Evidence map›Paper›PMID 37365517›Full record

ArticleBMC genomics2023

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Burcu Gurun, Wesley Horton, Dhaarini Murugan, Biqing Zhu, Patrick Leyshock, Sushil Kumar, Katelyn T Byrne, Robert H Vonderheide, Adam A Margolin, Motomi Mori and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Trial
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Burcu GurunKnight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. gurundem@ohsu.edu.ORCID http://orcid.org/0000-0003-0786-8059
Wesley HortonKnight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Dhaarini MuruganDepartment of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Biqing ZhuComputational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA.
Patrick LeyshockKnight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Sushil KumarDepartment of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Katelyn T ByrneDepartment of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
Robert H VonderheideAbramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Adam A MargolinNextVivo, Palo Alto, CA, USA.
Motomi MoriDepartment of Biostatistics, St. Jude's Children's Research Hospital, Memphis, TN, USA.
Paul T SpellmanKnight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. spellmap@ohsu.edu.
Lisa M CoussensKnight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. coussenl@ohsu.edu.
Terence P SpeedBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. terry@wehi.edu.au.

Funding

Understanding the origins of rapid recurrence of pancreatic cancer after resectionP30CA069533 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI Luiz Eduardo Bertassoni · 1997 to 2026
$60.5M
Leukocyte Biomarkers for Predicting Human Breast Cancer OutcomesU54CA163123 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COUSSENS, LISA M., DALDRUP-LINK, HEIKE ELIZABETH · 2011 to 2015
$2.0M
Regulation of Inflammation-Associated Epithelial Cancer DevelopmentR01CA130980 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COUSSENS, LISA M. · 2008 to 2012
$1.6M
Regulating the Immune Microenvironment in Breast CancerR01CA155331 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COUSSENS, LISA M. · 2011 to 2015
$1.6M
NCI NIH HHS CA130980NCI NIH HHS CA155331NCI NIH HHS CA163123NCI NIH HHS P30 CA069533NCI NIH HHS RO1 CA217176NCI NIH HHS U54 CA163123Susan G. Komen KG110560
6 · The paper itself

Abstract

T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.

Indexed as

High-Throughput Nucleotide SequencingT-LymphocytesBase SequenceChromosome MappingReceptors, Antigen, T-Cell, alpha-betaReceptors, Antigen, T-Cell, alpha-betaAmplification biasCDR3Clonotype countsCount normalizationMultiplex PCRNegative binomialNormalizationSynthetic TCR templatesSynthetic templatesTCR sequencing

Identifiers

PMID37365517
PMCPMC10291816

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.