Evidence map›Paper›PMID 26360253›Full record

ArticleClinical immunology (Orlando, Fla.)2015

High-throughput sequencing reveals an altered T cell repertoire in X-linked agammaglobulinemia.

Manish Ramesh, Noa Simchoni, David Hamm, Charlotte Cunningham-Rundles

Open access · greenAbstract read
In one paragraph

Article in Clinical immunology (Orlando, Fla.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.6field-weighted citation impact, top 35% 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

6 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. T Cell Abnormalities in X-Linked Agammaglobulinaemia: an Updated Review.Clinical reviews in allergy & immunology · 2023
    Review
  3. Article
  4. Article
  5. Article
  6. 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

4 authors at 3 institutions in 1 country.

Manish RameshMontefiore Medical Center, Bronx, NY, United States.
Noa SimchoniIcahn School of Medicine at Mount Sinai, New York, NY, United States.
David HammAdaptive Biotech, Seattle, WA, United States.
Charlotte Cunningham-RundlesIcahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Pediatrics, The Immunology Institute, Box 1089, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, United States.
Icahn School of Medicine at Mount Sinai · USAdaptive Biotechnologies (United States) · USMontefiore Medical Center · US

Funding

Regulation of IgA class switching in the intestinal mucosaP01AI061093 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2004 to 2021
$29.8M
MOUNT SINAI MEDICAL SCIENTIST TRAINING PROGRAMT32GM007280 · NIGMS · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI BARON, MARGARET H · 1985 to 2021
$22.8M
Resources to Assist Investigations in Primary Immunodeficiency Diseases (U24)U24AI086037 · NIAID · IMMUNE DEFICIENCY FOUNDATION · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2010 to 2019
$6.5M
TARGETING PRIMARY IMMUNODEFICIENCY AMONG MINORITIESR18AI048693 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CUNNINGHAM-RUNDLES, CHARLOTTE · 2000 to 2016
$6.2M
Exposporium determinants of Bacillus anthracisR21AI101093 · NIAID · UNIVERSITY OF MISSOURI-COLUMBIA · PI STEWART, GEORGE C. · 2012 to 2013
$390k
NIAID NIH HHS AI-086037NIAID NIH HHS AI 101093NIAID NIH HHS AI-48693NIAID NIH HHS P01 AI061093NIAID NIH HHS R18 AI048693NIAID NIH HHS R21 AI101093NIAID NIH HHS U24 AI086037NIGMS NIH HHS T32 GM007280NIGMS NIH HHS T32-GM007280
6 · The paper itself

Abstract

To examine the T cell receptor structure in the absence of B cells, the TCR β CDR3 was sequenced from DNA of 15 X-linked agammaglobulinemia (XLA) subjects and 18 male controls, using the Illumina HiSeq platform and the ImmunoSEQ analyzer. V gene usage and the V-J combinations, derived from both productive and non-productive sequences, were significantly different between XLA samples and controls. Although the CDR3 length was similar for XLA and control samples, the CDR3 region of the XLA T cell receptor contained significantly fewer deletions and insertions in V, D, and J gene segments, differences intrinsic to the V(D)J recombination process and not due to peripheral T cell selection. XLA CDR3s demonstrated fewer charged amino acid residues, more sharing of CDR3 sequences, and almost completely lacked a population of highly modified Vβ gene segments found in control DNA, suggesting both a skewed and contracted T cell repertoire in XLA.

Indexed as

AdolescentAdultAgammaglobulinemiaB-LymphocytesCase-Control StudiesChildChild, PreschoolDNAGenetic Diseases, X-LinkedHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Variable RegionInfantMaleMiddle AgedReceptor-CD3 Complex, Antigen, T-CellDNAImmunoglobulin Variable RegionReceptor-CD3 Complex, Antigen, T-CellReceptors, Antigen, T-CellAmino acid sequenceHigh throughput sequencingJunctional diversityT cell receptorXLA

Identifiers

PMID26360253
PMCPMC4658265
OpenAlexW1421986272

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.