FaceBase Kick-Off Meeting Nov 15-16, 2009 Bethesda. Oral Clefts: Moving from Genome Wide Studies Toward Functional Genomics TH Beaty for Alan F Scott, Ingo Ruczinski, Hong Kai Ji, Kung Yee Liang Johns Hopkins University. Starting point: Genome wide association study (GWAS) of oral clefts.
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Oral Clefts: Moving from Genome Wide Studies Toward Functional GenomicsTH Beaty for
Alan F Scott, Ingo Ruczinski,
Hong Kai Ji, Kung Yee Liang
Johns Hopkins University
Genome wide significant
CHR 8q24: Estimated genotypic relative risk (GRR) & 95%CI under an additive model obtained from a conditional logistic regression model for 78 SNPs in chr. 8q24 showing genome wide significance. The SNP showing the strongest signal was rs987525 (denoted by the star) is identical to that reported by 2 previous studies.
Statistical signal from 78 SNPs in 8q24 and pairwise LD for A) CL/P case-parent trios of European ancestry; B) CL/P case-parent trios of Asian ancestry.
Comparing sequence to 1000 genomes genotypes & sequence
MAFB on chr 20q11: A total 18 SNPs in the 3’UTR 20kb from MAFB showed genome wide significance (left). Estimated genotypic relative risk (GRR) & 95%CI under an additive model are shown over the region of signal.
ABCA4 on chr 1q22 spans 150kb & showed multiple SNPs attaining genome wide significance ( left). Estimated GRR from a conditional logistic regression model & 95%CI for each SNP in this region.