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

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Osoegawa, KazutoyoStanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA (author)

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

Article/chapterEnglish2019

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ELSEVIER SCIENCE INC,2019
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LIBRIS-ID:oai:DiVA.org:uu-382508
https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-382508URI
https://doi.org/10.1016/j.humimm.2019.01.009DOI

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Language:English
Summary in:English

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

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.

Subject headings and genre

MEDICIN OCH HÄLSOVETENSKAP Klinisk medicin Endokrinologi och diabetes hsv//swe
MEDICAL AND HEALTH SCIENCES Clinical Medicine Endocrinology and Diabetes hsv//eng
NGS HLA typing
Proficiency testing
Reference cell panel
Quality control

Added entries (persons, corporate bodies, meetings, titles ...)

Vayntrub, Tamara A.Stanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA (author)
Wenda, SabineMed Univ Vienna, Dept Blood Grp Serol & Transfus Med, Vienna, Austria (author)
De Santis, DianneFiona Stanley Hosp, PathWest, Murdoch, WA, Australia (author)
Barsakis, KonstantinosUniv Crete, Biol Dept, Iraklion, Greece;Stanford Univ, Dept Pathol, Sch Med, Stanford, CA 94305 USA (author)
Ivanova, MilenaAlexandrovska Hosp, Sofia, Bulgaria (author)
Hsu, SusanAmer Red Cross, Histocompatibil Mol Genet, Philadelphia, PA USA (author)
Barone, Jonathan gAmer Red Cross, Histocompatibil Mol Genet, Philadelphia, PA USA (author)
Holdsworth, RhondaAustralian Red Cross Blood Serv, Melbourne, Vic, Australia (author)
Diviney, MaryAustralian Red Cross Blood Serv, Melbourne, Vic, Australia (author)
Askar, MedhatBaylor Univ, Med Ctr, Dallas, TX USA (author)
Willis, AmandaBaylor Univ, Med Ctr, Dallas, TX USA (author)
Railton, DawnCambridge Univ Hosp NHS Fdn Trust, Cambridge, England (author)
Laflin, SophieCambridge Univ Hosp NHS Fdn Trust, Cambridge, England (author)
Gendzekhadze, KetevanCity Hope Natl Med Ctr, 1500 E Duarte Rd, Duarte, CA 91010 USA (author)
Oki, ArisaCity Hope Natl Med Ctr, 1500 E Duarte Rd, Duarte, CA 91010 USA (author)
Sacchi, NicolettaEnte Osped Osped Galliera, Genoa, Italy (author)
Mazzocco, MichelaEnte Osped Osped Galliera, Genoa, Italy (author)
Andreani, MarcoIst Mediterraneo Ematol, Fdn IME, Rome, Italy (author)
Ameen, ReemKuwait Univ, Hlth Sci Ctr, Jabriya, Kuwait (author)
Stavropoulos-Giokas, Catherine (author)
Dinou, AmaliaHellen Cord Blood Bank, Athens, Greece (author)
Torres, MargarethHosp Albert Einstein, Sao Paulo, Brazil (author)
Francisco, Rodrigo dos SantosHosp Albert Einstein, Sao Paulo, Brazil (author)
Serra-Pages, CariesHosp Clin Barcelona, Ctr Diagonost Biomed, Barcelona, Spain (author)
Goodridge, DamianHosp Clin Barcelona, Ctr Diagonost Biomed, Barcelona, Spain (author)
Balladares, SandraIllumina Inc, San Diego, CA USA (author)
Bettinotti, Maria P.Illumina Inc, San Diego, CA USA (author)
Iglehart, BrianJohns Hopkins Univ, Sch Med, Baltimore, MD USA (author)
Kashi, ZahraJohns Hopkins Univ, Sch Med, Baltimore, MD USA (author)
Martin, RussellKashi Clin Labs Inc, Portland, OR USA (author)
Saw, Chee LoongKashi Clin Labs Inc, Portland, OR USA (author)
Ragoussis, JiannisMcGill Univ, Hlth Ctr, Montreal, PQ, Canada (author)
Downing, JonathanMcGill Univ, Hlth Ctr, Montreal, PQ, Canada (author)
Navarrete, CristinaEpsom, New Zealand Blood Serv, Auckland, New Zealand (author)
Chong, WinnieNatl H&I Serv Dev Lab NHS Blood & Transplant, London, England (author)
Saito, KatsuyukiThermo Fisher Sci, One Lambda, Canoga Pk, CA USA (author)
Petrek, Martin (author)
Tokic, StanaPalacky Univ, Fac Med & Dent, Olomouc, Czech Republic (author)
Padros, KarinCABA, Fd Favaloro, Primer Ctr Argentina Immunogenet PRICAI, Mexico City, DF, Mexico (author)
Rodriguez, Ma BeatrizCABA, Fd Favaloro, Primer Ctr Argentina Immunogenet PRICAI, Mexico City, DF, Mexico (author)
Zakharovaa, ViktoriaRogachev Fed Res Ctr Pediat Hematol Oncol & Immun, Moscow, Russia (author)
Shragina, OlgaRogachev Fed Res Ctr Pediat Hematol Oncol & Immun, Moscow, Russia (author)
Marino, Susana R.Univ Chicago Med, Chicago, IL USA (author)
Brown, Nicholas K.Univ Chicago Med, Chicago, IL USA (author)
Shiina, TakashiTokai Univ, Sch Med, Kanagawa, Japan (author)
Suzuki, ShingoTokai Univ, Sch Med, Kanagawa, Japan (author)
Spierings, EricUniv Med Ctr Utrecht, Utrecht, Netherlands (author)
Zhang, QiuhengUniv Calif Los Angeles, Immunogenet Ctr, Los Angeles, CA USA (author)
Yin, YuxinUniv Calif Los Angeles, Immunogenet Ctr, Los Angeles, CA USA (author)
Morris, Gerald P.Univ Calif San Diego, La Jolla, CA 92093 USA (author)
Hernandez, AnaUniv Miami, Miller Sch Med, Coral Gables, FL 33124 USA (author)
Ruiz, PhillipUniv Miami, Miller Sch Med, Coral Gables, FL 33124 USA (author)
Khor, Seik-SoonUniv Tokyo, Tokyo, Japan (author)
Tokunaga, KatsushiUniv Tokyo, Tokyo, Japan (author)
Geretz, AvivaWalter Reed Army Inst Res, Silver Spring, MD USA;Henry M Jackson Fdn Adv Mil Med, Bethesda, MD USA (author)
Thomas, RasmiWalter Reed Army Inst Res, Silver Spring, MD USA;Henry M Jackson Fdn Adv Mil Med, Bethesda, MD USA (author)
Yamamoto, FumikoStanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA (author)
Mallempati, Kalyan C.Stanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA (author)
Gangavarapu, SrideviStanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA (author)
Kanga, UmaAll India Inst Med Sci, New Delhi, India (author)
Tyagi, ShwetaAll India Inst Med Sci, New Delhi, India (author)
Marsh, Steven G. E.Anthony Nolan Res Inst, Royal Free Campus, London, England;UCL, Canc Inst, Royal Free Campus, London, England (author)
Bultitude, Will P.Anthony Nolan Res Inst, Royal Free Campus, London, England;UCL, Canc Inst, Royal Free Campus, London, England (author)
Liu, XiangjunBo Fu Rui BFR Transplant Diagnost, Beijing, Peoples R China (author)
Cao, DajiangBo Fu Rui BFR Transplant Diagnost, Beijing, Peoples R China (author)
Penning, MaartenGenDx, Utrecht, Netherlands (author)
Hurley, Carolyn K.Georgetown Univ, Med Ctr, Washington, DC 20007 USA (author)
Cesbron, AnneHistocompatibil & Immunogenet Lab, Nantes, France (author)
Mueller, ClaudiaUniv Tubingen, Transplantat & Immunol, Tubingen, Germany (author)
Mytilineos, JoannisTransplantat Immunol, Ulm, Germany (author)
Weimer, Eric T.Univ N Carolina, Sch Med, Dept Pathol & Lab Med, Chapel Hill, NC 27515 USA (author)
Bengtsson, MatsUppsala universitet,Klinisk immunologi(Swepub:uu)matsbs (author)
Fischer, GottfriedMed Univ Vienna, Dept Blood Grp Serol & Transfus Med, Vienna, Austria (author)
Hansen, John A.Fred Hutchinson Canc Res Ctr, Div Clin Res, Seattle, WA USA;Univ Washington, Dept Pediat, Sch Med, Seattle, WA 98195 USA (author)
Chang, Chia-JungStanford Genome Technol Ctr, Palo Alto, CA USA (author)
Mack, Steven J.Childrens Hosp Oakland Res Inst, Ctr Genet, Oakland, CA USA (author)
Creary, Lisa E. (author)
Fernandez-Vina, Marcelo A.McGill Univ, Dept Human Genet, Montreal, PQ, Canada (author)
Stanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USAMed Univ Vienna, Dept Blood Grp Serol & Transfus Med, Vienna, Austria (creator_code:org_t)

