Illumina SNP chip genotyping The Icelandic chip-typed samples were assayed with the Illumina HumanHap300, HumanCNV370, HumanHap610, HumanHap1M, HumanHap660, Omni-1, Omni 2.5 or Omni Express bead chips (Illumina, San Diego, CA, USA) at deCODE genetics. SNPs were excluded if they had (i) yield lower than 95%, (ii) minor allele frequency <1% in the population, (iii) significant deviation from Hardy–Weinberg equilibrium in the controls (P<0.001), (iv) if they produced an excessive inheritance error rate (over 0.001) or (v) if there was substantial difference in allele frequency between chip types (from just a single chip if the problem that resolved all differences, but from all chips otherwise). All samples with a call rate below 97% were excluded from the analysis. For the HumanHap series of chips, 308 840 SNPs were used for long-range phasing, whereas for the Omni series of chips 642 079 SNPs were included.
