Evidence map›Paper›PMID 37205487›Full record

ArticlemedRxiv : the preprint server for health sciences2023

Transcriptome-Wide Association Analysis Identifies Novel Candidate Susceptibility Genes for Prostate-Specific Antigen Levels in Men Without Prostate Cancer.

Dorothy M Chen, Ruocheng Dong, Linda Kachuri, Thomas Hoffmann, Yu Jiang, Sonja I Berndt, John P Shelley, Kerry R Schaffer, Mitchell J Machiela, Neal D Freedman and 11 more

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

Article in medRxiv : the preprint server for health sciences, 2023. 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
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

5 · Who and what money

Authors and funding

21 authors at 8 institutions in 2 countries.

Dorothy M ChenDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
Ruocheng DongDepartment of Epidemiology and Population Health, Stanford University, Stanford, CA, 94305, USA.
Linda KachuriDepartment of Epidemiology and Population Health, Stanford University, Stanford, CA, 94305, USA.
Thomas HoffmannDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
Yu JiangDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
Sonja I BerndtDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
John P ShelleyDepartment of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
Kerry R SchafferDivision of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
Mitchell J MachielaDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
Neal D FreedmanDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
Wen-Yi HuangDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
Shengchao A LiDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
Hans LiljaDepartments of Pathology and Laboratory Medicine, Surgery, Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
Stephen K Van Den EedenDivision of Research, Kaiser Permanente Northern California, Oakland, CA, 94612, USA.
Stephen ChanockDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20814, USA.
Christopher A HaimanCenter for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA.
David V ContiCenter for Genetic Epidemiology, Department of Population and Preventive Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90032, USA.
Robert J KleinDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
Jonathan D MosleyDepartments of Internal Medicine and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
John S WitteDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
Rebecca E GraffDepartment of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
National Cancer Institute · USUniversity of California, San Francisco · USUniversity of Southern California · USStanford University · USVanderbilt University Medical Center · USIcahn School of Medicine at Mount Sinai · USKaiser Permanente · USMemorial Sloan Kettering Cancer Center · US

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI SELWYN M VICKERS · 1985 to 2026
$347.4M
Understanding Population Differences in Cancer: The MEC StudyU01CA164973 · NCI · UNIVERSITY OF HAWAII AT MANOA · PI HAIMAN, CHRISTOPHER ALAN, LE MARCHAND, LOIC · 2015 to 2025
$37.4M
MEDICAL SCIENTIST TRAINING PROGRAMT32GM007347 · NIGMS · VANDERBILT UNIVERSITY · PI WILLIAMS, CHRISTOPHER S. · 1985 to 2023
$26.3M
Modeling to Improve Prostate Cancer Outcomes Across Diverse PopulationsU01CA199338 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI DE KONING, HARRY J, ETZIONI, RUTH D · 2015 to 2019
$5.2M
Medical Scientist Training ProgramT32GM152284 · NIGMS · VANDERBILT UNIVERSITY · PI Christopher S. Williams · 2024 to 2026
$4.8M
Genetic Predictors of Prostate Cancer SurvivalR01CA244948 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI ROBERT J. KLEIN · 2021 to 2026
$4.1M
Precision Prostate Cancer Screening with Genetically Adjusted Prostate-Specific Antigen LevelsR01CA241410 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI John S. Witte · 2020 to 2026
$3.7M
Improving prostate cancer screening by integration of SNPs with blood biomarkersR01CA175491 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI KLEIN, ROBERT J. · 2013 to 2018
$2.8M
Comprehensive Investigation of Multiple Myeloma Genetic Susceptibility in African AmericansR00CA246076 · NCI · STANFORD UNIVERSITY · PI KACHURI, MIRLINDA · 2022 to 2024
$747k
NCI NIH HHS P30 CA008748NCI NIH HHS R00 CA246076NCI NIH HHS R01 CA175491NCI NIH HHS R01 CA241410NCI NIH HHS R01 CA244948NCI NIH HHS U01 CA164973NCI NIH HHS U01 CA199338NIGMS NIH HHS T32 GM007347NIGMS NIH HHS T32 GM152284
6 · The paper itself

Abstract

Deciphering the genetic basis of prostate-specific antigen (PSA) levels may improve their utility to screen for prostate cancer (PCa). We thus conducted a transcriptome-wide association study (TWAS) of PSA levels using genome-wide summary statistics from 95,768 PCa-free men, the MetaXcan framework, and gene prediction models trained in Genotype-Tissue Expression (GTEx) project data. Tissue-specific analyses identified 41 statistically significant (p < 0.05/12,192 = 4.10e-6) associations in whole blood and 39 statistically significant (p < 0.05/13,844 = 3.61e-6) associations in prostate tissue, with 18 genes associated in both tissues. Cross-tissue analyses that combined associations across 45 tissues identified 155 genes that were statistically significantly (p < 0.05/22,249 = 2.25e-6) associated with PSA levels. Based on conditional analyses that assessed whether TWAS associations were attributable to a lead GWAS variant, we found 20 novel genes (11 single-tissue, 9 cross-tissue) that were associated with PSA levels in the TWAS. Of these novel genes, five showed evidence of colocalization (colocalization probability > 0.5):

Identifiers

PMID37205487
PMCPMC10187439
OpenAlexW4372349335

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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.