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In:Human Immunology: ELSEVIER SCIENCE INC80:4, s. 228-2360198-88591879-1166

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By the author/editor: Osoegawa, Kazuto ...; Vayntrub, Tamara ...; Wenda, Sabine; De Santis, Diann ...; Barsakis, Konsta ...; Ivanova, Milena; show more...; Hsu, Susan; Barone, Jonathan ...; Holdsworth, Rhon ...; Diviney, Mary; Askar, Medhat; Willis, Amanda; Railton, Dawn; Laflin, Sophie; Gendzekhadze, Ke ...; Oki, Arisa; Sacchi, Nicolett ...; Mazzocco, Michel ...; Andreani, Marco; Ameen, Reem; Stavropoulos-Gio ...; Dinou, Amalia; Torres, Margaret ...; Francisco, Rodri ...; Serra-Pages, Car ...; Goodridge, Damia ...; Balladares, Sand ...; Bettinotti, Mari ...; Iglehart, Brian; Kashi, Zahra; Martin, Russell; Saw, Chee Loong; Ragoussis, Jiann ...; Downing, Jonatha ...; Navarrete, Crist ...; Chong, Winnie; Saito, Katsuyuki; Petrek, Martin; Tokic, Stana; Padros, Karin; Rodriguez, Ma Be ...; Zakharovaa, Vikt ...; Shragina, Olga; Marino, Susana R ...; Brown, Nicholas ...; Shiina, Takashi; Suzuki, Shingo; Spierings, Eric; Zhang, Qiuheng; Yin, Yuxin; Morris, Gerald P ...; Hernandez, Ana; Ruiz, Phillip; Khor, Seik-Soon; Tokunaga, Katsus ...; Geretz, Aviva; Thomas, Rasmi; Yamamoto, Fumiko; Mallempati, Kaly ...; Gangavarapu, Sri ...; Kanga, Uma; Tyagi, Shweta; Marsh, Steven G. ...; Bultitude, Will ...; Liu, Xiangjun; Cao, Dajiang; Penning, Maarten; Hurley, Carolyn ...; Cesbron, Anne; Mueller, Claudia; Mytilineos, Joan ...; Weimer, Eric T.; Bengtsson, Mats; Fischer, Gottfri ...; Hansen, John A.; Chang, Chia-Jung; Mack, Steven J.; Creary, Lisa E.; Fernandez-Vina, ...; show less...

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