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

Kazutoyo Osoegawa, Tamara A. Vayntrub, Sabine Wenda, Dianne De Santis, Konstantinos Barsakis, Milena Ivanova, Susan Hsu, Jonathan Barone, Rhonda Holdsworth, Mary Diviney, Medhat Askar, Amanda Willis, Dawn Railton, Sophie Laflin, Ketevan Gendzekhadze, Arisa Oki, Nicoletta Sacchi, Michela Mazzocco, Marco Andreani, Reem Ameen & 59 others Catherine Stavropoulos-Giokas, Amalia Dinou, Margareth Torres, Rodrigo dos Santos Francisco, Carles Serra-Pages, Damian Goodridge, Sandra Balladares, Maria Bettinotti, Brian Iglehart, Zahra Kashi, Russell Martin, Chee Loong Saw, Jiannis Ragoussis, Jonathan Downing, Cristina Navarrete, Winnie Chong, Katsuyuki Saito, Martin Petrek, Stana Tokic, Karin Padros, Ma Beatriz Rodriguez, Viktoria Zakharova, Olga Shragina, Susana R. Marino, Nicholas K. Brown, Takashi Shiina, Shingo Suzuki, Eric Spierings, Qiuheng Zhang, Yuxin Yin, Gerald P. Morris, Ana Hernandez, Phillip Ruiz, Seik Soon Khor, Katsushi Tokunaga, Aviva Geretz, Rasmi Thomas, Fumiko Yamamoto, Kalyan C. Mallempati, Sridevi Gangavarapu, Uma Kanga, Shweta Tyagi, Steven G.E. Marsh, Will P. Bultitude, Xiangjun Liu, Dajiang Cao, Maarten Penning, Carolyn K. Hurley, Anne Cesbron, Claudia Mueller, Joannis Mytilineos, Eric T. Weimer, Mats Bengtsson, Gottfried Fischer, John A. Hansen, Chia Jung Chang, Steven J. Mack, Lisa E. Creary, Marcelo A. Fernandez-Viña

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)228-236
Number of pages9
JournalHuman Immunology
Volume80
Issue number4
DOIs
StatePublished - Apr 1 2019

Fingerprint

Immunogenetics
Quality Control
Education
HLA-C Antigens
HLA-DRB1 Chains
Cell Line
Histocompatibility Testing
HLA-A Antigens
HLA-B Antigens
Software
HLA-DRB4 Chains
HLA-DRB5 Chains
HLA-DRB3 Chains
Genotype
Consensus Sequence
Alleles
Costs and Cost Analysis

Keywords

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

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

Cite this

Osoegawa, K., Vayntrub, T. A., Wenda, S., De Santis, D., Barsakis, K., Ivanova, M., ... Fernandez-Viña, M. A. (2019). Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. Human Immunology, 80(4), 228-236. https://doi.org/10.1016/j.humimm.2019.01.009

Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. / Osoegawa, Kazutoyo; Vayntrub, Tamara A.; Wenda, Sabine; De Santis, Dianne; Barsakis, Konstantinos; Ivanova, Milena; Hsu, Susan; Barone, Jonathan; Holdsworth, Rhonda; Diviney, Mary; Askar, Medhat; Willis, Amanda; Railton, Dawn; Laflin, Sophie; Gendzekhadze, Ketevan; Oki, Arisa; Sacchi, Nicoletta; Mazzocco, Michela; Andreani, Marco; Ameen, Reem; Stavropoulos-Giokas, Catherine; Dinou, Amalia; Torres, Margareth; dos Santos Francisco, Rodrigo; Serra-Pages, Carles; Goodridge, Damian; Balladares, Sandra; Bettinotti, Maria; Iglehart, Brian; Kashi, Zahra; Martin, Russell; Saw, Chee Loong; Ragoussis, Jiannis; Downing, Jonathan; Navarrete, Cristina; Chong, Winnie; Saito, Katsuyuki; Petrek, Martin; Tokic, Stana; Padros, Karin; Beatriz Rodriguez, Ma; Zakharova, Viktoria; Shragina, Olga; Marino, Susana R.; Brown, Nicholas K.; Shiina, Takashi; Suzuki, Shingo; Spierings, Eric; Zhang, Qiuheng; Yin, Yuxin; Morris, Gerald P.; Hernandez, Ana; Ruiz, Phillip; Khor, Seik Soon; Tokunaga, Katsushi; Geretz, Aviva; Thomas, Rasmi; Yamamoto, Fumiko; Mallempati, Kalyan C.; Gangavarapu, Sridevi; Kanga, Uma; Tyagi, Shweta; Marsh, Steven G.E.; Bultitude, Will P.; Liu, Xiangjun; Cao, Dajiang; Penning, Maarten; Hurley, Carolyn K.; Cesbron, Anne; Mueller, Claudia; Mytilineos, Joannis; Weimer, Eric T.; Bengtsson, Mats; Fischer, Gottfried; Hansen, John A.; Chang, Chia Jung; Mack, Steven J.; Creary, Lisa E.; Fernandez-Viña, Marcelo A.

