Whole Exome Sequencing Analysis of Family 489

In this study, we analyzed the WES data from four affected and two unaffected members of family 489 (both parents, the proband, and three siblings; Figure 1a,b). Exome capture was performed using the Nextera Rapid Capture Enrichment kit (expanded; includes untranslated genomic regions; San Diego, CA, USA) from Illumina (Illumina Nextera DNA exome; San Diego, CA, USA), which covers ≥ 98% of RefSeq, CCD, and Ensemble coding content of genes. The captured exomes were sequenced using the Illumina HighSeq instrument with paired-end sequencing at the University of Nebraska Medical Center Genomics Core Facility. The high-quality sequencing data were mapped to the human reference genome (hg19) using the Burrows—Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) best practices pipeline [36 (link),37 (link)]. The resulting VCF file was processed to identify coding and non-coding variants after removing low quality calls. Low-quality calls did not meet at least one of the following criteria: QUAL ≥ 50 (quality score), VQSLOD ≥ 0 (variant quality score log-odds of being a true variant versus being false based on the trained Gaussian mixture model), DP ≥ 5 (read depth) for all individuals in a family, and QD > 5 (quality by depth = QUAL score divided by allele depth).