April 21, 2020  |  

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

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

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. Copyright © 2019 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Journal: Human immunology
DOI: 10.1016/j.humimm.2019.01.009
Year: 2019

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