Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

Kazutoyo Osoegawa¹, Tamara A Vayntrub², Sabine Wenda³, Dianne De Santis⁴, Konstantinos Barsakis⁵, Milena Ivanova⁶, Susan Hsu⁷, Jonathan Barone⁷, Rhonda Holdsworth⁸, Mary Diviney⁸, Medhat Askar⁹, Amanda Willis⁹, Dawn Railton¹⁰, Sophie Laflin¹⁰, Ketevan Gendzekhadze¹¹, Arisa Oki¹¹, Nicoletta Sacchi¹², Michela Mazzocco¹², Marco Andreani¹³, Reem Ameen¹⁴, Catherine Stavropoulos-Giokas¹⁵, Amalia Dinou¹⁵, Margareth Torres¹⁶, Rodrigo Dos Santos Francisco¹⁶, Carles Serra-Pages¹⁷, Damian Goodridge¹⁸, Sandra Balladares¹⁸, Maria P Bettinotti¹⁹, Brian Iglehart¹⁹, Zahra Kashi²⁰, Russell Martin²⁰, Chee Loong Saw²¹, Jiannis Ragoussis²², Jonathan Downing²³, Cristina Navarrete²⁴, Winnie Chong²⁴, Katsuyuki Saito²⁵, Martin Petrek²⁶, Stana Tokic²⁶, Karin Padros²⁷, Ma Beatriz Rodriguez²⁷, Viktoria Zakharova²⁸, Olga Shragina²⁸, Susana R Marino²⁹, Nicholas K Brown²⁹, Takashi Shiina³⁰, Shingo Suzuki³⁰, Eric Spierings³¹, Qiuheng Zhang³², Yuxin Yin³², Gerald P Morris³³, Ana Hernandez³⁴, Phillip Ruiz³⁴, Seik-Soon Khor³⁵, Katsushi Tokunaga³⁵, Aviva Geretz³⁶, Rasmi Thomas³⁶, Fumiko Yamamoto², Kalyan C Mallempati², Sridevi Gangavarapu², Uma Kanga³⁷, Shweta Tyagi³⁷, Steven G E Marsh³⁸, Will P Bultitude³⁸, Xiangjun Liu³⁹, Dajiang Cao³⁹, Maarten Penning⁴⁰, Carolyn K Hurley⁴¹, Anne Cesbron⁴², Claudia Mueller⁴³, Joannis Mytilineos⁴⁴, Eric T Weimer⁴⁵, Mats Bengtsson⁴⁶, Gottfried Fischer³, John A Hansen⁴⁷, Chia-Jung Chang⁴⁸, Steven J Mack⁴⁹, Lisa E Creary⁵⁰, Marcelo A Fernandez-Viña⁵⁰

Affiliations

¹ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA. Electronic address: kazutoyo@stanford.edu.
² Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
³ Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
⁴ PathWest, Fiona Stanley Hospital, Murdoch, WA, Australia.
⁵ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; University of Crete, Biology Department, Heraklion, Greece; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Alexandrovska Hospital, Sofia, Bulgaria.
⁷ Histocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA.
⁸ Australian Red Cross Blood Services, Melbourne, Australia.
⁹ Baylor University Medical Center, Dallas, TX, USA.
¹⁰ Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
¹¹ City of Hope National Medical Center, Duarte, CA, USA.
¹² Ente Ospedaliero Ospedali Galliera, Genova, Italy.
¹³ Fondazione I.M.E. Istituto Mediterraneo Di Ematologia, Rome, Italy.
¹⁴ Health Sciences Center, Kuwait University, Jabriya, Kuwait.
¹⁵ Hellenic Cord Blood Bank, Athens, Greece.
¹⁶ Hospital Albert Einstein, Sao Paulo, Brazil.
¹⁷ Centro de Diagonóstico Biomédico, Hospital Clínic de Barcelona, Barcelona, Spain.
¹⁸ Illumina, Inc., San Diego, CA, USA.
¹⁹ Johns Hopkins University School of Medicine, Baltimore, MD, USA.
²⁰ Kashi Clinical Laboratories, Inc., Portland, OR, USA.
²¹ McGill University Health Centre, Montreal, QC, Canada.
²² McGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
²³ New Zealand Blood Service, Epsom, Auckland, New Zealand.
²⁴ National H&I Service Development Laboratory NHS Blood and Transplant, London, UK.
²⁵ One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
²⁶ Palacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic.
²⁷ Primer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina.
²⁸ Rogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation.
²⁹ The University of Chicago Medicine, Chicago, IL, USA.
³⁰ Tokai University School of Medicine, Kanagawa, Japan.
³¹ University Medical Center Utrecht, Netherlands.
³² University of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA.
³³ University of California San Diego, La Jolla, CA, USA.
³⁴ University of Miami Miller School of Medicine, USA.
³⁵ University of Tokyo, Tokyo, Japan.
³⁶ Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
³⁷ All India Institute of Medical Sciences, New Delhi, India.
³⁸ Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK.
³⁹ Bo Fu Rui (BFR) Transplant Diagnostics, Beijing, China.
⁴⁰ GenDx, Utrecht, Netherlands.
⁴¹ Georgetown University Medical Center, Washington DC, USA.
⁴² Histocompatibility and Immunogenetics Laboratory, Nantes, France.
⁴³ Transplantation and Immunology, Universitat Tuebingen, Germany.
⁴⁴ Transplantation Immunology, Ulm, Germany.
⁴⁵ Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, NC, USA.
⁴⁶ Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
⁴⁷ Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
⁴⁸ Stanford Genome Technology Center, Palo Alto, CA, USA.
⁴⁹ Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
⁵⁰ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

