NGS Panels
Testquality type A, C or A/C
NGS panel genes can be analysed with difference in quality. To gain more insight into this quality, the tests are classified as follows (Matthijs G et al., Eur J Hum Genet 2015; doi: 10.1038).
- Kwaliteit Type A: alle genen wordt volledig dekkend geanalyseerd. Gebieden met een lage coverage (<30 reads) in de NGS test worden alsnog met behulp van Sanger sequencing geanalyseerd.
- Kwaliteit Type C: alleen NGS analyse. Er wordt geen aanvullende analyse gedaan van eventuele gebieden met een lage coverage.
Core-NL genes
Core-NL: the genes in this list are considered essential for making a reliable diagnosis (Weiss MM et al., Human Mut 2013; 34: 1313-1321). This list was drawn up in national consultation with the Dutch laboratories and clinics. A core gene is always analyzed with full coverage (quality A). See https://www.dnadiagnostiek.nl/core-genen.
It is indicated per analysis where a Core-NL package is offered.
Incidentical findings
Reporting incidental findings: When requesting WES-based (package) analyses, we assume that the applicant has discussed the risk of incidental findings with the patient. For more information (in Dutch only): https://www.vkgn.org/nieuws/landelijk-beleid-voor-het-melden-van-nevenbevindingen-in-de-klinisch-genetische-diagnostiek/
CNV analyses
In indicated NGS panels, copy number variation (CNV) analysis is performed to detect exon deletions/duplications This CNV test ONLY works reliably on submitted EDTA blood and NOT on submitted DNA
Coverage
For quality A: Sanger sequencing is used for the analysis of areas with coverage below 30 reads. All coding exons and the flanking nucleotides in the intron are analyzed.
Based on validation experiments, we estimate the sensitivity of the combined assay (NextGen and Sanger) to nucleotide substitutions and deletions, insertions and duplications up to 68 nucleotides to be > 99%.
Test reports
Class 1 en 2 variants will not be reported.