Evidence map›Paper›PMID 25990418›Full record

SynthesisScientific reports2015

A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer.

Nada A Al-Tassan, Nicola Whiffin, Fay J Hosking, Claire Palles, Susan M Farrington, Sara E Dobbins, Rebecca Harris, Maggie Gorman, Albert Tenesa, Brian F Meyer and 26 more

Erratum issuedOpen access · goldAbstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 82 papers, 5 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
82citing papers in PubMed, 5 pooled it
12.4field-weighted citation impact, top 1% 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

82 citing papers in PubMed, 5 syntheses or guidelines pooled it, 126 citations in OpenAlex.

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22 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

36 authors at 15 institutions in 6 countries.

Nada A Al-TassanDepartment of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia.
Nicola WhiffinDivision of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Fay J HoskingDivision of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Claire PallesWellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
Susan M FarringtonColon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
Sara E DobbinsDivision of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Rebecca HarrisInstitute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
Maggie GormanWellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
Albert Tenesa1] Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK [2] The Roslin Institute, University of Edinburgh, Easter Bush, Roslin, EH25 9RG, UK.
Brian F MeyerDepartment of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia.
Salma M WakilDepartment of Genetics, King Faisal Specialist Hospital and Research Center, P.O.Box 3354, Riyadh 11211, Saudi Arabia.
Ben KinnersleyDivision of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Harry CampbellCentre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK.
Lynn MartinWellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
Christopher G SmithInstitute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
Shelley IdziaszczykInstitute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
Ella BarclayWellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
Timothy S MaughanCRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
Richard KaplanMRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK.
Rachel KerrOxford Cancer Centre, Department of Oncology, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LE, UK.
David KerrNuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
Daniel D Buchanan1] Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The Univers‡ity of Melbourne, Victoria, Australia [2] Centre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia.
Daniel D Buchannan
Aung Ko WinCentre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia.
John HopperCentre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia.
Mark JenkinsCentre for Epidemiology and Biostatistics, The University of Melbourne, Victoria, Australia.
Noralane M LindorDepartment of Health Sciences Research, Mayo Clinic, Scottsdale, AZ, USA.
Polly A NewcombCancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Steve GallingerSamuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
David ContiDepartment of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.
Fred SchumacherDepartment of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.
Graham CaseyDepartment of Preventive Medicine, University of Southern California, Los Angeles, CA, USA.
Malcolm G DunlopColon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Western General Hospital Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
Ian P TomlinsonWellcome Trust Centre for Human Genetics and NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
Jeremy P CheadleInstitute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
Richard S HoulstonDivision of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
Centre for Human Genetics · GBInstitute of Cancer Research · GBCardiff University · GBThe University of Melbourne · AUKing Faisal Specialist Hospital & Research Centre · SAUniversity of Southern California · USWestern General Hospital · GBChurchill Hospital · GBFred Hutch Cancer Center · USJohn Radcliffe Hospital · GBMayo Clinic in Arizona · USMount Sinai Hospital · CAMRC Clinical Trials Unit at UCL · GBUniversity of Edinburgh · GBUniversity of Oxford · GB

