Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer.
Genome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several of these tagSNPs are near bone morphogenetic protein (BMP) pathway loci. The penalty of multiple testing implicit in G...
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Public Library of Science (PLoS)
2011-06-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1002105 |
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| author | Ian P M Tomlinson Luis G Carvajal-Carmona Sara E Dobbins Albert Tenesa Angela M Jones Kimberley Howarth Claire Palles Peter Broderick Emma E M Jaeger Susan Farrington Annabelle Lewis James G D Prendergast Alan M Pittman Evropi Theodoratou Bianca Olver Marion Walker Steven Penegar Ella Barclay Nicola Whiffin Lynn Martin Stephane Ballereau Amy Lloyd Maggie Gorman Steven Lubbe COGENT Consortium CORGI Collaborators EPICOLON Consortium Bryan Howie Jonathan Marchini Clara Ruiz-Ponte Ceres Fernandez-Rozadilla Antoni Castells Angel Carracedo Sergi Castellvi-Bel David Duggan David Conti Jean-Baptiste Cazier Harry Campbell Oliver Sieber Lara Lipton Peter Gibbs Nicholas G Martin Grant W Montgomery Joanne Young Paul N Baird Steven Gallinger Polly Newcomb John Hopper Mark A Jenkins Lauri A Aaltonen David J Kerr Jeremy Cheadle Paul Pharoah Graham Casey Richard S Houlston Malcolm G Dunlop |
| author_facet | Ian P M Tomlinson Luis G Carvajal-Carmona Sara E Dobbins Albert Tenesa Angela M Jones Kimberley Howarth Claire Palles Peter Broderick Emma E M Jaeger Susan Farrington Annabelle Lewis James G D Prendergast Alan M Pittman Evropi Theodoratou Bianca Olver Marion Walker Steven Penegar Ella Barclay Nicola Whiffin Lynn Martin Stephane Ballereau Amy Lloyd Maggie Gorman Steven Lubbe COGENT Consortium CORGI Collaborators EPICOLON Consortium Bryan Howie Jonathan Marchini Clara Ruiz-Ponte Ceres Fernandez-Rozadilla Antoni Castells Angel Carracedo Sergi Castellvi-Bel David Duggan David Conti Jean-Baptiste Cazier Harry Campbell Oliver Sieber Lara Lipton Peter Gibbs Nicholas G Martin Grant W Montgomery Joanne Young Paul N Baird Steven Gallinger Polly Newcomb John Hopper Mark A Jenkins Lauri A Aaltonen David J Kerr Jeremy Cheadle Paul Pharoah Graham Casey Richard S Houlston Malcolm G Dunlop |
| author_sort | Ian P M Tomlinson |
| collection | DOAJ |
| description | Genome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several of these tagSNPs are near bone morphogenetic protein (BMP) pathway loci. The penalty of multiple testing implicit in GWAS increases the attraction of complementary approaches for disease gene discovery, including candidate gene- or pathway-based analyses. The strongest candidate loci for additional predisposition SNPs are arguably those already known both to have functional relevance and to be involved in disease risk. To investigate this proposition, we searched for novel CRC susceptibility variants close to the BMP pathway genes GREM1 (15q13.3), BMP4 (14q22.2), and BMP2 (20p12.3) using sample sets totalling 24,910 CRC cases and 26,275 controls. We identified new, independent CRC predisposition SNPs close to BMP4 (rs1957636, P = 3.93×10(-10)) and BMP2 (rs4813802, P = 4.65×10(-11)). Near GREM1, we found using fine-mapping that the previously-identified association between tagSNP rs4779584 and CRC actually resulted from two independent signals represented by rs16969681 (P = 5.33×10(-8)) and rs11632715 (P = 2.30×10(-10)). As low-penetrance predisposition variants become harder to identify-owing to small effect sizes and/or low risk allele frequencies-approaches based on informed candidate gene selection may become increasingly attractive. Our data emphasise that genetic fine-mapping studies can deconvolute associations that have arisen owing to independent correlation of a tagSNP with more than one functional SNP, thus explaining some of the apparently missing heritability of common diseases. |
| format | Article |
| id | doaj-art-c10c8a90b2ce4383b4aa02c682b34728 |
