The genomic integrity of all iPSC lines was assessed using eSNP-karyotyping analysis. The eSNP-karyotyping was conducted as previously described (44). Briefly, SNPs were identified using GATK HaplotypeCaller and then filtered by read depth and allelic frequency to minimize errors. SNPs with low coverage (under 20 reads) or minor allele frequency below 0.2 were excluded. For each SNP, the major-to-minor frequency ratio was computed and organized by chromosomal position. Visualization involved plotting moving medians of these ratios along chromosomal positions. Statistical significance was determined with a one-tailed t test, adjusted for multiple testing using false discovery rate. G-band karyotyping analysis of the selected iPSCs was conducted by Cell Line Genetics (https://clgenetics.com/our-services/g-band-karyotyping/).
