TY - JOUR
T1 - Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-Lymphoblastoid cell lines
T2 - report from the 17th International HLA and Immunogenetics Workshop
AU - Creary, Lisa E
AU - Guerra, Sandra G
AU - Chong, Winnie
AU - Brown, Colin J
AU - Turner, Thomas R
AU - Robinson, James
AU - Bultitude, Will P
AU - Mayor, Neema P
AU - Marsh, Steven G E
AU - Saito, Katsuyuki
AU - Lam, Kevin
AU - Duke, Jamie L
AU - Mosbruger, Timothy L
AU - Ferriola, Deborah
AU - Monos, Dimitrios
AU - Willis, Amanda
AU - Askar, Medhat
AU - Fischer, Gottfried
AU - Loong Saw, Chee
AU - Ragoussis, Ioannis
AU - Petrek, Martin
AU - Serra-Pagés, Carles
AU - Juan Otero, Manel
AU - Stavropoulos-Giokas, Catherine
AU - Dinou, Amalia
AU - Ameen, Reem
AU - Al Shemmari, Salem
AU - Spierings, Eric
AU - Gendzekhadze, Ketevan
AU - Morris, Gerald P
AU - Zhang, Quiheng
AU - Kashi, Zahra
AU - Hsu, Susan
AU - Gangavarapu, Sridevi
AU - Mallempati, Kalyan C
AU - Yamamoto, Fumiko
AU - Osoegawa, Kazutoyo
AU - Vayntrub, Tamara
AU - Chang, Chia-Jung
AU - Hansen, John A
AU - Fernández-Viňa, Marcelo A
N1 - Funding Information:
We gratefully acknowledge the Fred Hutchinson Cancer Research center for providing the IHWG DNA samples, in particular Mr. Emil Madraimov and Ms. Angela Bryce for distributing samples to participating laboratories. We are also immensely grateful to the many vendors that provided reagents and software free of charge to some of the investigators. We extend thanks to the Stanford Blood center for their financial and general administrative support for the 17th IHIW. LEC and MFV (Stanford University) were supported by grant U19NS095774 from the U.S. National Institutes of Health (NIH). MP (Palacky University) was supported by RVO: 61989592. SAS (Kuwait University) was supported by grant 2012-130-204 from the Kuwait Foundation for Advancement of Science (KFAS). JR (McGill University) was supported by the Genome Canada Science Technology Innovation Centre, Compute Canada Resource Allocation Project (WST-164-AB) and Genome Innovation Node (244819). LEC was involved in the conception of the study, analysed the data and drafted the manuscript. MFV was involved in the conception of the study. JH provided DNA samples to participants. TV helped to coordinate distribution of the samples to participants. CJH assisted in data analysis. JR, TRT, NPM, and WPB assisted in data analysis and performed NGS genotyping assays. The remaining authors performed NGS genotyping assays. The authors declare no competing financial or other interests.
Funding Information:
We gratefully acknowledge the Fred Hutchinson Cancer Research center for providing the IHWG DNA samples, in particular Mr. Emil Madraimov and Ms. Angela Bryce for distributing samples to participating laboratories. We are also immensely grateful to the many vendors that provided reagents and software free of charge to some of the investigators. We extend thanks to the Stanford Blood center for their financial and general administrative support for the 17 th IHIW. LEC and MFV (Stanford University) were supported by grant U19NS095774 from the U.S. National Institutes of Health (NIH). MP (Palacky University) was supported by RVO : 61989592 . SAS (Kuwait University) was supported by grant 2012-130-204 from the Kuwait Foundation for Advancement of Science (KFAS). JR (McGill University) was supported by the Genome Canada Science Technology Innovation Centre, Compute Canada Resource Allocation Project (WST-164-AB) and Genome Innovation Node (244819).
Publisher Copyright:
© 2019
PY - 2019/7/1
Y1 - 2019/7/1
N2 - Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
AB - Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.
KW - B-lymphoblastoid cell lines
KW - Human leukocyte antigen
KW - International HLA and Immunogenetics Workshop
KW - Multiple-laboratory testing
KW - Next-generation sequencing
UR - http://www.scopus.com/inward/record.url?scp=85064602232&partnerID=8YFLogxK
U2 - 10.1016/j.humimm.2019.03.001
DO - 10.1016/j.humimm.2019.03.001
M3 - Article
C2 - 30844424
SN - 0198-8859
VL - 80
SP - 449
EP - 460
JO - Human Immunology
JF - Human Immunology
IS - 7
ER -