Evidence map›Paper›PMID 25784652›Full record

ArticleOncotarget2015

Multilevel-analysis identify a cis-expression quantitative trait locus associated with risk of renal cell carcinoma.

Xiang Shu, Mark P Purdue, Yuanqing Ye, Christopher G Wood, Meng Chen, Zhaoming Wang, Demetrius Albanes, Xia Pu, Maosheng Huang, Victoria L Stevens and 9 more

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

Article in Oncotarget, 2015. 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 98% 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, 0 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

19 authors at 6 institutions in 3 countries.

Xiang ShuDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Mark P PurdueDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.
Yuanqing YeDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Christopher G WoodUrology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Meng ChenDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Zhaoming WangCancer Genomics Research Laboratory, SAIC-Frederick Inc., National Cancer Institute-Frederick, Frederick, Maryland, USA.
Demetrius AlbanesDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.
Xia PuDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Maosheng HuangDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Victoria L StevensEpidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA.
W Ryan DiverEpidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA.
Susan M GapsturEpidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA.
Jarmo VirtamoDepartment of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Wong-Ho ChowDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Nizar M TannirGenitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Colin P DinneyUrology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Nathaniel RothmanDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.
Stephen J ChanockDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA.
Xifeng WuDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
The University of Texas MD Anderson Cancer Center · USNational Cancer Institute · USAmerican Cancer Society · USFinnish Institute for Health and Welfare · FINational Institutes of Health · USSpanish Oncology Genitourinary Group · ES

Funding

Molecular pathways linking obesity and RCC tumorigenesis (PQ1)R01CA170298 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI GU, JIAN · 2012 to 2015
$2.1M
NCI NIH HHS R01 CA170298
6 · The paper itself

Abstract

We conducted multilevel analyses to identify potential susceptibility loci for renal cell carcinoma (RCC), which may be overlooked in traditional genome-wide association studies (GWAS). A gene set enrichment analysis was performed utilizing a GWAS dataset comprised of 894 RCC cases and 1,516 controls using GenGen, SNP ratio test, and ALIGATOR. The antigen processing and presentation pathway was consistently significant (P = 0.001, = 0.004, and < 0.001, respectively). Versatile gene-based association study approach was applied to the top-ranked pathway and identified the driven genes. By comparing the expression of the genes in RCC tumor and adjacent normal tissues, we observed significant overexpression of HLA genes in tumor tissues, which was also supported by public databases. We sought to validate genetic variants in antigen processing and presentation pathway in an independent GWAS dataset comprised of 1,311 RCC cases and 3,424 control subjects from the National Cancer Institute; one SNP, rs1063355, was significant in both populations (P(meta-analysis) = 9.15 × 10⁻⁴, P(heterogeneity) = 0.427). Strong correlation indicated that rs1063355 was a cis-expression quantitative trait loci which associated with HLA-DQB1 expression (Spearman's rank r = -0.59, p = 5.61 × 10⁻⁶). The correlation was further validated using a public dataset. Our results highlighted the role of immune-related pathway and genes in the etiology of RCC.

Indexed as

Quantitative Trait LociCarcinoma, Renal CellCase-Control StudiesFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansKidney NeoplasmsMalePolymorphism, Single Nucleotide

Identifiers

PMID25784652
PMCPMC4414175
OpenAlexW1496822420

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.