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Pregled bibliografske jedinice broj: 988943

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

Osoegawa, Kazutoyo; Vayntrub, A Tamara; Wenda, Sabine; De Santis, Dianne; Barsakis, Konstantinos; Ivanova, Milena; Hsu, Susan; Barone, Jonathan; Holdsworth, Rhonda; Divine, Mary et al.
Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop // Human immunology, 80 (2019), 4; 228-236 doi:10.1016/j.humimm.2019.01.009 (međunarodna recenzija, članak, znanstveni)

CROSBI ID: 988943 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

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

Autori
Osoegawa, Kazutoyo ; Vayntrub, A Tamara ; Wenda, Sabine ; De Santis, Dianne ; Barsakis, Konstantinos ; Ivanova, Milena ; Hsu, Susan ; Barone, Jonathan ; Holdsworth, Rhonda ; Divine, Mary ; Askar, Medhat ; Willis, Amanda ; Railton, Dawn ; Laflin, Sophie ; Gendzekhadze, Ketevan ; Oki, Arisa ; Sacchi, Nicoletta ; Mazzocco, Michela ; Andreani, Marco ; Ameenn, Reem ; Stavropoulos-Giokas, Catherine ; Dinou, Amalia ; Torres, Margareth ; dos Santos Francisco, Rodrigo ; Serra-Pages, Carles ; Goodridge, Damian ; Balladares, Sandra ; Bettinotti, Maria P ; Iglehart, Brian ; Kashi, Zahra ; Martin, Russell ; Saw, Chee Loong ; Saw ; Ragoussis, Jiannis ; Downing, Jonathan ; Navarrete, Cristina ; Chong, Winnie ; Saito, Katsuyuki ; Petrek, Martin ; Tokić, Stana ; Padros, Karin ; MaBeatriz Rodriguez, Ma Beatriz ; 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 ; Marshal, Steven GE ; Bultitude, Will P ; Liu, Xiangjun ; Cao, Daijang ; Penning, Maarten ; Hurley, Carolyn K ; Cesbron, Anne ; Mueller, Claudia ; Mytilineos, Joannis ; Weimeras, Eric T ; Bengtsson, Mats ; Fischer, Gottfried ; Hansen, John A ; Chang, Chia-Jung ; Mack, Steven J ; Creary, Lisa E ; Fernandez- Viñaae, Marcelo A.

Izvornik
Human immunology (0198-8859) 80 (2019), 4; 228-236

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

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

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Biotehnologija u biomedicini (prirodno područje, biomedicina i zdravstvo, biotehničko područje)



POVEZANOST RADA

Ustanove:
Medicinski fakultet, Osijek,
Sveučilište J. J. Strossmayera u Osijeku

Profili:

Avatar Url Stana Tokić (autor)

Poveznice na cjeloviti tekst rada:

doi

Citiraj ovu publikaciju:

