Primary alignment of the sequencing reads to the reference genome and subsequent base calling was performed using the instrument provided Torrent Suite software v.5.0.4 (Thermo Fisher Scientific). The Torrent Suite software pipeline was adapted in view of the highly optimized analysis parameters specific to Ion instrument data. The human genome build 19 was used for the alignment, calling and annotations of potential variant changes in the specimen. Subsequently, the generated BAM files were uploaded to the Ion Reporter Cloud. Detailed annotation of the individual variant calls was generated by the Ion Reporter v.5.2 (Thermo Fisher Scientific) software as shown previously.7 (link) In addition to the Ion Reporter annotation, a custom built software pipeline composed of Linux bash scripts was used to confirm the somatic variants of single nucleotide variants (SNVs) and insertion-deletion (indel) changes called by Ion Reporter. For the purposes of variant calling, we set a coverage threshold of 200X reads for SNVs and 350X reads Indels at a variant allele fraction of 5%. Anything below these limits was not called.