Infinium humancytosnp 12 beadchip

Infinium HumanCytoSNP-12 BeadChip (Illumina, San Diego, CA) analysis was performed at the Genomic Shared Resource at Roswell Park Comprehensive Cancer Center. Data analysis was performed in Illumina’s GenomeStudio (v2.0) Genotyping Module (v2.0.4). Illumina’s BlueFuse Multi Analysis Software (v4.5) was used for cytogenetic visualization.

Genotyping was performed using the Infinium HumanCytoSNP-12 BeadChip (Illumina Inc., San Diego, CA, USA), which interrogates 299,140 single-nucleotide polymorphism (SNP) markers, following the manufacturer’s instructions. Data quality control included removing SNPs with possible genotyping errors that were detected through Mendelian inconsistences (PedCheck) and double recombination events over short genetic distances (Merlin).^{(17 (link),18 (link))} Analysis of the genotype data was performed using parametric multipoint and two-point linkage analysis (Allegro 1.2) and homozygosity mapping (HomozygosityMapper).^{(19 (link),20 (link))} For the linkage analysis, a fully penetrant autosomal recessive mode of inheritance was assumed with a disease frequency of 1.0×10⁻⁴. Marker allele frequencies were estimated from founders and reconstructed founders of the Pakistani families that were genotyped at the same time.