Bipolar Disorder Candidate Gene Custom SNP Panel: Design and Preliminary Results
Burmeister Margit
University of Michigan
Scott Laura J.
Univ. of Michigan
Li Yun
Univ. of Michigan
Thompson Robert C. Univ. of Michigan
Li Jun
Stanford Univ.
Meng Fan
Univ. of Michigan
Guan Weihua
Univ. of Michigan
Absher Devin
Stanford Univ.
Vawter Marquis P. UC
Choudary Prabhakara UC
Tomita Hiroaki
UC
Evans Simon J.
Univ. of Michigan
Bunney William E, UC
Jones Edward G.
UC
Barchas Jack D.
Cornell
Akil Huda
Univ. of Michigan
Watson Stanley J.
Univ. of Michigan
Myers Richard M.
Stanford Univ.
Boehnke Michael
Univ. of Michigan
We designed a Bipolar Disorder candidate gene panel for the 1536 SNP
Illumina Golden Gate assay. Inclusion criteria were association with
Bipolar Disorder in 1 large study or >2 smaller studies, reproducible or
RT-PCR confirmed difference in express ion between bipolar disorder and
controls in microarray studies from brain mRNA, strong evidence of
biological implication or mouse model with relevant phenotypes. Genes were
defined as all exons and introns, plus 10 kb 5’ to the start of
transcri ption and 5 kb 3’ to the last base of the longest transcript.
HapMap II SNPs with minor allele frequency > 0.05 were identified for all
SNPs in > 120 genes. After eliminating SNPs with an Illumina design score
<0.6, optimal SNPs were chosen to cove r all HAPMAP bins and singletons by
at least 1 SNP within LD of r2 >0.8. All nonsynonymous SNPs were added
regardless of MAF and HapMap. Some large genes with > 100 HapMap SNPs had
to be excluded for efficiency, as were genes without HapMap SNPs, us ually
due to genome map uncertainty. The final list includes 96 genes, with a
median of 10 SNPs per gene (average 16; range 0 to 176).
We will present preliminary results using this panel in an association
study of 476 cases and 470 controls fro m the NIMH genetic initiative.