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

被引：24

作者：

Osoegawa, Kazutoyo ^{[1
]}

Vayntrub, Tamara A. ^{[1
]}

Wenda, Sabine ^{[2
]}

De Santis, Dianne ^{[3
]}

Barsakis, Konstantinos ^{[4
,5
]}

Ivanova, Milena ^{[6
]}

Hsu, Susan ^{[7
]}

Barone, Jonathan g ^{[7
]}

Holdsworth, Rhonda ^{[8
]}

Diviney, Mary ^{[8
]}

Askar, Medhat ^{[9
]}

Willis, Amanda ^{[9
]}

Railton, Dawn ^{[10
]}

Laflin, Sophie ^{[10
]}

Gendzekhadze, Ketevan ^{[11
]}

Oki, Arisa ^{[11
]}

Sacchi, Nicoletta ^{[12
]}

Mazzocco, Michela ^{[12
]}

Andreani, Marco ^{[13
]}

Ameen, Reem ^{[14
]}

Stavropoulos-Giokas, Catherine ^{[15
]}

Dinou, Amalia ^{[15
]}

Torres, Margareth ^{[16
]}

Francisco, Rodrigo dos Santos ^{[16
]}

Serra-Pages, Caries ^{[17
]}

Goodridge, Damian ^{[17
]}

Balladares, Sandra ^{[18
]}

Bettinotti, Maria P. ^{[18
]}

Iglehart, Brian ^{[19
]}

Kashi, Zahra ^{[19
]}

Martin, Russell ^{[20
]}

Saw, Chee Loong ^{[20
]}

Ragoussis, Jiannis ^{[21
]}

Downing, Jonathan ^{[21
]}

Navarrete, Cristina ^{[22
]}

Chong, Winnie ^{[23
]}

Saito, Katsuyuki ^{[24
]}

Petrek, Martin

Tokic, Stana ^{[25
]}

Padros, Karin ^{[26
]}

Rodriguez, Ma Beatriz ^{[26
]}

Zakharovaa, Viktoria ^{[27
]}

Shragina, Olga ^{[27
]}

Marino, Susana R. ^{[28
]}

Brown, Nicholas K. ^{[28
]}

Shiina, Takashi ^{[29
]}

Suzuki, Shingo ^{[29
]}

Spierings, Eric ^{[30
]}

Zhang, Qiuheng ^{[31
]}

Yin, Yuxin ^{[31
]}

机构：

[1] Stanford Blood Ctr, Histocompatibil Immunogenet & Dis Profiling Lab, 3155 Porter Dr, Palo Alto, CA 94304 USA

[2] Med Univ Vienna, Dept Blood Grp Serol & Transfus Med, Vienna, Austria

[3] Fiona Stanley Hosp, PathWest, Murdoch, WA, Australia

[4] Univ Crete, Biol Dept, Iraklion, Greece

[5] Stanford Univ, Dept Pathol, Sch Med, Stanford, CA 94305 USA

[6] Alexandrovska Hosp, Sofia, Bulgaria

[7] Amer Red Cross, Histocompatibil Mol Genet, Philadelphia, PA USA

[8] Australian Red Cross Blood Serv, Melbourne, Vic, Australia

[9] Baylor Univ, Med Ctr, Dallas, TX USA

[10] Cambridge Univ Hosp NHS Fdn Trust, Cambridge, England

[11] City Hope Natl Med Ctr, 1500 E Duarte Rd, Duarte, CA 91010 USA

[12] Ente Osped Osped Galliera, Genoa, Italy

[13] Ist Mediterraneo Ematol, Fdn IME, Rome, Italy

[14] Kuwait Univ, Hlth Sci Ctr, Jabriya, Kuwait

[15] Hellen Cord Blood Bank, Athens, Greece

[16] Hosp Albert Einstein, Sao Paulo, Brazil

[17] Hosp Clin Barcelona, Ctr Diagonost Biomed, Barcelona, Spain

[18] Illumina Inc, San Diego, CA USA

[19] Johns Hopkins Univ, Sch Med, Baltimore, MD USA

[20] Kashi Clin Labs Inc, Portland, OR USA

[21] McGill Univ, Hlth Ctr, Montreal, PQ, Canada

[22] Epsom, New Zealand Blood Serv, Auckland, New Zealand

[23] Natl H&I Serv Dev Lab NHS Blood & Transplant, London, England

[24] Thermo Fisher Sci, One Lambda, Canoga Pk, CA USA

[25] Palacky Univ, Fac Med & Dent, Olomouc, Czech Republic

[26] CABA, Fd Favaloro, Primer Ctr Argentina Immunogenet PRICAI, Mexico City, DF, Mexico

[27] Rogachev Fed Res Ctr Pediat Hematol Oncol & Immun, Moscow, Russia

[28] Univ Chicago Med, Chicago, IL USA

[29] Tokai Univ, Sch Med, Kanagawa, Japan

[30] Univ Med Ctr Utrecht, Utrecht, Netherlands

[31] Univ Calif Los Angeles, Immunogenet Ctr, Los Angeles, CA USA

[32] Univ Calif San Diego, La Jolla, CA 92093 USA

[33] Univ Miami, Miller Sch Med, Coral Gables, FL 33124 USA

[34] Univ Tokyo, Tokyo, Japan

[35] Walter Reed Army Inst Res, Silver Spring, MD USA

[36] Henry M Jackson Fdn Adv Mil Med, Bethesda, MD USA

[37] All India Inst Med Sci, New Delhi, India

[38] Anthony Nolan Res Inst, Royal Free Campus, London, England

[39] UCL, Canc Inst, Royal Free Campus, London, England

[40] Bo Fu Rui BFR Transplant Diagnost, Beijing, Peoples R China

[41] GenDx, Utrecht, Netherlands

[42] Georgetown Univ, Med Ctr, Washington, DC 20007 USA

[43] Histocompatibil & Immunogenet Lab, Nantes, France

[44] Univ Tubingen, Transplantat & Immunol, Tubingen, Germany

[45] Transplantat Immunol, Ulm, Germany

[46] Univ N Carolina, Sch Med, Dept Pathol & Lab Med, Chapel Hill, NC 27515 USA

[47] Uppsala Univ, Dept Immunol Genet & Pathol, Uppsala, Sweden

[48] Fred Hutchinson Canc Res Ctr, Div Clin Res, Seattle, WA USA

[49] Univ Washington, Dept Pediat, Sch Med, Seattle, WA 98195 USA

[50] Stanford Genome Technol Ctr, Palo Alto, CA USA

来源：

HUMAN IMMUNOLOGY | 2019年 / 80卷 / 04期

基金：

美国国家卫生研究院;

关键词：

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

D O I：

10.1016/j.humimm.2019.01.009

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

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.

引用

页码：228 / 236

页数：9

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