Chunk #12 — METHODS — Multi-dimensional scaling analysis of SNP genotypes

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Characterization of bipolar disorder patient-specific induced pluripotent stem cells from a family reveals neurodevelopmental and mRNA expression abnormalities.

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For multi-dimensional analysis of SNP profiles, Family-811 quartet genotype data was merged with data from STEP and HapMap 2, and retained only those genotypes shared between all three datasets (N=180,564). Using PLINK35, LD-based SNPs were pruned to 97,171 SNPs and then multi-dimensional scaling was run. Individuals from CEU (60) Western European, YRB (60) Yoruban, HCB (90) Han Chinese, STEP-BP (1753) and Family-811 (4) were analyzed.