Evidence map›Paper›PMID 30738112›Full record

ReviewHuman immunology2019

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 and 69 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Human immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

15 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. HLA Genetics for the Human Diseases.Advances in experimental medicine and biology · 2024
    Review
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

79 authors.

Kazutoyo OsoegawaHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA. Electronic address: kazutoyo@stanford.edu.
Tamara A VayntrubHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Sabine WendaDepartment of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
Dianne De SantisPathWest, Fiona Stanley Hospital, Murdoch, WA, Australia.
Konstantinos BarsakisHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; University of Crete, Biology Department, Heraklion, Greece; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Milena IvanovaAlexandrovska Hospital, Sofia, Bulgaria.
Susan HsuHistocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA.
Jonathan BaroneHistocompatibility/Molecular Genetics, American Red Cross, Philadelphia, PA, USA.
Rhonda HoldsworthAustralian Red Cross Blood Services, Melbourne, Australia.
Mary DivineyAustralian Red Cross Blood Services, Melbourne, Australia.
Medhat AskarBaylor University Medical Center, Dallas, TX, USA.
Amanda WillisBaylor University Medical Center, Dallas, TX, USA.
Dawn RailtonCambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
Sophie LaflinCambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
Ketevan GendzekhadzeCity of Hope National Medical Center, Duarte, CA, USA.
Arisa OkiCity of Hope National Medical Center, Duarte, CA, USA.
Nicoletta SacchiEnte Ospedaliero Ospedali Galliera, Genova, Italy.
Michela MazzoccoEnte Ospedaliero Ospedali Galliera, Genova, Italy.
Marco AndreaniFondazione I.M.E. Istituto Mediterraneo Di Ematologia, Rome, Italy.
Reem AmeenHealth Sciences Center, Kuwait University, Jabriya, Kuwait.
Catherine Stavropoulos-GiokasHellenic Cord Blood Bank, Athens, Greece.
Amalia DinouHellenic Cord Blood Bank, Athens, Greece.
Margareth TorresHospital Albert Einstein, Sao Paulo, Brazil.
Rodrigo Dos Santos FranciscoHospital Albert Einstein, Sao Paulo, Brazil.
Carles Serra-PagesCentro de Diagonóstico Biomédico, Hospital Clínic de Barcelona, Barcelona, Spain.
Damian GoodridgeIllumina, Inc., San Diego, CA, USA.
Sandra BalladaresIllumina, Inc., San Diego, CA, USA.
Maria P BettinottiJohns Hopkins University School of Medicine, Baltimore, MD, USA.
Brian IglehartJohns Hopkins University School of Medicine, Baltimore, MD, USA.
Zahra KashiKashi Clinical Laboratories, Inc., Portland, OR, USA.
Russell MartinKashi Clinical Laboratories, Inc., Portland, OR, USA.
Chee Loong SawMcGill University Health Centre, Montreal, QC, Canada.
Jiannis RagoussisMcGill University Health Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
Jonathan DowningNew Zealand Blood Service, Epsom, Auckland, New Zealand.
Cristina NavarreteNational H&I Service Development Laboratory NHS Blood and Transplant, London, UK.
Winnie ChongNational H&I Service Development Laboratory NHS Blood and Transplant, London, UK.
Katsuyuki SaitoOne Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
Martin PetrekPalacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic.
Stana TokicPalacky University, Faculty of Medicine and Dentistry, Olomouc, Czech Republic.
Karin PadrosPrimer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina.
Ma Beatriz RodriguezPrimer Centro Argentino de Immunogenetica (PRICAI), Fundación Favaloro, CABA, Argentina.
Viktoria ZakharovaRogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation.
Olga ShraginaRogachev Federal Research Centre of Pediatric Hematology,Oncology and Immunology, Moscow, Russian Federation.
Susana R MarinoThe University of Chicago Medicine, Chicago, IL, USA.
Nicholas K BrownThe University of Chicago Medicine, Chicago, IL, USA.
Takashi ShiinaTokai University School of Medicine, Kanagawa, Japan.
Shingo SuzukiTokai University School of Medicine, Kanagawa, Japan.
Eric SpieringsUniversity Medical Center Utrecht, Netherlands.
Qiuheng ZhangUniversity of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA.
Yuxin YinUniversity of California, Los Angeles, Immunogenetics Center, Los Angeles, CA, USA.
Gerald P MorrisUniversity of California San Diego, La Jolla, CA, USA.
Ana HernandezUniversity of Miami Miller School of Medicine, USA.
Phillip RuizUniversity of Miami Miller School of Medicine, USA.
Seik-Soon KhorUniversity of Tokyo, Tokyo, Japan.
Katsushi TokunagaUniversity of Tokyo, Tokyo, Japan.
Aviva GeretzWalter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Rasmi ThomasWalter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
Fumiko YamamotoHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Kalyan C MallempatiHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Sridevi GangavarapuHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Uma KangaAll India Institute of Medical Sciences, New Delhi, India.
Shweta TyagiAll India Institute of Medical Sciences, New Delhi, India.
Steven G E MarshAnthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK.
Will P BultitudeAnthony Nolan Research Institute and UCL Cancer Institute, Royal Free Campus, London, UK.
Xiangjun LiuBo Fu Rui (BFR) Transplant Diagnostics, Beijing, China.
Dajiang CaoBo Fu Rui (BFR) Transplant Diagnostics, Beijing, China.
Maarten PenningGenDx, Utrecht, Netherlands.
Carolyn K HurleyGeorgetown University Medical Center, Washington DC, USA.
Anne CesbronHistocompatibility and Immunogenetics Laboratory, Nantes, France.
Claudia MuellerTransplantation and Immunology, Universitat Tuebingen, Germany.
Joannis MytilineosTransplantation Immunology, Ulm, Germany.
Eric T WeimerDepartment of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, NC, USA.
Mats BengtssonDepartment of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
Gottfried FischerDepartment of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
John A HansenDivision of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.
Chia-Jung ChangStanford Genome Technology Center, Palo Alto, CA, USA.
Steven J MackCenter for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
Lisa E CrearyHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Marcelo A Fernandez-ViñaHistocompatibility, Immunogenetics, and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Funding

KIR association studies in neurological diseasesU19NS095774 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERNANDEZ-VINA, MARCELO, OKSENBERG, JORGE R. · 2015 to 2019
$7.0M
Integrated Exchange and Storage of Current- and Future-Generation Immunogenomic DataR01AI128775 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JILL Allison HOLLENBACH, STEVEN JOHN MACK · 2017 to 2026
$4.5M
Integrated Exchange & Storage of Current and Future-Generation Immunogenomic DataR01GM109030 · NIGMS · CHILDREN'S HOSPITAL & RES CTR AT OAKLAND · PI HOLLENBACH, JILL ALLISON, MACK, STEVEN JOHN · 2014 to 2016
$919k
Department of Health RP-PG-0310-1003NIAID NIH HHS R01 AI128775NIGMS NIH HHS R01 GM109030NINDS NIH HHS U19 NS095774
6 · The paper itself

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.

Indexed as

GenotypeImmunogeneticsAllelesConsensus Statements as TopicHigh-Throughput Nucleotide SequencingHistocompatibility TestingHLA AntigensHumansInternational CooperationPilot ProjectsQuality ControlSoftwareHLA AntigensNGS HLA typingProficiency testingQuality controlReference cell panel

Identifiers

PMID30738112
PMCPMC6446570

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.