Evidence map›Paper›PMID 36595917›Full record

ArticleSTAR protocols2022

Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors.

Rosalyn W Sayaman, Mohamad Saad, Carolina Heimann, Donglei Hu, Khalid Kunji, Jessica Roelands, Denise M Wolf, Scott Huntsman, Michele Ceccarelli, Vésteinn Thorsson and 2 more

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

Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 47% 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

3 citing papers in PubMed, 3 citations in OpenAlex.

  1. Review
  2. Article
  3. 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

12 authors at 8 institutions in 5 countries.

Rosalyn W SayamanDepartment of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: rwsayaman@gmail.com.
Mohamad SaadQatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar; Neuroscience Research Center, Faculty of Medical Sciences, Lebanese University, Beirut, Lebanon.
Carolina HeimannInstitute for Systems Biology, Seattle, WA 98109, USA.
Donglei HuDepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
Khalid KunjiQatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
Jessica RoelandsHuman Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
Denise M WolfDepartment of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
Scott HuntsmanDepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
Michele CeccarelliDepartment of Electrical Engineering and Information Technology, University of Naples "Federico II", 80128 Naples, Italy; BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy.
Vésteinn ThorssonInstitute for Systems Biology, Seattle, WA 98109, USA.
Elad ZivDepartment of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: elad.ziv@ucsf.edu.
Davide BedognettiHuman Immunology Department, Cancer Program, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar; Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, 16132 Genoa, Italy. Electronic address: dbedognetti@sidra.org.
Hamad bin Khalifa University · QAInstitute for Systems Biology · USUCSF Helen Diller Family Comprehensive Cancer Center · USUniversity of California, San Francisco · USLawrence Berkeley National Laboratory · USLeiden University Medical Center · NLUniversity of Genoa · ITUniversity of Naples Federico II · IT

Funding

(8) Genetics of Immune Related Adverse Events and Response to ImmunotherapyR01CA227466 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZIV, ELAD · 2018 to 2023
$3.3M
Genetics of mammographic density and breast cancer risk in LatinasK24CA169004 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZIV, ELAD · 2012 to 2021
$1.8M
Cancer Metabolism Training ProgramT32CA221709 · NCI · BECKMAN RESEARCH INSTITUTE/CITY OF HOPE · PI David K. Ann, Victoria L. Seewaldt · 2018 to 2026
$1.8M
NCI NIH HHS K24 CA169004NCI NIH HHS R01 CA227466NCI NIH HHS T32 CA221709
6 · The paper itself

Abstract

Germline genetic variants modulate human immune response. We present analytical pipelines for assessing the contribution of hosts' genetic background to the immune landscape of solid tumors using harmonized data from more than 9,000 patients in The Cancer Genome Atlas (TCGA). These include protocols for heritability, genome-wide association studies (GWAS), colocalization, and rare variant analyses. These workflows are developed around the structure of TCGA but can be adapted to explore other repositories or in the context of cancer immunotherapy. For complete details on the use and execution of this protocol, please refer to Sayaman et al. (2021).

Indexed as

Genome-Wide Association StudyNeoplasmsGenomeGerm CellsHumansImmunityBioinformaticsCancerGene expressionGeneticsGenomicsImmunology

Identifiers

PMID36595917
PMCPMC9772839
OpenAlexW4311327057

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.