Evidence map›Paper›PMID 30844424›Full record

ArticleHuman immunology2019

Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-lymphoblastoid cell lines: Report from the 17th International HLA and Immunogenetics Workshop.

Lisa E Creary, Sandra G Guerra, Winnie Chong, Colin J Brown, Thomas R Turner, James Robinson, Will P Bultitude, Neema P Mayor, Steven G E Marsh, Katsuyuki Saito and 31 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
1.5field-weighted citation impact, top 18% of its field
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

12 citing papers in PubMed, 20 citations in OpenAlex.

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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

41 authors at 19 institutions in 9 countries.

Lisa E CrearyDepartment of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA. Electronic address: lcreary@stanford.edu.
Sandra G GuerraHistocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK.
Winnie ChongHistocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK.
Colin J BrownDepartment of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK.
Thomas R TurnerAnthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
James RobinsonAnthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
Will P BultitudeAnthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
Neema P MayorAnthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
Steven G E MarshAnthony Nolan Research Institute, Royal Free Hospital, London, UK; UCL Cancer Institute, Royal Free Campus, London, UK.
Katsuyuki SaitoMolecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
Kevin LamMolecular Biology Research Department, One Lambda, Thermo Fisher Scientific, Canoga Park, CA, USA.
Jamie L DukeImmunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Timothy L MosbrugerImmunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Deborah FerriolaImmunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Dimitrios MonosImmunogenetics Laboratory, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Lab Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Amanda WillisDepartment of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA.
Medhat AskarDepartment of Pathology and Laboratory Medicine, Baylor University Medical Center, Dallas, USA.
Gottfried FischerDepartment for Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria.
Chee Loong SawHLA Laboratory, Division of Haematology, McGill University Health Centre, Montreal, Canada.
Jiannis RagoussisDepartment of Human Genetics, McGill University & McGill University and Genome Quèbec Innovation Centre, Montreal, Canada.
Martin PetrekDepartment of Pathological Physiology and Immunogenomics, IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
Carles Serra-PagésImmunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain.
Manel JuanImmunology Department, Hospital Clinic de Barcelona, University of Barcelona, IDIBAPS, Barcelona, Spain.
Catherine Stavropoulos-GiokasBiomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece.
Amalia DinouBiomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece.
Reem AmeenHealth Sciences Center, Kuwait University, Kuwait.
Salem Al ShemmariHealth Sciences Center, Kuwait University, Kuwait.
Eric SpieringsLaboratory of Translational Immunology, UMC Utrecht, Utrecht, Netherlands.
Ketevan GendzekhadzeHLA Laboratory, City of Hope, Duarte, CA, USA.
Gerald P MorrisDepartment of Pathology, University of California San Diego, La Jolla, CA, USA.
Qiuheng ZhangDepartment of Pathology and Laboratory Medicine, UCLA Immunogenetics Center, Los Angeles, CA, USA.
Zahra KashiHLA Department, Kashi Clinical Laboratories, Inc., Portland, OR, USA.
Susan HsuHLA Laboratory, American Red Cross, Philadelphia, PA, USA.
Sridevi GangavarapuHistocompatibility, 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.
Fumiko YamamotoHistocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Kazutoyo OsoegawaHistocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Tamara VayntrubHistocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Chia-Jung ChangStanford Genome Technology Center, Palo Alto, CA, USA.
John A HansenFred Hutchinson Cancer Research Center, Seattle, WA, USA.
Marcelo A Fernández-ViňaDepartment of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA.
Stanford Blood Center · USAnthony Nolan · GBChildren's Hospital of Philadelphia · USNHS Blood and Transplant · GBAcademy of Athens · GRBaylor University Medical Center · USHospital Clínic de Barcelona · ESKuwait University · KWThermo Fisher Scientific (United States) · USAmerican Red Cross · USCity of Hope · USFred Hutch Cancer Center · USMcGill University and Génome Québec Innovation Centre · CAMcGill University Health Centre · CAMedical University of Vienna · ATOregon Medical Research Center · USPalacký University Olomouc · CZUniversity Medical Center Utrecht · NLUniversity of California San Diego · US

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
NINDS NIH HHS U19 NS095774
6 · The paper itself

Abstract

Extended molecular characterization of HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLA genotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II genes was variable; the lowest observed at HLA-DRB3 (84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.

Indexed as

AllelesB-LymphocytesCell Line, TransformedCell Transformation, ViralData AccuracyExonsGenetic LociGenetic VariationGenotypeHaplotypesHerpesvirus 4, HumanHigh-Throughput Nucleotide SequencingHistocompatibilityHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHistocompatibility TestingHistocompatibility Antigens Class IHistocompatibility Antigens Class IIHLA AntigensB-lymphoblastoid cell linesHuman leukocyte antigenInternational HLA and Immunogenetics WorkshopMultiple-laboratory testingNext-generation sequencing

Identifiers

PMID30844424
PMCPMC6599558
OpenAlexW2918529223

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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.