Evidence map›Paper›PMID 26162851›Full record

ArticleHuman molecular genetics2015

Integration of multiethnic fine-mapping and genomic annotation to prioritize candidate functional SNPs at prostate cancer susceptibility regions.

Ying Han, Dennis J Hazelett, Fredrik Wiklund, Fredrick R Schumacher, Daniel O Stram, Sonja I Berndt, Zhaoming Wang, Kristin A Rand, Robert N Hoover, Mitchell J Machiela and 78 more

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In one paragraph

Article in Human molecular genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
30citing papers in PubMed, 3 pooled it
–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

30 citing papers in PubMed, 3 syntheses or guidelines pooled it.

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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

88 authors.

Ying HanDepartment of Preventive Medicine, Keck School of Medicine.
Dennis J HazelettDepartment of Preventive Medicine, Keck School of Medicine.
Fredrik WiklundDepartment of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.
Fredrick R SchumacherDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Daniel O StramDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Sonja I BerndtDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Zhaoming WangDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA.
Kristin A RandDepartment of Preventive Medicine, Keck School of Medicine.
Robert N HooverDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Mitchell J MachielaDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Merideth YeagerCancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA.
Laurie BurdetteDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA.
Charles C ChungDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Amy HutchinsonDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-DCEG, SAIC-Frederick Inc., Frederick, MD, USA.
Kai YuDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Jianfeng XuProgram for Personalized Cancer Care and Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA.
Ruth C TravisCancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
Timothy J KeyCancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
Afshan SiddiqDepartment of Genomics of Common Disease, School of Public Health.
Federico CanzianGenomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany.
Atsushi TakahashiLaboratory for Statistical Analysis.
Michiaki KuboLaboratory for Genotyping Development.
Janet L StanfordDivision of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.
Suzanne KolbDivision of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Susan M GapsturEpidemiology Research Program, American Cancer Society, Atlanta, GA, USA.
W Ryan DiverEpidemiology Research Program, American Cancer Society, Atlanta, GA, USA.
Victoria L StevensEpidemiology Research Program, American Cancer Society, Atlanta, GA, USA.
Sara S StromDepartment of Epidemiology.
Curtis A PettawayDepartment of Urology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
Ali Amin Al OlamaCentre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Zsofia Kote-JaraiThe Institute of Cancer Research, London, UK.
Rosalind A EelesThe Institute of Cancer Research, London, UK, Royal Marsden National Health Services (NHS) Foundation Trust, London and Sutton, UK.
Edward D YeboahKorle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana.
Yao TetteyKorle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana.
Richard B BiritwumKorle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana.
Andrew A AdjeiKorle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana.
Evelyn TayKorle Bu Teaching Hospital, Accra, Ghana, University of Ghana Medical School, Accra, Ghana.
Ann TrueloveWestat, Rockville, MD, USA.
Shelley NiwaWestat, Rockville, MD, USA.
Anand P ChokkalingamSchool of Public Health, University of California, Berkeley, CA, USA.
William B IsaacsJames Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institution, Baltimore, MD, USA.
Constance ChenProgram in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology.
Sara LindstromProgram in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology.
Loic Le MarchandEpidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA.
Edward L GiovannucciDepartment of Nutrition, Department of Epidemiology.
Mark PomerantzDepartment of Medical Oncology.
Henry LongDepartment of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
Fugen LiDepartment of Medical Oncology, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
Jing MaChanning Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
Meir StampferDepartment of Nutrition, Department of Epidemiology.
Esther M JohnCancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
Sue A InglesDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Rick A KittlesUniversity of Arizona College of Medicine and University of Arizona Cancer Center, Tucson, AZ, USA.
Adam B MurphyDepartment of Urology, Northwestern University, Chicago, IL, USA.
William J BlotInternational Epidemiology Institute, Rockville, MD, USA, Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
Lisa B SignorelloDepartment of Epidemiology.
Wei ZhengDivision of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
Demetrius AlbanesDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Jarmo VirtamoDepartment of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland.
Stephanie WeinsteinDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Barbara NemesureDepartment of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA.
John CarptenThe Translational Genomics Research Institute, Phoenix, AZ, USA.
M Cristina LeskeDepartment of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA.
Suh-Yuh WuDepartment of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA.
Anselm J M HennisDepartment of Preventive Medicine, Stony Brook University, Stony Brook, NY, USA, Chronic Disease Research Centre and Faculty of Medical Sciences, University of the West Indies, Bridgetown, Barbados.
Benjamin A RybickiDepartment of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA.
Christine Neslund-DudasDepartment of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA.
Ann W HsingCancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
Lisa ChuCancer Prevention Institute of California, Fremont, CA, USA, Division of Epidemiology, Department of Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
Phyllis J GoodmanSWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Eric A KleinDepartment of Urology, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA.
S Lilly ZhengCenter for Cancer Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.
John S WitteDepartment of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, CA, USA and.
Graham CaseyDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Elio RiboliDepartment of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK.
Qiyuan LiMedical College, Xiamen University, Xiamen 361102, China.
Matthew L FreedmanDepartment of Medical Oncology.
David J HunterProgram in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology.
Henrik GronbergDepartment of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.
Michael B CookDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Hidewaki NakagawaLaboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.
Peter KraftProgram in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
Stephen J ChanockDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Douglas F EastonCentre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Brian E HendersonDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Gerhard A CoetzeeDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
David V ContiDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center.
Christopher A HaimanDepartment of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, haiman@usc.edu.

