Evidence map›Paper›PMID 28811643›Full record

ArticleScientific reports2017

Overexpressed somatic alleles are enriched in functional elements in Breast Cancer.

Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2017. 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
–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

3 citing papers in PubMed.

  1. Article
  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

14 authors.

Paula RestrepoDepartment of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Mercedeh MovassaghUniversity of Massachusetts Medical School, Program in Bioinformatics and Integrative Biology, Worcester, MA, 01605, USA.
Nawaf AlomranMcCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Christian MillerMcCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Muzi LiMcCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Chris TrenkovMcCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Yulian ManchevMcCormick Genomics and Proteomics Center, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Sonali BahlDepartment of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Stephanie WarnkenComputational Biology Institute, The George Washington University, Washington, DC, 20037, USA.ORCID 0000-0003-1591-3921
Liam SpurrDepartment of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA.
Tatiyana ApanasovichDepartment of Statistics, The George Washington University, Washington, DC, 20037, USA.
Keith CrandallComputational Biology Institute, The George Washington University, Washington, DC, 20037, USA.ORCID 0000-0002-0836-3389
Nathan EdwardsDepartment of Biochemistry and Molecular and Cellular Biology, Georgetown University, School of Medicine, Washington, DC, 20057, USA.
Anelia HorvathDepartment of Pharmacology and Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, 20037, USA. horvatha@gwu.edu.ORCID 0000-0003-4117-013X

Funding

Clinical and Translational Science Institute at Children's NationalUL1TR000075 · NCATS · CHILDREN'S RESEARCH INSTITUTE · PI GUAY-WOODFORD, LISA MARIE · 2012 to 2015
$13.7M
NCATS NIH HHS UL1 TR000075
6 · The paper itself

Abstract

Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC). We document significant allele-preferential expression of functional variants in CGC genes and across the entire dataset. Notably, we find frequent allele-specific overexpression of variants in tumor-suppressor genes. We also report a list of over-expressed variants from non-CGC genes. Overall, our analysis presents an integrated set of features of somatic allele expression and points to the vast information content of the asymmetric alleles in the cancer transcriptome.

Indexed as

AllelesGene Expression Regulation, NeoplasticResponse ElementsBreast NeoplasmsFemaleGene Expression ProfilingGenetic VariationGenotypeHumansMutationTranscriptome

Identifiers

PMID28811643
PMCPMC5557904

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.