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Target enrichment array design

JB Joseph S. Baxter
OL Olivia C. Leavy
ND Nicola H. Dryden
SM Sarah Maguire
NJ Nichola Johnson
VF Vita Fedele
NS Nikiana Simigdala
LM Lesley-Ann Martin
SA Simon Andrews
SW Steven W. Wingett
IA Ioannis Assiotis
KF Kerry Fenwick
RC Ritika Chauhan
AR Alistair G. Rust
NO Nick Orr
FD Frank Dudbridge
SH Syed Haider
OF Olivia Fletcher
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74 SNPs mapping to 68 GWAS risk loci were selected based on all available published GWAS and replication studies as of 31/01/2015. Capture regions were defined as the region that included all SNPs that were correlated (r2 ≥ 0.2) with the published SNP based on 1000 Genomes pilot data (http://www.1000genomes.org/; Supplementary Data 1). Biotinylated 120-mer RNA baits were designed to target both ends of the HindIII restriction fragments that mapped within these capture regions using Agilent eArray software (Agilent, Santa Clara, CA, USA), using 2 × tiling, moderately stringent repeat masking and maximum performance boosting options.

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