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

Kazutoyo Osoegawa, Tamara A. Vayntrub, Sabine Wenda, Dianne De Santis, Konstantinos Barsakis, Milena Ivanova, Susan Hsu, Jonathan Barone, Rhonda Holdsworth, Mary Diviney, Medhat Askar, Amanda Willis, Dawn Railton, Sophie Laflin, Ketevan Gendzekhadze, Arisa Oki, Nicoletta Sacchi, Michela Mazzocco, Marco Andreani, Reem AmeenCatherine Stavropoulos-Giokas, Amalia Dinou, Margareth Torres, Rodrigo dos Santos Francisco, Carles Serra-Pages, Damian Goodridge, Sandra Balladares, Maria P. Bettinotti, Brian Iglehart, Zahra Kashi, Russell Martin, Chee Loong Saw, Jiannis Ragoussis, Jonathan Downing, Cristina Navarrete, Winnie Chong, Katsuyuki Saito, Martin Petrek, Stana Tokic, Karin Padros, Ma Beatriz Rodriguez, Viktoria Zakharova, Olga Shragina, Susana R. Marino, Nicholas K. Brown, Takashi Shiina, Shingo Suzuki, Eric Spierings, Qiuheng Zhang, Yuxin Yin, Gerald P. Morris, Ana Hernandez, Phillip Ruiz, Seik Soon Khor, Katsushi Tokunaga, Aviva Geretz, Rasmi Thomas, Fumiko Yamamoto, Kalyan C. Mallempati, Sridevi Gangavarapu, Uma Kanga, Shweta Tyagi, Steven G.E. Marsh, Will P. Bultitude, Xiangjun Liu, Dajiang Cao, Maarten Penning, Carolyn K. Hurley, Anne Cesbron, Claudia Mueller, Joannis Mytilineos, Eric T. Weimer, Mats Bengtsson, Gottfried Fischer, John A. Hansen, Chia Jung Chang, Steven J. Mack, Lisa E. Creary, Marcelo A. Fernandez-Viña

Research output: Contribution to journalArticle

4 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)228-236
Number of pages9
JournalHuman Immunology
Volume80
Issue number4
DOIs
StatePublished - Apr 2019

Keywords

  • NGS HLA typing
  • Proficiency testing
  • Quality control
  • Reference cell panel

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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    Osoegawa, K., Vayntrub, T. A., Wenda, S., De Santis, D., Barsakis, K., Ivanova, M., Hsu, S., Barone, J., Holdsworth, R., Diviney, M., Askar, M., Willis, A., Railton, D., Laflin, S., Gendzekhadze, K., Oki, A., Sacchi, N., Mazzocco, M., Andreani, M., ... Fernandez-Viña, M. A. (2019). Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. Human Immunology, 80(4), 228-236. https://doi.org/10.1016/j.humimm.2019.01.009