Evidence map›Paper›PMID 34059054›Full record

ArticleBMC medical genomics2021

Exonic variants undergoing allele-specific selection in cancers.

Qiyuan Li, Yuanyuan Zeng, Janet Wang, Hongkun Fang, Jintao Guo, Liying Yu, Taoling Zhong, Chaoqun Xu, Matthew Freedman, Thomas LaFramboise

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

Article in BMC medical genomics, 2021. 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 95% 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, 1 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

10 authors at 5 institutions in 2 countries.

Qiyuan Li *Department of Hematology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361102, China.
Yuanyuan Zeng *Department of Obstetrics and Gynecology, The First Affiliated Hospital, Army Medical University, Chong Qing, China.
Janet WangDepartment of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44122, USA.
Hongkun FangNational Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
Jintao GuoNational Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
Liying YuState Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
Taoling ZhongNational Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
Chaoqun XuNational Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
Matthew Freedman *Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
Thomas LaFramboise *Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44122, USA. thomas.laframboise@case.edu.
Xiamen University · CNArmy Medical University · CNBroad Institute · USCase Western Reserve University · USUniversity School · US

Funding

THE CANCER EPITOPE DATABASE AND ANALYSIS RESOURCEU24CA248138 · NCI · LA JOLLA INSTITUTE FOR IMMUNOLOGY · PI PETERS, BJOERN, SETTE, ALESSANDRO · 2021 to 2025
$4.6M
Defining the epigenetic landscape in human prostate cancerR01CA193910 · NCI · DANA-FARBER CANCER INST · PI BROWN, MYLES A, FREEDMAN, MATTHEW L · 2015 to 2019
$3.1M
Identifying causal variants and genes underlying breast cancer risk lociR01CA204954 · NCI · DANA-FARBER CANCER INST · PI FREEDMAN, MATTHEW L · 2016 to 2020
$3.0M
Tools and Data for Bayesian Modeling of Mitochondrial Genome Dynamics in Human DiseaseR01LM013067 · NLM · CASE WESTERN RESERVE UNIVERSITY · PI BRYNJARSDOTTIR, JENNY, LAFRAMBOISE, THOMAS LOUIS · 2020 to 2024
$1.5M
Integrating Clues from the Somatic Genome in the Search for Rare Germline Cancer Susceptibility VariantsR21CA249138 · NCI · CASE WESTERN RESERVE UNIVERSITY · PI LAFRAMBOISE, THOMAS LOUIS · 2020 to 2021
$414k
Epigenetic Effects of ResveratrolR21CA124818 · NCI · UNIVERSITY OF NORTH DAKOTA · PI SAUTER, EDWARD R · 2007 to 2008
$314k
NCI NIH HHS R01 CA193910NCI NIH HHS R01 CA204954NCI NIH HHS R21 CA124818NCI NIH HHS R21 CA249138NCI NIH HHS U24 CA248138NLM NIH HHS R01 LM013067
6 · The paper itself

Abstract

backgroundAllelic imbalance (AI) in tumors is caused by chromosomal and sub-chromosomal gains and losses.

resultsWe evaluated AI at 109,086 germline exonic SNP loci in four cancer types, and identified a set of SNPs that demonstrate strong tumor allele specificity in AI events. Further analyses demonstrated that these alleles show consistently different frequencies in the cancer population compared to the healthy population and are significantly enriched for predicted protein-damaging variants. Moreover, genes harboring SNPs that demonstrate allele specificity are enriched for cancer-related biological processes and are more likely to be essential in cancer cells.

conclusionsIn summary, our study provides a unique and complementary method to identify genes and variants that are relevant to carcinogenesis.

Indexed as

AllelesExonsNeoplasmsPolymorphism, Single NucleotideAllelic ImbalanceHumansAllelic imbalanceCancerCopy numberExonic variantsSomatic selection

Identifiers

PMID34059054
PMCPMC8166126
OpenAlexW3165470539

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.