| institution | DOAJ |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2011-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-c10c8a90b2ce4383b4aa02c682b347282025-08-20T03:10:22ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042011-06-0176e100210510.1371/journal.pgen.1002105Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer.Ian P M TomlinsonLuis G Carvajal-CarmonaSara E DobbinsAlbert TenesaAngela M JonesKimberley HowarthClaire PallesPeter BroderickEmma E M JaegerSusan FarringtonAnnabelle LewisJames G D PrendergastAlan M PittmanEvropi TheodoratouBianca OlverMarion WalkerSteven PenegarElla BarclayNicola WhiffinLynn MartinStephane BallereauAmy LloydMaggie GormanSteven LubbeCOGENT ConsortiumCORGI CollaboratorsEPICOLON ConsortiumBryan HowieJonathan MarchiniClara Ruiz-PonteCeres Fernandez-RozadillaAntoni CastellsAngel CarracedoSergi Castellvi-BelDavid DugganDavid ContiJean-Baptiste CazierHarry CampbellOliver SieberLara LiptonPeter GibbsNicholas G MartinGrant W MontgomeryJoanne YoungPaul N BairdSteven GallingerPolly NewcombJohn HopperMark A JenkinsLauri A AaltonenDavid J KerrJeremy CheadlePaul PharoahGraham CaseyRichard S HoulstonMalcolm G DunlopGenome-wide association studies (GWAS) have identified 14 tagging single nucleotide polymorphisms (tagSNPs) that are associated with the risk of colorectal cancer (CRC), and several of these tagSNPs are near bone morphogenetic protein (BMP) pathway loci. The penalty of multiple testing implicit in GWAS increases the attraction of complementary approaches for disease gene discovery, including candidate gene- or pathway-based analyses. The strongest candidate loci for additional predisposition SNPs are arguably those already known both to have functional relevance and to be involved in disease risk. To investigate this proposition, we searched for novel CRC susceptibility variants close to the BMP pathway genes GREM1 (15q13.3), BMP4 (14q22.2), and BMP2 (20p12.3) using sample sets totalling 24,910 CRC cases and 26,275 controls. We identified new, independent CRC predisposition SNPs close to BMP4 (rs1957636, P = 3.93×10(-10)) and BMP2 (rs4813802, P = 4.65×10(-11)). Near GREM1, we found using fine-mapping that the previously-identified association between tagSNP rs4779584 and CRC actually resulted from two independent signals represented by rs16969681 (P = 5.33×10(-8)) and rs11632715 (P = 2.30×10(-10)). As low-penetrance predisposition variants become harder to identify-owing to small effect sizes and/or low risk allele frequencies-approaches based on informed candidate gene selection may become increasingly attractive. Our data emphasise that genetic fine-mapping studies can deconvolute associations that have arisen owing to independent correlation of a tagSNP with more than one functional SNP, thus explaining some of the apparently missing heritability of common diseases.https://doi.org/10.1371/journal.pgen.1002105 |
| spellingShingle | Ian P M Tomlinson Luis G Carvajal-Carmona Sara E Dobbins Albert Tenesa Angela M Jones Kimberley Howarth Claire Palles Peter Broderick Emma E M Jaeger Susan Farrington Annabelle Lewis James G D Prendergast Alan M Pittman Evropi Theodoratou Bianca Olver Marion Walker Steven Penegar Ella Barclay Nicola Whiffin Lynn Martin Stephane Ballereau Amy Lloyd Maggie Gorman Steven Lubbe COGENT Consortium CORGI Collaborators EPICOLON Consortium Bryan Howie Jonathan Marchini Clara Ruiz-Ponte Ceres Fernandez-Rozadilla Antoni Castells Angel Carracedo Sergi Castellvi-Bel David Duggan David Conti Jean-Baptiste Cazier Harry Campbell Oliver Sieber Lara Lipton Peter Gibbs Nicholas G Martin Grant W Montgomery Joanne Young Paul N Baird Steven Gallinger Polly Newcomb John Hopper Mark A Jenkins Lauri A Aaltonen David J Kerr Jeremy Cheadle Paul Pharoah Graham Casey Richard S Houlston Malcolm G Dunlop Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genetics |
| title | Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. |
| title_full | Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. |
| title_fullStr | Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. |
| title_full_unstemmed | Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. |
| title_short | Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. |
| title_sort | multiple common susceptibility variants near bmp pathway loci grem1 bmp4 and bmp2 explain part of the missing heritability of colorectal cancer |
| url | https://doi.org/10.1371/journal.pgen.1002105 |
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