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
SWOG Foreign AccrualsU10CA037429 · NCI · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI BLANKE, CHARLES D., MEYSKENS, FRANK L. · 1985 to 2014
$205.2M
Tumor Immunology and Microenvironment Research ProgramP30CA068485 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI MATTHEW J TYSKA · 1995 to 2026
$172.8M
Tumor Environment and Metastasis (TEAM) Research ProgramP30CA060553 · NCI · NORTHWESTERN UNIVERSITY AT CHICAGO · PI Daniela E Matei · 1993 to 2026
$153.9M
SWOG NCORP Research BaseUG1CA189974 · NCI · THE HOPE FOUNDATION · PI CHARLES D. BLANKE, DAWN HERSHMAN · 2014 to 2026
$80.6M
Southern Community Cohort StudyR01CA092447 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI BLOT, WILLIAM J., ZHENG, WEI · 2001 to 2015
$74.0M
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
PLCO Trial Etiologic and Early Marker StudyZIACP010152 · NCI · DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS · PI MOORE, STEVEN · 2009 to 2025
$29.9M
Targeting Tumor Microenvironment-Induced Therapy Resistance in Prostate Cancer Bone MetastasisP50CA140388 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI LOGOTHETIS, CHRISTOPHER J., THOMPSON, TIMOTHY CHARLES · 2009 to 2022
$23.4M
GENETIC SUSCEPTIBILITY TO CANCER IN MULTIETHNIC COHORTSR01CA063464 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI HENDERSON, BRIAN E · 2001 to 2005
$23.2M
Multiethnic Cohort Study of Diet and CancerR37CA054281 · NCI · UNIVERSITY OF HAWAII AT MANOA · PI KOLONEL, LAURENCE N. · 2003 to 2012
$23.2M
CALIFORNIA'S PARTICIPATION IN THE NATIONAL CANCER PREVENTION AND CONTRO PROGRAMU58DP000807 · DP · PUBLIC HEALTH INSTITUTE · PI SNIPES, KURT P · 2007 to 2011
$22.5M
Cancer Research UK 15007Cancer Research UK 16491Cancer Research UK 16563Cancer Research UK 17528Cancer Research UK 19170CCR NIH HHS N01 RC037004CCR NIH HHS N01-RC-37004CCR NIH HHS N01-RC-45035Intramural NIH HHSNCCDPHP CDC HHS 1U58DP000807-3NCI NIH HHS 5UM1CA182883NCI NIH HHS CA056678NCI NIH HHS CA082664NCI NIH HHS CA092447NCI NIH HHS CA092579NCI NIH HHS CA098758NCI NIH HHS CA127298NCI NIH HHS CA1326792NCI NIH HHS CA136924NCI NIH HHS CA140388NCI NIH HHS CA148085NCI NIH HHS CA148537NCI NIH HHS CA37429NCI NIH HHS CA54281NCI NIH HHS CA63464NCI NIH HHS CA68485NCI NIH HHS CA68578NCI NIH HHS CA88164NCI NIH HHS HHSN261201000006CNCI NIH HHS N01 CN045165NCI NIH HHS N01-CN-45165NCI NIH HHS N01 PC035139NCI NIH HHS N01-PC-35139NCI NIH HHS P30 CA060553NCI NIH HHS P30 CA068485NCI NIH HHS P50 CA140388NCI NIH HHS R01 CA054281NCI NIH HHS R01 CA056678NCI NIH HHS R01 CA063464NCI NIH HHS R01 CA068578NCI NIH HHS R01 CA082664NCI NIH HHS R01 CA088164NCI NIH HHS R01 CA092447NCI NIH HHS R01 CA092579NCI NIH HHS R01 CA136924NCI NIH HHS R35 CA197449NCI NIH HHS R37 CA054281NCI NIH HHS RC2 CA148085NCI NIH HHS U01 CA063464NCI NIH HHS U01 CA098216NCI NIH HHS U01 CA098233NCI NIH HHS U01 CA098710NCI NIH HHS U01 CA098758NCI NIH HHS U01 CA127298NCI NIH HHS U01 CA164973NCI NIH HHS U01-CA98216NCI NIH HHS U01-CA98233NCI NIH HHS U01-CA98710NCI NIH HHS U01-CA98758NCI NIH HHS U10 CA037429NCI NIH HHS UG1 CA189974NCI NIH HHS UM1 CA182883NHGRI NIH HHS HG004726NHGRI NIH HHS U01 HG004446NHGRI NIH HHS U01 HG004726NHGRI NIH HHS U01 HG004726-01NIEHS NIH HHS ES007784NIEHS NIH HHS ES011126NIEHS NIH HHS P30 ES007784NIEHS NIH HHS R01 ES011126NIGMS NIH HHS R01 GM107427NIGMS NIH HHS S06 GM008016NIGMS NIH HHS S06GM08016
6 · The paper itself

