Evidence map›Paper›PMID 30936866›Full record

ReviewFrontiers in immunology2019

Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming.

Mats Ohlin, Cathrine Scheepers, Martin Corcoran, William D Lees, Christian E Busse, Davide Bagnara, Linnea Thörnqvist, Jean-Philippe Bürckert, Katherine J L Jackson, Duncan Ralph and 15 more

Open access · goldAbstract readReview
In one paragraph

Review in Frontiers in immunology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.

0numbers the graph read from it
0cells of the map it votes in
44citing papers in PubMed
4.5field-weighted citation impact, top 5% 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

44 citing papers in PubMed, 73 citations in OpenAlex.

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  14. Adaptive immune receptor genotyping using theFrontiers in immunology · 2023
    Article
  15. Article
  16. Review
  17. IMGTBiomolecules · 2022
    Article
  18. Article
  19. Review
  20. 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

25 authors at 20 institutions in 12 countries.

Mats OhlinDepartment of Immunotechnology, Lund University, Lund, Sweden.
Cathrine ScheepersCenter for HIV and STIs, National Institute for Communicable Diseases, Johannesburg, South Africa.
Martin CorcoranDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden.
William D LeesInstitute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
Christian E BusseDivision of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany.
Davide BagnaraDepartment of Experimental Medicine, University of Genoa, Genoa, Italy.
Linnea ThörnqvistDepartment of Immunotechnology, Lund University, Lund, Sweden.
Jean-Philippe BürckertBISC Global Inc., Boston, MA, United States.
Katherine J L JacksonImmunology Division, The Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
Duncan RalphFred Hutchinson Cancer Research Center, Seattle, WA, United States.
Chaim A SchrammVaccine Research Center, National Institutes of Health, Washington, DC, United States.
Nishanth MarthandanDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
Felix BredenDepartment of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
Jamie ScottDepartment of Molecular Biology and Biochemistry, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.
Frederick A Matsen IvFred Hutchinson Cancer Research Center, Seattle, WA, United States.
Victor GreiffDepartment of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
Gur YaariFaculty of Engineering, Bar Ilan University, Ramat Gan, Israel.
Steven H KleinsteinDepartment of Pathology, Yale University, New Haven, CT, United States.
Scott ChristleyDepartment of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States.
Jacob S SherkowInnovation Center for Law and Technology, New York Law School, New York, NY, United States.
Sofia KossidaIMGT®, The International ImMunoGenetics information system® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France.
Marie-Paule LefrancIMGT®, The International ImMunoGenetics information system® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), CNRS, Institut de Génétique Humaine, Université de Montpellier, Montpellier, France.
Menno C van ZelmDepartment of Immunology and Pathology, Central Clinical School, The Alfred Hospital, Monash University, Melbourne, VIC, Australia.
Corey T WatsonDepartment of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, United States.
Andrew M CollinsSchool of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
Simon Fraser University · CACentre National de la Recherche Scientifique · FRFred Hutch Cancer Center · USLund University · SEBar-Ilan University · ILCenter for Global Development · USGarvan Institute of Medical Research · AUGerman Cancer Research Center · DEKarolinska Institutet · SENational Institutes of Health · USNew York Law School · USThe Alfred Hospital · AUThe University of Texas Southwestern Medical Center · USUniversity of Genoa · ITUniversity of London · GBUniversity of Louisville · USUniversity of Oslo · NOUniversity of the Witwatersrand · ZAUNSW Sydney · AUYale University · US

Funding

University of Washington/Fred Hutch Center for AIDS ResearchP30AI027757 · NIAID · UNIVERSITY OF WASHINGTON · PI Kenneth Sherr · 1988 to 2026
$104.9M
Modeling the dynamics and evolution of immune responses to influenza virusesU19AI117891 · NIAID · EMORY UNIVERSITY · PI AHMED, RAFI, ANTIA, RUSTOM NOSHIR · 2015 to 2019
$8.4M
An ethnically diverse genomic reference resource for the human heavy and light chain immunoglobulin lociR24AI138963 · NIAID · UNIVERSITY OF LOUISVILLE · PI Melissa Laird Smith, Corey Taylor Watson · 2018 to 2026
$5.5M
Comprehensive profiling of SARS-CoV-2 antibody responses and escape pathwaysR01AI138709 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI OVERBAUGH, JULIE M. · 2018 to 2022
$5.0M
DEFINING THE INFANT IMMUNE RESPONSE TO HIVR01AI120961 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI OVERBAUGH, JULIE M. · 2016 to 2020
$4.1M
COMPUTATIONAL TOOLS FOR THE ANALYSIS OF HIGH-THROUGHPUT IMMUNOGLOBULIN SEQUENCING EXPERIMENTSR01AI104739 · NIAID · YALE UNIVERSITY · PI KLEINSTEIN, STEVEN H. · 2014 to 2022
$3.6M
RepServer: Antigen Receptor Repertoire Analysis Pipelines via the WWWR01AI097403 · NIAID · UT SOUTHWESTERN MEDICAL CENTER · PI COWELL, LINDSAY G. · 2012 to 2016
$3.2M
Leveraing deep sequencing data to understand antibody maturationR01GM113246 · NIGMS · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2014 to 2018
$1.9M
Population level characterization of human immunoglobulin heavy chain germline variants with impacts on variability in the Ab repertoire of healthy adultsR21AI142590 · NIAID · UNIVERSITY OF LOUISVILLE · PI MARASCO, WAYNE A., WATSON, COREY TAYLOR · 2019 to 2020
$477k
NIAID NIH HHS P30 AI027757NIAID NIH HHS R01 AI097403NIAID NIH HHS R01 AI104739NIAID NIH HHS R01 AI120961NIAID NIH HHS R01 AI138709NIAID NIH HHS R21 AI142590NIAID NIH HHS R24 AI138963NIAID NIH HHS U19 AI117891NIGMS NIH HHS R01 GM113246
6 · The paper itself

Abstract

Immunoglobulins or antibodies are the main effector molecules of the B-cell lineage and are encoded by hundreds of variable (V), diversity (D), and joining (J) germline genes, which recombine to generate enormous IG diversity. Recently, high-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) of recombined V-(D)-J genes has offered unprecedented insights into the dynamics of IG repertoires in health and disease. Faithful biological interpretation of AIRR-seq studies depends upon the annotation of raw AIRR-seq data, using reference germline gene databases to identify the germline genes within each rearrangement. Existing reference databases are incomplete, as shown by recent AIRR-seq studies that have inferred the existence of many previously unreported polymorphisms. Completing the documentation of genetic variation in germline gene databases is therefore of crucial importance. Lymphocyte receptor genes and alleles are currently assigned by the Immunoglobulins, T cell Receptors and Major Histocompatibility Nomenclature Subcommittee of the International Union of Immunological Societies (IUIS) and managed in IMGT

Indexed as

AllelesGenes, ImmunoglobulinTerminology as TopicV(D)J RecombinationBase SequenceDatabases, GeneticDatasets as TopicGene LibraryGenetic VariationGerm-Line MutationHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionPolymerase Chain ReactionSequence AlignmentImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionAIRR-seqallelic variationIGHVimmunoglobulininferenceV(D)J rearrangement

Identifiers

PMID30936866
PMCPMC6431624
OpenAlexW2922017807

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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.