Computational protocol: Clinical diagnostic exome evaluation for an infant with a lethal disorder: genetic diagnosis of TARP syndrome and expansion of the phenotype in a patient with a newly reported RBM10 alteration

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Protocol publication

[…] Exome library preparation, sequencing, bioinformatics, and data analysis were performed as previously described [, –]. Briefly, samples were prepared using IDT xGen Exome Research Panel V1.0 and sequenced using paired-end, 150-cycle chemistry on the Illumina HiSeq 2500 (Illumina, San Diego, CA). Approximately 92% of characterized Mendelian disease genes are fully covered (100%) at > 20X (Farwell et al. []). The sequence data were aligned to the reference human genome (GRCh37) and variant calls were generated using CASAVA and Pindel []. Stepwise filtering included the removal of common SNPs, intergenic and 3’/5’ UTR variants, non-splice-related intronic variants, and lastly synonymous variants. Variants were then filtered further based on family history and possible inheritance models. Data are annotated with the Ambry Variant Analyzer tool (AVA) []. Identified candidate alterations were confirmed using automated fluorescence dideoxy sequencing. […]

Pipeline specifications

Software tools BaseSpace, Pindel
Application WES analysis
Organisms Homo sapiens