Evidence map›Paper›PMID 27276420›Full record

ArticleBiometrics2017

A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data.

Rong Fu, Pei Wang, Weiping Ma, Ayumu Taguchi, Chee-Hong Wong, Qing Zhang, Adi Gazdar, Samir M Hanash, Qinghua Zhou, Hua Zhong and 1 more

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

Article in Biometrics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact, top 97% 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

0 citing papers in PubMed, 2 citations in OpenAlex.

No citing paper in PubMed yet.

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 at 2 institutions in 2 countries.

Rong FuDepartment of Biostatistics, University of Washington, Seattle, Washington, U.S.A.
Pei WangDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A.
Weiping MaDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, U.S.A.
Ayumu TaguchiProgram of Molecular Diagnosis, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A.
Chee-Hong WongProgram of Molecular Diagnosis, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A.
Qing ZhangProgram of Molecular Diagnosis, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A.
Adi GazdarHamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas, U.S.A.
Samir M HanashProgram of Molecular Diagnosis, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A.
Qinghua ZhouSichuang Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
Hua ZhongDepartment of Population Health, New York University, New York, U.S.A.
Ziding FengDepartment of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas, U.S.A.
Sichuan University · CNUniversity of Washington · US

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
The Early Detection Research Network: Data Management and Coordinating CenterU24CA086368 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI RUTH D ETZIONI, Ziding Feng · 2010 to 2026
$75.7M
UNIVERSITY OF TEXAS--SPORE IN LUNG CANCERP50CA070907 · NCI · UT SOUTHWESTERN MEDICAL CENTER · PI GIBBONS, DON LYNN · 1996 to 2024
$57.4M
EDRN--DATA MANAGEMENT AND COORDINATING CENTERU01CA086368 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI FENG, ZIDING · 2000 to 2010
$16.9M
Proteo-genomic Discovery, Prioritization and Verification of Cancer BiomarkersU24CA160034 · NCI · BROAD INSTITUTE, INC. · PI CARR, STEVEN A, PAULOVICH, AMANDA G · 2011 to 2016
$16.2M
Use of Biomarkers in Diagnosis, Prognosis, Risk Prediction and Early Detection ofP01CA053996 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI HSU, LI · 1991 to 2015
$9.4M
Systems Biology based Proteogenomic Translator for Cancer Marker Discovery towards Precision MedicineU24CA210993 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SCHADT, ERIC E, WANG, PEI · 2016 to 2020
$4.6M
Integrative multivariate association and genomic analysesR01GM108711 · NIGMS · UNIVERSITY OF CHICAGO · PI CHEN, LIN · 2014 to 2022
$3.1M
Statistical Methods for Integrative Analysis of Genomics and Proteomics DataR01GM082802 · NIGMS · FRED HUTCHINSON CANCER RESEARCH CENTER · PI WANG, PEI · 2008 to 2012
$1.4M
NCI NIH HHS P01 CA053996NCI NIH HHS P30 CA016672NCI NIH HHS P50 CA070907NCI NIH HHS U01 CA086368NCI NIH HHS U24 CA086368NCI NIH HHS U24 CA160034NCI NIH HHS U24 CA210993NIGMS NIH HHS R01 GM082802NIGMS NIH HHS R01 GM108711
6 · The paper itself

Abstract

In this article, we propose a new statistical method-MutRSeq-for detecting differentially expressed single nucleotide variants (SNVs) based on RNA-seq data. Specifically, we focus on nonsynonymous mutations and employ a hierarchical likelihood approach to jointly model observed mutation events as well as read count measurements from RNA-seq experiments. We then introduce a likelihood ratio-based test statistic, which detects changes not only in overall expression levels, but also in allele-specific expression patterns. In addition, this method can jointly test multiple mutations in one gene/pathway. The simulation studies suggest that the proposed method achieves better power than a few competitors under a range of different settings. In the end, we apply this method to a breast cancer data set and identify genes with nonsynonymous mutations differentially expressed between the triple negative breast cancer tumors and other subtypes of breast cancer tumors.

Indexed as

Gene Expression Regulation, NeoplasticHigh-Throughput Nucleotide SequencingModels, StatisticalBreast NeoplasmsFemaleGene Expression ProfilingHumansLikelihood FunctionsMutationPolymorphism, Single NucleotideSequence Analysis, RNASoftwareAllele-specific expressionBreast cancer tumorsDifferential expressionLikelihood ratio testRNA-seq

Identifiers

PMID27276420
PMCPMC5151178
OpenAlexW2414674452

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.