| Literature DB >> 30738112 |
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.
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.Entities:
Keywords: NGS HLA typing; Proficiency testing; Quality control; Reference cell panel
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Year: 2019 PMID： 30738112 PMCID： PMC6446570 DOI： 10.1016/j.humimm.2019.01.009
Source DB: PubMed Journal: Hum Immunol ISSN： 0198-8859 Impact factor: 2.850