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Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop |
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| Authors: | Lisa E. Creary Sandra G. Guerra Winnie Chong Colin J. Brown Thomas R. Turner James Robinson Will P. Bultitude Neema P. Mayor Steven G.E. Marsh Katsuyuki Saito Kevin Lam Jamie L. Duke Timothy L. Mosbruger Deborah Ferriola Dimitrios Monos Amanda Willis Medhat Askar Gottfried Fischer Marcelo A. Fernández-Viňa |
| Affiliation: | 1. Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA;2. Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK;3. Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK;4. Anthony Nolan Research Institute, Royal Free Hospital, London, UK;5. UCL Cancer Institute, Royal Free Campus, London, UK;6. Molecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA;7. Immunogenetics Laboratory, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA;8. Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA;9. Department of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA;10. Department for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria;11. HLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada;12. Department of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada;13. Department of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic;14. Immunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain;15. Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece;p. Health Sciences Center, Kuwait University, Kuwait;q. Laboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands;r. HLA Laboratory, City of Hope, Duarte, CA, USA;s. Department of Pathology, University of California San Diego, La Jolla, CA, USA;t. Department of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA;u. HLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA;v. HLA Laboratory, American Red Cross, Philadelphia, PA, USA;w. Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA;x. Stanford Genome Technology Center, Palo Alto, CA, USA;y. Fred Hutchinson Cancer Research Center, Seattle, WA, USA |
| Abstract: | 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. |
| Keywords: | Corresponding author. Human leukocyte antigen Next-generation sequencing B-lymphoblastoid cell lines International HLA and Immunogenetics Workshop Multiple-laboratory testing HLA Human leukocyte antigen B-LCL B-lymphoblastoid cell lines NGS Next-generation sequencing IHIW International HLA and Immunogenetics Workshop IHWG International Histocompatibility Working Group |
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