Fig. 4.

Whole Genome analysis conducted on two iPSC lines generated using the cGMP compliant manufacturing process. a. WGS data characterisation pipeline. This figure outlines the work flow followed in this study. The filters applied at various stages have been mentioned in the methods section. The fastq files were aligned using Isaac aligner to generate bam file. The bam file generated was checked for its mapping quality using samstat. The fastq files were also used for prediction of HLA types using HLAVBseq. The variants called by Issac variant caller was annotated using SnpEff and this data was used for predicting blood groups using BOOGIE. Only non-synonymous variants were considered for its implication with PD and cross validated with expression data. Structural variation (deletions and duplications) were filtered (see methods) and annotated for genes using UCSC. This data was cross validated with expression and microarray data. The differentially expressed genes were verified for gene enrichment relevant to disease and pathway through DAVID. b. The x-axis shows the various chromosomes and Y-axis represents the max-depth computed by Issac Variant Caller across each chromosome on a log scale for both the cell lines under study. c. Bar graph representing number of variants identified for SNPs, small Insertions, small deletions, synonymous, non-synonymous variants, CNVs and different types of structural variants including duplications, large insertions (length > 50), large deletions (length > −50), inversions and translocations. Deletions were higher in number than other types of SVs