High density SNP-array
DNAs were quantified using PicoGreen [Invitrogen Corporation,
Carlsbad, United States]. A genome‐wide scan of 850,000 tag SNPs was
conducted on III4, using Illumina CytoSNP‐850k BeadChip according to
manufacturer’s specifications [Illumina, San Diego, United States].
GenCall scores <0.15 at any locus were considered ”no-calls”.
Image data were analyzed using the Chromosome Viewer tool contained in
Genome Studio [Illumina, San Diego, United States]. The metric used
was the logR ratio which is the log (base 2) ratio of the observed
normalized R-value for a SNP divided by the expected normalized R-value
(under manufacturer’s specifications). In addition, an allele frequency
analysis was applied for all SNPs. Genomic positions were based upon
GRCh37.
Whole genome sequencing (WGS) analysis
WGS was performed in III4 using a HiSeq instrument [Illumina, San
Diego, United States] by Macrogen services [Republic of Korea].
Bioinformatics analysis included a quality control with FASTX-toolkit
(v.0.0.13.2), reads mapping to the Reference Genome (GRCh38.p12) with
Burrows-Wheeler Aligner tool (BWA v.0.7.15) and visualization of results
with the Integrative Genomics Viewer software (IGV v.2.80).