Mutation Detection Rate

EpiRapid can detect >99.9% of described sequencing mutations in the included genes and deletion/duplication mutations in MECP2, when present (analytic sensitivity).

Test Description

EpiRapid includes 16 genes with reported therapeutic associations: ALDH7A1, FOLR1, KCNQ2, KCNQ3, KCNT1, MECP2, PCDH19, PNPO, POLG, PRRT2, SCN1A, SCN8A, SLC2A1, STXBP1, TSC1, and TSC2. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using a standardized kit and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology using long biotinylated oligonucleotide probes, followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). 

Sanger sequencing is performed for any regions missing, or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.¹ This assay targets all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions. Gross deletion/duplication analysis is performed using a custom pipeline based on read-depth from NGS data and/or targeted chromosomal microarray with confirmatory MLPA when applicable.

1. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.