Both MGPT and TP53 gene-specific tests were performed from DNA isolated from whole blood or saliva samples. NGS analysis (Illumina, San Diego, CA) was performed in all coding domains plus at least five bases into the 5′ and 3′ ends of the introns and untranslated regions (5′UTR and 3′UTR) for all cancer susceptibility genes. EPCAM and GREM1 were only analyzed for gross deletions and duplications, if included on the panel. Depending on the panel ordered by the clinician, 5–49 genes, including TP53, were analyzed. Sanger sequencing was performed for any region with insufficient depth of coverage (<10X), for verification of all variants (other than known benign variants), and for those with decreased mutant to wild-type allele ratios. A targeted chromosomal microarray and/or MLPA was used for the detection of gross deletions and duplications.
A five-tier classification schema—pathogenic; variant, likely pathogenic; variant of unknown significance; variant, likely benign; and benign—was used to classify variants.29 (link)
A five-tier classification schema—pathogenic; variant, likely pathogenic; variant of unknown significance; variant, likely benign; and benign—was used to classify variants.29 (link)