Funding

USC Consortium:Colorectal Cancer Family RegistryU01CA074799 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI HAILE, ROBERT WILLIAM · 1997 to 2008
$20.4M
SEATTLE FAMILIAL COLORECTAL CANCER REGISTRYU01CA074794 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI NEWCOMB, POLLY A · 1997 to 2007
$14.1M
ONTARIO REGISTRY FOR STUDIES OF FAMILIAL COLON CANCERU01CA074783 · NCI · CANCER CARE ONTARIO · PI GALLINGER, STEVEN · 1997 to 2008
$12.5M
Colon Cancer Family Registry CohortUM1CA167551 · NCI · STANFORD UNIVERSITY · PI HAILE, ROBERT WILLIAM, JENKINS, MARK A · 2013 to 2017
$11.3M
FAMILIAL COLORECTAL NEOPLASIA COLLABORATIVE GROUPU01CA074800 · NCI · MAYO CLINIC ROCHESTER · PI LINDOR, NORALANE MOREY · 1997 to 2007
$9.1M
Inherited colorectal cancer risk variants: from association to biologyR01CA143237 · NCI · UNIVERSITY OF VIRGINIA · PI CASEY, GRAHAM · 2010 to 2020
$8.4M
The Colon Cancer Family Registry: USC ConsortiumU24CA074799 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI HAILE, ROBERT WILLIAM · 2008 to 2011
$7.6M
Genomic Wide Association Study of Colorectal CancerU01CA122839 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CASEY, GRAHAM · 2006 to 2010
$7.3M
The Colon Cancer Family Registry: SeattleU24CA074794 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI NEWCOMB, POLLY A · 2008 to 2011
$7.0M
AUSTRALASIAN COLORECTAL CANCER FAMILY REGISTRYU01CA097735 · NCI · UNIVERSITY OF MELBOURNE · PI HOPPER, JOHN L · 2002 to 2007
$6.9M
The Colon Cancer Family Registry: AustralasiaU24CA097735 · NCI · UNIVERSITY OF MELBOURNE · PI HOPPER, JOHN L · 2008 to 2011
$6.2M
HAWAII FAMILY REGISTRY OF COLON CANCERU01CA074806 · NCI · UNIVERSITY OF HAWAII AT MANOA · PI LE MARCHAND, LOIC · 1997 to 2008
$6.1M
Cancer Research UK 12076Cancer Research UK 13154Cancer Research UK 15116Cancer Research UK 16459Cancer Research UK 20240Cancer Research UK C1298/A8362Cancer Research UK C348/A12076Medical Research Council G0701770Medical Research Council G1001799Medical Research Council MC_PC_U127527198Medical Research Council MC_U122861325Medical Research Council MC_UU_12023/20Medical Research Council MC_UU_12023/3Medical Research Council MR/K018647/1Medical Research Council MR/N01104X/1NCI NIH HHS R01 CA143237NCI NIH HHS U01 CA074783NCI NIH HHS U01 CA074794NCI NIH HHS U01 CA074799NCI NIH HHS U01 CA074800NCI NIH HHS U01 CA074806NCI NIH HHS U01 CA097735NCI NIH HHS U01 CA122839NCI NIH HHS U01/U24 CA074783NCI NIH HHS U01/U24 CA074794NCI NIH HHS U01/U24 CA074799NCI NIH HHS U01/U24 CA074800NCI NIH HHS U01/U24 CA074806NCI NIH HHS U01/U24 CA097735NCI NIH HHS U24 CA074783NCI NIH HHS U24 CA074794NCI NIH HHS U24 CA074799NCI NIH HHS U24 CA074800NCI NIH HHS U24 CA074806NCI NIH HHS U24 CA097735NCI NIH HHS UM1 CA167551Wellcome TrustWellcome Trust 090532/Z/09/Z
6 · The paper itself

Abstract

Genome-wide association studies (GWAS) of colorectal cancer (CRC) have identified 23 susceptibility loci thus far. Analyses of previously conducted GWAS indicate additional risk loci are yet to be discovered. To identify novel CRC susceptibility loci, we conducted a new GWAS and performed a meta-analysis with five published GWAS (totalling 7,577 cases and 9,979 controls of European ancestry), imputing genotypes utilising the 1000 Genomes Project. The combined analysis identified new, significant associations with CRC at 1p36.2 marked by rs72647484 (minor allele frequency [MAF] = 0.09) near CDC42 and WNT4 (P = 1.21 × 10(-8), odds ratio [OR] = 1.21 ) and at 16q24.1 marked by rs16941835 (MAF = 0.21, P = 5.06 × 10(-8); OR = 1.15) within the long non-coding RNA (lncRNA) RP11-58A18.1 and ~500 kb from the nearest coding gene FOXL1. Additionally we identified a promising association at 10p13 with rs10904849 intronic to CUBN (MAF = 0.32, P = 7.01 × 10(-8); OR = 1.14). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to CRC. Additionally, our analysis further demonstrates that imputation can be used to exploit GWAS data to identify novel disease-causing variants.

Indexed as

Genetic Predisposition to DiseaseBiomarkers, TumorChromosome MappingColorectal NeoplasmsFemaleForkhead Transcription FactorsGene FrequencyGenome-Wide Association StudyHumansMaleMiddle AgedPolymorphism, Single NucleotideReceptors, Cell SurfaceBiomarkers, TumorForkhead Transcription FactorsFOXL1 protein, humanintrinsic factor-cobalamin receptorReceptors, Cell Surface

Identifiers

PMID25990418
PMCPMC4438486
OpenAlexW1940833630

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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.