Abstract

Interpretation of biological mechanisms underlying genetic risk associations for prostate cancer is complicated by the relatively large number of risk variants (n = 100) and the thousands of surrogate SNPs in linkage disequilibrium. Here, we combined three distinct approaches: multiethnic fine-mapping, putative functional annotation (based upon epigenetic data and genome-encoded features), and expression quantitative trait loci (eQTL) analyses, in an attempt to reduce this complexity. We examined 67 risk regions using genotyping and imputation-based fine-mapping in populations of European (cases/controls: 8600/6946), African (cases/controls: 5327/5136), Japanese (cases/controls: 2563/4391) and Latino (cases/controls: 1034/1046) ancestry. Markers at 55 regions passed a region-specific significance threshold (P-value cutoff range: 3.9 × 10(-4)-5.6 × 10(-3)) and in 30 regions we identified markers that were more significantly associated with risk than the previously reported variants in the multiethnic sample. Novel secondary signals (P < 5.0 × 10(-6)) were also detected in two regions (rs13062436/3q21 and rs17181170/3p12). Among 666 variants in the 55 regions with P-values within one order of magnitude of the most-associated marker, 193 variants (29%) in 48 regions overlapped with epigenetic or other putative functional marks. In 11 of the 55 regions, cis-eQTLs were detected with nearby genes. For 12 of the 55 regions (22%), the most significant region-specific, prostate-cancer associated variant represented the strongest candidate functional variant based on our annotations; the number of regions increased to 20 (36%) and 27 (49%) when examining the 2 and 3 most significantly associated variants in each region, respectively. These results have prioritized subsets of candidate variants for downstream functional evaluation.

Indexed as

Polymorphism, Single NucleotideAsian PeopleBlack PeopleChromosome MappingGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHispanic or LatinoHumansLinkage DisequilibriumMaleMolecular Sequence AnnotationProstatic NeoplasmsQuantitative Trait LociWhite People

Identifiers

PMID26162851
PMCPMC4572069

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