PMID: 30738112
PMCID: PMC6446570
DOI: 10.1016/j.humimm.2019.01.009

Review

Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

Kazutoyo Osoegawa et al. Hum Immunol. 2019 Apr.

. 2019 Apr;80(4):228-236.

doi: 10.1016/j.humimm.2019.01.009. Epub 2019 Feb 6.

Authors

Affiliations

¹ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA. Electronic address: kazutoyo@stanford.edu.
² Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
³ Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
⁴ PathWest, Fiona Stanley Hospital, Murdoch, WA, Australia.
⁵ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; University of Crete, Biology Department, Heraklion, Greece; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Alexandrovska Hospital, Sofia, Bulgaria.
⁷ Histocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA.
⁸ Australian Red Cross Blood Services, Melbourne, Australia.
⁹ Baylor University Medical Center, Dallas, TX, USA.
¹⁰ Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
¹¹ City of Hope National Medical Center, Duarte, CA, USA.
¹² Ente Ospedaliero Ospedali Galliera, Genova, Italy.
¹³ Fondazione I.M.E. Istituto Mediterraneo Di Ematologia, Rome, Italy.
¹⁴ Health Sciences Center, Kuwait University, Jabriya, Kuwait.
¹⁵ Hellenic Cord Blood Bank, Athens, Greece.
¹⁶ Hospital Albert Einstein, Sao Paulo, Brazil.
¹⁷ Centro de Diagonóstico Biomédico, Hospital Clínic de Barcelona, Barcelona, Spain.
¹⁸ Illumina, Inc., San Diego, CA, USA.
¹⁹ Johns Hopkins University School of Medicine, Baltimore, MD, USA.
²⁰ Kashi Clinical Laboratories, Inc., Portland, OR, USA.
²¹ McGill University Health Centre, Montreal, QC, Canada.
²² McGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
²³ New Zealand Blood Service, Epsom, Auckland, New Zealand.
²⁴ National H&I Service Development Laboratory NHS Blood and Transplant, London, UK.
²⁵ One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
²⁶ Palacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic.
²⁷ Primer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina.
²⁸ Rogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation.
²⁹ The University of Chicago Medicine, Chicago, IL, USA.
³⁰ Tokai University School of Medicine, Kanagawa, Japan.
³¹ University Medical Center Utrecht, Netherlands.
³² University of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA.
³³ University of California San Diego, La Jolla, CA, USA.
³⁴ University of Miami Miller School of Medicine, USA.
³⁵ University of Tokyo, Tokyo, Japan.
³⁶ Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
³⁷ All India Institute of Medical Sciences, New Delhi, India.
³⁸ Anthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK.
³⁹ Bo Fu Rui (BFR) Transplant Diagnostics, Beijing, China.
⁴⁰ GenDx, Utrecht, Netherlands.
⁴¹ Georgetown University Medical Center, Washington DC, USA.
⁴² Histocompatibility and Immunogenetics Laboratory, Nantes, France.
⁴³ Transplantation and Immunology, Universitat Tuebingen, Germany.
⁴⁴ Transplantation Immunology, Ulm, Germany.
⁴⁵ Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, NC, USA.
⁴⁶ Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
⁴⁷ Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
⁴⁸ Stanford Genome Technology Center, Palo Alto, CA, USA.
⁴⁹ Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
⁵⁰ Histocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

PMID: 30738112
PMCID: PMC6446570
DOI: 10.1016/j.humimm.2019.01.009

Abstract

The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.

Keywords: NGS HLA typing; Proficiency testing; Quality control; Reference cell panel.

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References

1. Histocompatibility Testing; Report of a Conference and Workshop Sponsored by the Division of Medical Sciences, National Academy of Sciences, National Research Council, 7–12 June, 1964 Washington: National Academy of Sciences; 1965.
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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

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