Osoegawa, Kazutoyo; Vayntrub, A Tamara; Wenda, Sabine; De Santis, Dianne; Barsakis, Konstantinos; Ivanova, Milena; Hsu, Susan; Barone, Jonathan; Holdsworth, Rhonda; Divine, Mary et al.
Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop // Human immunology, 80 (2019), 4; 228-236 doi:10.1016/j.humimm.2019.01.009 (međunarodna recenzija, članak, znanstveni)
Osoegawa, K., Vayntrub, A., Wenda, S., De Santis, D., Barsakis, K., Ivanova, M., Hsu, S., Barone, J., Holdsworth, R. & Divine, M. (2019) Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop. Human immunology, 80 (4), 228-236 doi:10.1016/j.humimm.2019.01.009.
@article{article, author = {Osoegawa, Kazutoyo and Vayntrub, A Tamara and Wenda, Sabine and De Santis, Dianne and Barsakis, Konstantinos and Ivanova, Milena and Hsu, Susan and Barone, Jonathan and Holdsworth, Rhonda and Divine, Mary and Askar, Medhat and Willis, Amanda and Railton, Dawn and Laflin, Sophie and Gendzekhadze, Ketevan and Oki, Arisa and Sacchi, Nicoletta and Mazzocco, Michela and Andreani, Marco and Ameenn, Reem and Stavropoulos-Giokas, Catherine and Dinou, Amalia and Torres, Margareth and dos Santos Francisco, Rodrigo and Serra-Pages, Carles and Goodridge, Damian and Balladares, Sandra and Bettinotti, Maria P and Iglehart, Brian and Kashi, Zahra and Martin, Russell and Saw, Chee Loong and Ragoussis, Jiannis and Downing, Jonathan and Navarrete, Cristina and Chong, Winnie and Saito, Katsuyuki and Petrek, Martin and Toki\'{c}, Stana and Padros, Karin and MaBeatriz Rodriguez, Ma Beatriz and Zakharova, Viktoria and Shragina, Olga and Marino, Susana R and Brown, Nicholas K and Shiina, Takashi and Suzuki, Shingo and Spierings, Eric and Zhang, Qiuheng and Yin, Yuxin and Morris, Gerald P and Hernandez, Ana and Ruiz, Phillip and Khor, Seik-Soon and Tokunaga, Katsushi and Geretz, Aviva and Thomas, Rasmi and Yamamoto, Fumiko and Mallempati, Kalyan C and Gangavarapu, Sridevi and Kanga, Uma and Tyagi, Shweta and Marshal, Steven GE and Bultitude, Will P and Liu, Xiangjun and Cao, Daijang and Penning, Maarten and Hurley, Carolyn K and Cesbron, Anne and Mueller, Claudia and Mytilineos, Joannis and Weimeras, Eric T and Bengtsson, Mats and Fischer, Gottfried and Hansen, John A and Chang, Chia-Jung and Mack, Steven J and Creary, Lisa E and Fernandez- Vi\~{n}aae, Marcelo A.}, year = {2019}, pages = {228-236}, DOI = {10.1016/j.humimm.2019.01.009}, keywords = {NGS HLA typing, Proficiency testing, Quality control, Reference cell panel}, journal = {Human immunology}, doi = {10.1016/j.humimm.2019.01.009}, volume = {80}, number = {4}, issn = {0198-8859}, title = {Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop}, keyword = {NGS HLA typing, Proficiency testing, Quality control, Reference cell panel} }
@article{article, author = {Osoegawa, Kazutoyo and Vayntrub, A Tamara and Wenda, Sabine and De Santis, Dianne and Barsakis, Konstantinos and Ivanova, Milena and Hsu, Susan and Barone, Jonathan and Holdsworth, Rhonda and Divine, Mary and Askar, Medhat and Willis, Amanda and Railton, Dawn and Laflin, Sophie and Gendzekhadze, Ketevan and Oki, Arisa and Sacchi, Nicoletta and Mazzocco, Michela and Andreani, Marco and Ameenn, Reem and Stavropoulos-Giokas, Catherine and Dinou, Amalia and Torres, Margareth and dos Santos Francisco, Rodrigo and Serra-Pages, Carles and Goodridge, Damian and Balladares, Sandra and Bettinotti, Maria P and Iglehart, Brian and Kashi, Zahra and Martin, Russell and Saw, Chee Loong and Ragoussis, Jiannis and Downing, Jonathan and Navarrete, Cristina and Chong, Winnie and Saito, Katsuyuki and Petrek, Martin and Toki\'{c}, Stana and Padros, Karin and MaBeatriz Rodriguez, Ma Beatriz and Zakharova, Viktoria and Shragina, Olga and Marino, Susana R and Brown, Nicholas K and Shiina, Takashi and Suzuki, Shingo and Spierings, Eric and Zhang, Qiuheng and Yin, Yuxin and Morris, Gerald P and Hernandez, Ana and Ruiz, Phillip and Khor, Seik-Soon and Tokunaga, Katsushi and Geretz, Aviva and Thomas, Rasmi and Yamamoto, Fumiko and Mallempati, Kalyan C and Gangavarapu, Sridevi and Kanga, Uma and Tyagi, Shweta and Marshal, Steven GE and Bultitude, Will P and Liu, Xiangjun and Cao, Daijang and Penning, Maarten and Hurley, Carolyn K and Cesbron, Anne and Mueller, Claudia and Mytilineos, Joannis and Weimeras, Eric T and Bengtsson, Mats and Fischer, Gottfried and Hansen, John A and Chang, Chia-Jung and Mack, Steven J and Creary, Lisa E and Fernandez- Vi\~{n}aae, Marcelo A.}, year = {2019}, pages = {228-236}, DOI = {10.1016/j.humimm.2019.01.009}, keywords = {NGS HLA typing, Proficiency testing, Quality control, Reference cell panel}, journal = {Human immunology}, doi = {10.1016/j.humimm.2019.01.009}, volume = {80}, number = {4}, issn = {0198-8859}, title = {Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop}, keyword = {NGS HLA typing, Proficiency testing, Quality control, Reference cell panel} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE

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