Evidence map›Paper›PMID 35942349›Full record

ArticleSTAR protocols2022

Analysis of germline-driven ancestry-associated gene expression in cancers.

Nyasha Chambwe, Rosalyn W Sayaman, Donglei Hu, Scott Huntsman, Cancer Genome Analysis Network, Anab Kemal, Samantha Caesar-Johnson, Jean C Zenklusen, Elad Ziv, Rameen Beroukhim and 1 more

Abstract 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 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

11 authors.

Nyasha ChambweInstitute for Systems Biology, Seattle, WA 98109, USA.
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, Duarte, CA 91010, USA; Biological Sciences and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: rwsayaman@gmail.com.
Donglei HuDepartment of Medicine, Institute for Human Genetics, 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.
Cancer Genome Analysis Network
Anab KemalNational Cancer Institute, Bethesda, MD 20892, USA.
Samantha Caesar-JohnsonNational Cancer Institute, Bethesda, MD 20892, USA.
Jean C ZenklusenNational Cancer Institute, Bethesda, MD 20892, 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.
Rameen BeroukhimThe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: rameen_beroukhim@dfci.harvard.edu.
Andrew D CherniackThe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: achernia@broadinstitute.org.

Funding

Global Infrastructure for Collaborative High-throughput Cancer Genomics AnalysisU24CA210999 · NCI · BROAD INSTITUTE, INC. · PI GETZ, GAD A · 2016 to 2020
$4.7M
Visualization hub for genomics data exploration and translational discoveryU24CA210974 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI COLLISSON, ERIC, HAUSSLER, DAVID H · 2016 to 2020
$4.2M
(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
Integrative Cancer Epigenomic Data Analysis Center (ICE-DAC)U24CA210969 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI LAIRD, PETER W · 2016 to 2020
$2.5M
The joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor ProfilesU24CA210989 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, ZODY, MICHAEL C · 2016 to 2020
$2.4M
Center for the comprehensive analysis of somatic copy-number alterations in cancerU24CA210978 · NCI · BROAD INSTITUTE, INC. · PI BEROUKHIM, RAMEEN, CHERNIACK, ANDREW DAVID · 2016 to 2020
$2.3M
UCSC-Buck Specialized Genomic Data Analysis Center for the Genomic Data Analysis NetworkU24CA210990 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI STUART, JOSHUA MICHAEL · 2016 to 2020
$2.2M
OHSU Center for Specialized Data Analysis as part of the GDANU24CA210957 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI DEMIR, EMEK, SPELLMAN, PAUL T. · 2016 to 2020
$2.2M
RNA sequencing analysis of CancerU24CA210988 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, HOADLEY, KATHERINE A. · 2016 to 2020
$2.1M
Integrative miRNA data analysis for clinical cancer genomicsU24CA210952 · NCI · PROVINCIAL HEALTH SERVICES AUTHORITY · PI JONES, STEVEN JOHN, SHMULEVICH, ILYA · 2016 to 2020
$2.0M
Batch effects in molecular profiling data on cancers: detection, quantitation, interpretation, and correctionU24CA210949 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI AKBANI, REHAN, MILLS, GORDON B. · 2016 to 2020
$1.9M
Genetics of mammographic density and breast cancer risk in LatinasK24CA169004 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ZIV, ELAD · 2012 to 2021
$1.8M
NCI NIH HHS K24 CA169004NCI NIH HHS R01 CA227466NCI NIH HHS T32 CA221709NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210950NCI NIH HHS U24 CA210952NCI NIH HHS U24 CA210957NCI NIH HHS U24 CA210969NCI NIH HHS U24 CA210974NCI NIH HHS U24 CA210978NCI NIH HHS U24 CA210988NCI NIH HHS U24 CA210989NCI NIH HHS U24 CA210990NCI NIH HHS U24 CA210999NCI NIH HHS U24 CA211000NCI NIH HHS U24 CA211006
6 · The paper itself

Abstract

Differential mRNA expression between ancestry groups can be explained by both genetic and environmental factors. We outline a computational workflow to determine the extent to which germline genetic variation explains cancer-specific molecular differences across ancestry groups. Using multi-omics datasets from The Cancer Genome Atlas (TCGA), we enumerate ancestry-informative markers colocalized with cancer-type-specific expression quantitative trait loci (e-QTLs) at ancestry-associated genes. This approach is generalizable to other settings with paired germline genotyping and mRNA expression data for a multi-ethnic cohort. For complete details on the use and execution of this protocol, please refer to Carrot-Zhang et al. (2020), Robertson et al. (2021), and Sayaman et al. (2021).

Indexed as

NeoplasmsQuantitative Trait LociGene ExpressionGerm CellsHumansRNA, MessengerRNA, MessengerBioinformaticsCancerComputer sciencesGene ExpressionGenomicsRNAseqSequence analysis

Identifiers

PMID35942349
PMCPMC9356164

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.