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The OncoArray Consortium: A Network for Understanding the Genetic Architecture of Common Cancers
Authors
M Adams
A Amin Al Olama
+91 more
CI Amos
AC Antoniou
F Bacot
S Benlloch
A Berchuck
H Bickeböller
SE Bojesen
P Brennan
I Brüske-Hohlfeld
K Butterbach
J Byun
C Caga-Anan
G Casey
SJ Chanock
G Chenevix-Trench
GA Coetzee
DV Conti
FJ Couch
JM Cunningham
S Demetriades
J Dennis
K Doheny
AM Dunning
DF Easton
CK Edlund
RA Eeles
L Fachal
JK Field
L FitzGerald
JL Forman
SA Gayther
GG Giles
E Gillanders
DE Goldgar
MT Goodman
SB Gruber
CA Haiman
DJ Hazelett
BD Hicks
RJ Hung
DJ Hunter
A Kamal
LE Kelemen
Z Kote-Jarai
P Kraft
K Kuchenbaecker
S Laboissiere
A Lee
Y Li
S Lindström
H Ling
C Luccarini
J Manz
J Marchini
L McGuffog
JD McKay
K Michailidou
S Nelson
SF Nielsen
TA O'Mara
K Offit
L Ottini
SK Park
U Peters
PDP Pharoah
CM Phelan
E Pugh
M Riggan
A Risch
J Romm
SL Schmit
R Schmutzler
FR Schumacher
MF Seldin
TA Sellers
D Seminara
T Shelford
H Shen
Y Shi
J Simard
P Soucy
AB Spurdle
JA Taylor
D Tessier
M Thomassen
DJ Thompson
DJ Van Den Berg
D Vincent
M Waldenberger
Z Wang
X Xiao
Publication date
3 October 2016
Publisher
Doi
Cite
Abstract
BACKGROUND: Common cancers develop through a multistep process often including inherited susceptibility. Collaboration among multiple institutions, and funding from multiple sources, has allowed the development of an inexpensive genotyping microarray, the OncoArray. The array includes a genome-wide backbone, comprising 230,000 SNPs tagging most common genetic variants, together with dense mapping of known susceptibility regions, rare variants from sequencing experiments, pharmacogenetic markers, and cancer-related traits. METHODS: The OncoArray can be genotyped using a novel technology developed by Illumina to facilitate efficient genotyping. The consortium developed standard approaches for selecting SNPs for study, for quality control of markers, and for ancestry analysis. The array was genotyped at selected sites and with prespecified replicate samples to permit evaluation of genotyping accuracy among centers and by ethnic background. RESULTS: The OncoArray consortium genotyped 447,705 samples. A total of 494,763 SNPs passed quality control steps with a sample success rate of 97% of the samples. Participating sites performed ancestry analysis using a common set of markers and a scoring algorithm based on principal components analysis. CONCLUSIONS: Results from these analyses will enable researchers to identify new susceptibility loci, perform fine-mapping of new or known loci associated with either single or multiple cancers, assess the degree of overlap in cancer causation and pleiotropic effects of loci that have been identified for disease-specific risk, and jointly model genetic, environmental, and lifestyle-related exposures. IMPACT: Ongoing analyses will shed light on etiology and risk assessment for many types of cancer. Cancer Epidemiol Biomarkers Prev; 26(1); 126-35. ©2016 AACR
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