Chunk #11 — SNP Analysis — Rare variant analysis

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Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity.

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A rare variant analysis method implemented in CCRaVAT (Case-Control Rare Variant Analysis Tool, see URLs) was used to test for association with rare variants (MAF<0.05 in cases), collapsing within genes. Only directly genotyped SNPs for the discovery sample set were used, removing those that failed quality control. Cluster plots for SNPs contributing to any potential signals were manually re-called and checked.