Methodology

Method: Next-generation sequencing with CNV calling (NGS-CNV)

The technical sensitivity of sequencing is estimated to be >99% at detecting single nucleotide events. It will not reliably detect deletions greater than 20 base pairs, insertions, or rearrangements greater than 10 base pairs, or low-level mosaicism.

The copy number assessment methods used with this test cannot reliably detect copy number variants of less than 500 base pairs or mosaicism and cannot identify balanced chromosome aberrations. Assessment of exon-level copy number events is dependent on the inherent sequence properties of the targeted regions, including shared homology and exon size.

The following gene specific information applies. For CACNA1C, sequencing of exons 1-42 only, AKAP9, sequencing of the KCNQ1-binding domains only including Ser1570 residue, TTN, sequencing of exons 1-171 and 199-363 only. For PKP6, sequencing of exon 6 is not performed.

Gene specific exclusions for exon-level deletion/duplication testing for this panel are: FKRP, HRAS and 14 mitochondrial gene(s), no copy number testing, ALMS1, EMD, GATA5, HCN4, TAZ, TBX20 gene(s), only whole gene deletions or duplications may be detected, SCN5A gene, exon level coverage for exons 2-12 and 21-28 only. For mitochondrial genome testing, sequencing analysis is performed on the following genes: MT-ND1, MT-ND5, MT-ND6, MT-TD, MT-TG, MT-TH, MT-TI, MT-TK, MT-TL1, MT-TL2, MT-TM, MT-TQ, MT-TS1, MT-TS2. Next-generation sequencing may not detect mtDNA point variants present at 10 % heteroplasmy or lower.

Reportable variants include pathogenic variants, likely pathogenic variants and variants of uncertain significance. Likely benign and benign variants, if present, are not routinely reported.