Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Mark McIntosh,'s picture
PubMed URL: 
http://www.ncbi.nlm.nih.gov/pubmed/20360734
Author: 
Donnelly P
Author List: 
Wellcome Trust Case Control Consortium
Craddock N
Hurles ME
Cardin N
Pearson RD
Plagnol V
Robson S
Vukcevic D
Barnes C
Conrad DF
Giannoulatou E
Holmes C
Marchini JL
Stirrups K
Tobin MD
Wain LV
Yau C
Aerts J
Ahmad T
Andrews TD
Arbury H
Attwood A
Auton A
Ball SG
Balmforth AJ
Barrett JC
Barroso I
Barton A
Bennett AJ
Bhaskar S
Blaszczyk K
Bowes J
Brand OJ
Braund PS
Bredin F
Breen G
Brown MJ
Bruce IN
Bull J
Burren OS
Burton J
Byrnes J
Caesar S
Clee CM
Coffey AJ
Connell JM
Cooper JD
Dominiczak AF
Downes K
Drummond HE
Dudakia D
Dunham A
Ebbs B
Eccles D
Edkins S
Edwards C
Elliot A
Emery P
Evans DM
Evans G
Eyre S
Farmer A
Ferrier IN
Feuk L
Fitzgerald T
Flynn E
Forbes A
Forty L
Franklyn JA
Freathy RM
Gibbs P
Gilbert P
Gokumen O
Gordon-Smith K
Gray E
Green E
Groves CJ
Grozeva D
Gwilliam R
Hall A
Hammond N
Hardy M
Harrison P
Hassanali N
Hebaishi H
Hines S
Hinks A
Hitman GA
Hocking L
Howard E
Howard P
Howson JM
Hughes D
Hunt S
Isaacs JD
Jain M
Jewell DP
Johnson T
Jolley JD
Jones IR
Jones LA
Kirov G
Langford CF
Lango-Allen H
Lathrop GM
Lee J
Lee KL
Lees C
Lewis K
Lindgren CM
Maisuria-Armer M
Maller J
Mansfield J
Martin P
Massey DC
McArdle WL
McGuffin P
McLay KE
Mentzer A
Mimmack ML
Morgan AE
Morris AP
Mowat C
Myers S
Newman W
Nimmo ER
O'Donovan MC
Onipinla A
Onyiah I
Ovington NR
Owen MJ
Palin K
Parnell K
Pernet D
Perry JR
Phillips A
Pinto D
Prescott NJ
Prokopenko I
Quail MA
Rafelt S
Rayner NW
Redon R
Reid DM
Renwick
Ring SM
Robertson N
Russell E
St Clair D
Sambrook JG
Sanderson JD
Schuilenburg H
Scott CE
Scott R
Seal S
Shaw-Hawkins S
Shields BM
Simmonds MJ
Smyth DJ
Somaskantharajah E
Spanova K
Steer S
Stephens J
Stevens HE
Stone MA
Su Z
Symmons DP
Thompson JR
Thomson W
Travers ME
Turnbull C
Valsesia A
Walker M
Walker NM
Wallace C
Warren-Perry M
Watkins NA
Webster J
Weedon MN
Wilson AG
Woodburn M
Wordsworth BP
Young AH
Zeggini E
Carter NP
Frayling TM
Lee C
McVean G
Munroe PB
Palotie A
Sawcer SJ
Scherer SW
Strachan DP
Tyler-Smith C
Brown MA
Burton PR
Caulfield MJ
Compston A
Farrall M
Gough SC
Hall AS
Hattersley AT
Hill AV
Mathew CG
Pembrey M
Satsangi J
Stratton MR
Worthington J
Deloukas P
Duncanson A
Kwiatkowski DP
McCarthy MI
Ouwehand W
Parkes M
Rahman N
Todd JA
Samani NJ
Donnelly P
Journal: 
Nature
PubMed ID: 
20360734
Pagination: 
713-20
Volume: 
464
Issue: 
7289
Abstract: 
Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
Published Date: 
April, 2010

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