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Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop
K. Osoegawa, TA. Vayntrub, S. Wenda, D. De Santis, K. Barsakis, M. Ivanova, S. Hsu, J. Barone, R. Holdsworth, M. Diviney, M. Askar, A. Willis, D. Railton, S. Laflin, K. Gendzekhadze, A. Oki, N. Sacchi, M. Mazzocco, M. Andreani, R. Ameen, C....
Jazyk angličtina Země Spojené státy americké
Typ dokumentu časopisecké články, přehledy
Grantová podpora
R01 AI128775
NIAID NIH HHS - United States
R01 GM109030
NIGMS NIH HHS - United States
RP-PG-0310-1003
Department of Health - United Kingdom
U19 NS095774
NINDS NIH HHS - United States
- MeSH
- alely MeSH
- genotyp * MeSH
- HLA antigeny genetika MeSH
- imunogenetika * MeSH
- konsensuální konference jako téma MeSH
- lidé MeSH
- mezinárodní spolupráce MeSH
- pilotní projekty MeSH
- řízení kvality MeSH
- software MeSH
- testování histokompatibility metody MeSH
- vysoce účinné nukleotidové sekvenování metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
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.
Alexandrovska Hospital Sofia Bulgaria
All India Institute of Medical Sciences New Delhi India
Anthony Nolan Research Institute and UCL Cancer Institute Royal Free Campus London UK
Australian Red Cross Blood Services Melbourne Australia
Baylor University Medical Center Dallas TX USA
Bo Fu Rui Transplant Diagnostics Beijing China
Cambridge University Hospitals NHS Foundation Trust Cambridge UK
Center for Genetics Children's Hospital Oakland Research Institute Oakland CA USA
Centro de Diagonóstico Biomédico Hospital Clínic de Barcelona Barcelona Spain
City of Hope National Medical Center Duarte CA USA
Department of Human Genetics McGill University Montreal Quebec Canada
Department of Immunology Genetics and Pathology Uppsala University Uppsala Sweden
Department of Pathology Stanford University School of Medicine Stanford CA USA
Department of Pediatrics University of Washington School of Medicine Seattle WA USA
Division of Clinical Research Fred Hutchinson Cancer Research Center Seattle WA USA
Ente Ospedaliero Ospedali Galliera Genova Italy
Fondazione 1 M E Istituto Mediterraneo Di Ematologia Rome Italy
Georgetown University Medical Center Washington DC USA
Health Sciences Center Kuwait University Jabriya Kuwait
Hellenic Cord Blood Bank Athens Greece
Henry M Jackson Foundation for the Advancement of Military Medicine Bethesda MD USA
Histocompatibility and Immunogenetics Laboratory Nantes France
Histocompatibility Molecular Genetics American Red Cross Philadelphia PA USA
Hospital Albert Einstein Sao Paulo Brazil
Johns Hopkins University School of Medicine Baltimore MD USA
Kashi Clinical Laboratories Inc Portland OR USA
McGill University Health Centre Montreal QC Canada
National H and 1 Service Development Laboratory NHS Blood and Transplant London UK
New Zealand Blood Service Epsom Auckland New Zealand
One Lambda Thermo Fisher Scientific Canoga Park CA USA
Palacky University Faculty of Medicine and Dentistry Olomouc Czech Republic
PathWest Fiona Stanley Hospital Murdoch WA Australia
Primer Centro Argentino de Immunogenetica Fundación Favaloro CABA Argentina
Stanford Genome Technology Center Palo Alto CA USA
The University of Chicago Medicine Chicago IL USA
Tokai University School of Medicine Kanagawa Japan
Transplantation and Immunology Universitat Tuebingen Germany
Transplantation Immunology Ulm Germany
University Medical Center Utrecht Netherlands
University of California Los Angeles Immunogenetics Center Los Angeles CA USA
University of California San Diego La Jolla CA USA
University of Crete Biology Department Heraklion Greece
University of Miami Miller School of Medicine USA
Citace poskytuje Crossref.org
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