Case 1
DNA was extracted from proband’s whole blood and prepared using TruSeq
DNA PCR-free libraries (Illumina). The Illumina HiSeq X Ten System
(Illumina) was used to sequence the proband’s DNA to a median 84x
whole-genome coverage. Sequence reads were aligned to the GRCh37
reference genome (including decoy sequences from the GATK resource
bundle) using the BWA-MEM (Li, 2013). The resulting BAM files were
de-duplicated, INDEL realignment and base quality recalibration was
performed using Picard tools (Toolkit, 2019) followed by the GATK
variant discovery toolkit using a best practices workflow (DePristo et
al., 2011). Quality control metrics indicated high quality sequence,
alignment and variant calling. Sequence variant data for the proband in
VCF file format was loaded into the Fabric Genomics (formerly Omicia)
platform (https://fabricgenomics.com/), and genes involved in the
urea cycle were examined in detail within this framework to identify
variants that may have an impact on gene function.