In: Human Immunology, Vol. 80, No. 4, 01.04.2019, p. 228-236.

Research output: Contribution to journalArticle

Osoegawa, K, Vayntrub, TA, Wenda, S, De Santis, D, Barsakis, K, Ivanova, M, Hsu, S, Barone, J, Holdsworth, R, Diviney, M, Askar, M, Willis, A, Railton, D, Laflin, S, Gendzekhadze, K, Oki, A, Sacchi, N, Mazzocco, M, Andreani, M, Ameen, R, Stavropoulos-Giokas, C, Dinou, A, Torres, M, dos Santos Francisco, R, Serra-Pages, C, Goodridge, D, Balladares, S, Bettinotti, M, Iglehart, B, Kashi, Z, Martin, R, Saw, CL, Ragoussis, J, Downing, J, Navarrete, C, Chong, W, Saito, K, Petrek, M, Tokic, S, Padros, K, Beatriz Rodriguez, M, Zakharova, V, Shragina, O, Marino, SR, Brown, NK, Shiina, T, Suzuki, S, Spierings, E, Zhang, Q, Yin, Y, Morris, GP, Hernandez, A, Ruiz, P, Khor, SS, Tokunaga, K, Geretz, A, Thomas, R, Yamamoto, F, Mallempati, KC, Gangavarapu, S, Kanga, U, Tyagi, S, Marsh, SGE, Bultitude, WP, Liu, X, Cao, D, Penning, M, Hurley, CK, Cesbron, A, Mueller, C, Mytilineos, J, Weimer, ET, Bengtsson, M, Fischer, G, Hansen, JA, Chang, CJ, Mack, SJ, Creary, LE & Fernandez-Viña, MA 2019, 'Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop', Human Immunology, vol. 80, no. 4, pp. 228-236. https://doi.org/10.1016/j.humimm.2019.01.009
Osoegawa, Kazutoyo ; Vayntrub, Tamara A. ; Wenda, Sabine ; De Santis, Dianne ; Barsakis, Konstantinos ; Ivanova, Milena ; Hsu, Susan ; Barone, Jonathan ; Holdsworth, Rhonda ; Diviney, Mary ; Askar, Medhat ; Willis, Amanda ; Railton, Dawn ; Laflin, Sophie ; Gendzekhadze, Ketevan ; Oki, Arisa ; Sacchi, Nicoletta ; Mazzocco, Michela ; Andreani, Marco ; Ameen, Reem ; Stavropoulos-Giokas, Catherine ; Dinou, Amalia ; Torres, Margareth ; dos Santos Francisco, Rodrigo ; Serra-Pages, Carles ; Goodridge, Damian ; Balladares, Sandra ; Bettinotti, Maria ; Iglehart, Brian ; Kashi, Zahra ; Martin, Russell ; Saw, Chee Loong ; Ragoussis, Jiannis ; Downing, Jonathan ; Navarrete, Cristina ; Chong, Winnie ; Saito, Katsuyuki ; Petrek, Martin ; Tokic, Stana ; Padros, Karin ; Beatriz Rodriguez, Ma ; Zakharova, Viktoria ; Shragina, Olga ; Marino, Susana R. ; Brown, Nicholas K. ; Shiina, Takashi ; Suzuki, Shingo ; Spierings, Eric ; Zhang, Qiuheng ; Yin, Yuxin ; Morris, Gerald P. ; Hernandez, Ana ; Ruiz, Phillip ; Khor, Seik Soon ; Tokunaga, Katsushi ; Geretz, Aviva ; Thomas, Rasmi ; Yamamoto, Fumiko ; Mallempati, Kalyan C. ; Gangavarapu, Sridevi ; Kanga, Uma ; Tyagi, Shweta ; Marsh, Steven G.E. ; Bultitude, Will P. ; Liu, Xiangjun ; Cao, Dajiang ; Penning, Maarten ; Hurley, Carolyn K. ; Cesbron, Anne ; Mueller, Claudia ; Mytilineos, Joannis ; Weimer, Eric T. ; Bengtsson, Mats ; Fischer, Gottfried ; Hansen, John A. ; Chang, Chia Jung ; Mack, Steven J. ; Creary, Lisa E. ; Fernandez-Viña, Marcelo A. / Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. In: Human Immunology. 2019 ; Vol. 80, No. 4. pp. 228-236.
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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.",
keywords = "NGS HLA typing, Proficiency testing, Quality control, Reference cell panel",
author = "Kazutoyo Osoegawa and Vayntrub, {Tamara A.} and Sabine Wenda and {De Santis}, Dianne and Konstantinos Barsakis and Milena Ivanova and Susan Hsu and Jonathan Barone and Rhonda Holdsworth and Mary Diviney and Medhat Askar and Amanda Willis and Dawn Railton and Sophie Laflin and Ketevan Gendzekhadze and Arisa Oki and Nicoletta Sacchi and Michela Mazzocco and Marco Andreani and Reem Ameen and Catherine Stavropoulos-Giokas and Amalia Dinou and Margareth Torres and {dos Santos Francisco}, Rodrigo and Carles Serra-Pages and Damian Goodridge and Sandra Balladares and Maria Bettinotti and Brian Iglehart and Zahra Kashi and Russell Martin and Saw, {Chee Loong} and Jiannis Ragoussis and Jonathan Downing and Cristina Navarrete and Winnie Chong and Katsuyuki Saito and Martin Petrek and Stana Tokic and Karin Padros and {Beatriz Rodriguez}, Ma and Viktoria Zakharova and Olga Shragina and Marino, {Susana R.} and Brown, {Nicholas K.} and Takashi Shiina and Shingo Suzuki and Eric Spierings and Qiuheng Zhang and Yuxin Yin and Morris, {Gerald P.} and Ana Hernandez and Phillip Ruiz and Khor, {Seik Soon} and Katsushi Tokunaga and Aviva Geretz and Rasmi Thomas and Fumiko Yamamoto and Mallempati, {Kalyan C.} and Sridevi Gangavarapu and Uma Kanga and Shweta Tyagi and Marsh, {Steven G.E.} and Bultitude, {Will P.} and Xiangjun Liu and Dajiang Cao and Maarten Penning and Hurley, {Carolyn K.} and Anne Cesbron and Claudia Mueller and Joannis Mytilineos and Weimer, {Eric T.} and Mats Bengtsson and Gottfried Fischer and Hansen, {John A.} and Chang, {Chia Jung} and Mack, {Steven J.} and Creary, {Lisa E.} and Fernandez-Vi{\~n}a, {Marcelo A.}",
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T1 - Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop

AU - Osoegawa, Kazutoyo

AU - Vayntrub, Tamara A.

AU - Wenda, Sabine

AU - De Santis, Dianne

AU - Barsakis, Konstantinos

AU - Ivanova, Milena

AU - Hsu, Susan

AU - Barone, Jonathan

AU - Holdsworth, Rhonda

AU - Diviney, Mary

AU - Askar, Medhat

AU - Willis, Amanda

AU - Railton, Dawn

AU - Laflin, Sophie

AU - Gendzekhadze, Ketevan

AU - Oki, Arisa

AU - Sacchi, Nicoletta

AU - Mazzocco, Michela

AU - Andreani, Marco

AU - Ameen, Reem

AU - Stavropoulos-Giokas, Catherine

AU - Dinou, Amalia

AU - Torres, Margareth

AU - dos Santos Francisco, Rodrigo

AU - Serra-Pages, Carles

AU - Goodridge, Damian

AU - Balladares, Sandra

AU - Bettinotti, Maria

AU - Iglehart, Brian

AU - Kashi, Zahra

AU - Martin, Russell

AU - Saw, Chee Loong

AU - Ragoussis, Jiannis

AU - Downing, Jonathan

AU - Navarrete, Cristina

AU - Chong, Winnie

AU - Saito, Katsuyuki

AU - Petrek, Martin

AU - Tokic, Stana

AU - Padros, Karin

AU - Beatriz Rodriguez, Ma

AU - Zakharova, Viktoria

AU - Shragina, Olga

AU - Marino, Susana R.

AU - Brown, Nicholas K.

AU - Shiina, Takashi

AU - Suzuki, Shingo

AU - Spierings, Eric

AU - Zhang, Qiuheng

AU - Yin, Yuxin

AU - Morris, Gerald P.

AU - Hernandez, Ana

AU - Ruiz, Phillip

AU - Khor, Seik Soon

AU - Tokunaga, Katsushi

AU - Geretz, Aviva

AU - Thomas, Rasmi

AU - Yamamoto, Fumiko

AU - Mallempati, Kalyan C.

AU - Gangavarapu, Sridevi

AU - Kanga, Uma

AU - Tyagi, Shweta

AU - Marsh, Steven G.E.

AU - Bultitude, Will P.

AU - Liu, Xiangjun

AU - Cao, Dajiang

AU - Penning, Maarten

AU - Hurley, Carolyn K.

AU - Cesbron, Anne

AU - Mueller, Claudia

AU - Mytilineos, Joannis

AU - Weimer, Eric T.

AU - Bengtsson, Mats

AU - Fischer, Gottfried

AU - Hansen, John A.

AU - Chang, Chia Jung

AU - Mack, Steven J.

AU - Creary, Lisa E.

AU - Fernandez-Viña, Marcelo A.

PY - 2019/4/1

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N2 - 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.

AB - 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.

KW - NGS HLA typing

KW - Proficiency testing

KW - Quality control

KW - Reference cell panel

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