Methodology

Method: Next-generation sequencing with CNV calling (NGS-CNV) of nuclear and mitochondrial genomes. Alternative sequencing or other detection methods may be used to analyze or confirm mtDNA variants.

Average mean sequencing coverage for the proband is 30x across the genome. It is anticipated that approximately 97% of the coding region of an affected individual’s genome (i.e., the exome) will be assessed at 15x coverage.

This test also includes screening for several non-sequencing variants commonly related to human disease. This test can identify uniparental disomy (UPD) when parents are submitted, homozygous loss of exon 8 (formerly exon 7) in the SMN1 gene (spinal muscular atrophy), and expansion of the poly-nucleotide repeat regions in the FMR1 (FMR1-related disorders) and DMPK (myotonic dystrophy, type 1) genes. If detected, expansions of greater than 54 CGG repeats in the FMR1 gene and greater than 49 CTG repeats in the DMPK gene are confirmed via an appropriate orthogonal method and reported.

Next generation sequencing of the mitochondrial genome can detect mtDNA variants as low as 2% heteroplasmy and large-scale deletions (2 kb or larger) as low as 5% heteroplasmy. However, for large-scale deletions observed at less than 15% heteroplasmy a quantitative value will not be provided. This test is expected to detect greater than 98% of known pathogenic variants and deletions of the mitochondrial genome.

This is a phenotype-driven test of a very large number of genes; therefore, reported results are focused on pathogenic and likely pathogenic variants in genes related to the clinical information provided. Less frequently, variants of uncertain significance in candidate and differential diagnosis genes are reported.