conducted the study. We would also like to thank the following Sanofi Pasteur (SP) employees for their contribution to the organization of the CYD59 study activities: Sanjay Gurunathan for WRAIR and SP partnership liaison, Julien Bertrand for clinical program management, Chalit Kosolsak for study monitoring and logistics, Fabrice Bailleux as biostatistician, Elena Puente for her support in writing the study report, and Anne Dagot for data management. Authors also acknowledge Louis Macareo and his team from Armed Forces Research Institute of Medical Sciences in Bangkok, Thailand for saliva samples shipment from Bangkok to WRAIR. This research was supported by a cooperative agreement (W81XWH-07-2-0067) between the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., and the U.S. Department of Defense (DOD). This research was funded, in part, by the U.S. National Institute of Allergy and Infectious Disease . The views expressed are those of the authors and should not be construed to represent the positions of the U.S. Army or the DOD.
Publisher Copyright:
© 2018
PY - 2018/11
Y1 - 2018/11
N2 - The human leukocyte antigen (HLA) genes are highly variable and are known to play an important role in disease outcomes, including infectious diseases. Prior knowledge of HLA polymorphisms in a population usually forms the basis for an effective case-control study design. As a prelude to future disease association analyses, we report HLA class I and II diversity in 334 unrelated donors from a Dengue vaccine efficacy trial conducted in Thailand. Long-range PCR amplification of six HLA loci was performed on DNA extracted from saliva samples. HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 were genotyped using a next-generation sequencing method presented at the 17th International HLA and Immunogenetics Workshop. In total, we identified 201 HLA alleles, including 35 HLA-A, 57 HLA-B, 28 HLA-C, 24 HLA-DPB1, 21 HLA-DQB1 and 36 HLA-DRB1 alleles. Very common HLA alleles with frequencies greater than 10 percent were A∗11:01:01, A∗33:03:01, A∗24:02:01, B∗46:01:01, C∗07:02:01, C∗01:02:01, C∗08:01:01, DPB1∗05:01:01, DPB1∗13:01:01, DPB1∗04:01:01, DPB1∗02:01:02, DQB1∗03:01:01, DQB1∗05:02:01, DQB1∗03:03:02, DRB1∗12:02:01, DRB1∗09:01:02, and DRB1∗15:02:01. A novel HLA allele, B∗15:450, had a non-synonymous substitution and occurred in more than one donor. Population-based full-length NGS HLA typing is more conclusive and provides a sound foundation for exploring disease association in a given population.
AB - The human leukocyte antigen (HLA) genes are highly variable and are known to play an important role in disease outcomes, including infectious diseases. Prior knowledge of HLA polymorphisms in a population usually forms the basis for an effective case-control study design. As a prelude to future disease association analyses, we report HLA class I and II diversity in 334 unrelated donors from a Dengue vaccine efficacy trial conducted in Thailand. Long-range PCR amplification of six HLA loci was performed on DNA extracted from saliva samples. HLA-A, -B, -C, -DPB1, -DQB1 and -DRB1 were genotyped using a next-generation sequencing method presented at the 17th International HLA and Immunogenetics Workshop. In total, we identified 201 HLA alleles, including 35 HLA-A, 57 HLA-B, 28 HLA-C, 24 HLA-DPB1, 21 HLA-DQB1 and 36 HLA-DRB1 alleles. Very common HLA alleles with frequencies greater than 10 percent were A∗11:01:01, A∗33:03:01, A∗24:02:01, B∗46:01:01, C∗07:02:01, C∗01:02:01, C∗08:01:01, DPB1∗05:01:01, DPB1∗13:01:01, DPB1∗04:01:01, DPB1∗02:01:02, DQB1∗03:01:01, DQB1∗05:02:01, DQB1∗03:03:02, DRB1∗12:02:01, DRB1∗09:01:02, and DRB1∗15:02:01. A novel HLA allele, B∗15:450, had a non-synonymous substitution and occurred in more than one donor. Population-based full-length NGS HLA typing is more conclusive and provides a sound foundation for exploring disease association in a given population.
KW - Dengue
KW - HLA alleles
KW - Illumina
KW - Next-generation sequencing
KW - Thailand
UR - http://www.scopus.com/inward/record.url?scp=85054032786&partnerID=8YFLogxK
U2 - 10.1016/j.humimm.2018.09.005
DO - 10.1016/j.humimm.2018.09.005
M3 - Article
C2 - 30243890
AN - SCOPUS:85054032786
SN - 0198-8859
VL - 79
SP - 773
EP - 780
JO - Human Immunology
JF - Human Immunology
IS - 11
ER -