Diagnosis; Predictive; Prognostic

Patients with symptoms of CADASIL, CARASIL, Fabry Disease, COL4A1/2 related encephalopathy, Small Vessel Disease, FHM1-3, EA1, EA2, SCA6 or Epilepsy (relating to SCN1A). Test sequences ATP1A2, SCN1A, SCN2A, TREX1, FOXC1, KCNK18, HTRA1, KCNA1, COL4A1, COL4A2, PRRT2, NOTCH3, CACNA1A, ATP1A3 and GLA.

Is research allowed on the sample after clinical testing is complete? Help
The GRC performs research in the conditions for which we test. Patients may participate in this research. Please contact the laboratory for additional information.

Custom PCR based library construction for coding exons, intron/exon boundaries and 3' and 5' UTRs, followed by ion detection sequencing using Life Technologies sequencing chips.

Ion Torrent Proton OR Ion Torrent S5

Positive mutations confirmed by direct Sanger Sequencing.

Tests performed
Entire test performed in-house

Test performance comments
All components of the test are performed in-house. In case of instrument breakdown, the laboratory may use another NATA accredited sequencing facility to perform Sanger based testing.

Analytical validity was determined by re-sequencing 23 previously sequenced samples. Mutations were detected in 100% of re-sequenced samples. There is ongoing validation of samples through Sanger re-sequencing of samples and cross-batch comparison.

The assay has regions of low or no coverage. Mutations in these regions or deep in introns (greater than ~100bp from exons) will not be detected. The assay cannot identify insertions, deletions, inversions or translocations whose breakpoints are in gene areas of no coverage. We are developing controls to detect … The assay has regions of low or no coverage. Mutations in these regions or deep in introns (greater than ~100bp from exons) will not be detected. The assay cannot identify insertions, deletions, inversions or translocations whose breakpoints are in gene areas of no coverage. We are developing controls to detect copy number changes, but these are not reliably detected at present. Specific gene and target coverage is as follows: CACNA1A gene - Exons 1-41, 5’UTR, 3’UTR. (partial coverage Ex 1, 29, Int 11, 20, 25, 3’UTR) ATP1A2 gene - Exons 1-23, 5’UTR, 3’UTR (partial coverage for Ex 8, 3’UTR) SCN1A gene – Exons 1-27, 5’UTR, 3’UTR (partial coverage for 5’UTR, Ex 2, 6, 15, 16, 18, Int 21) Notch 3 gene - Exons 1-33, 5’UTR, 3’UTR (partial coverage for Ex 10, 30, 31, 3’UTR) TRESK gene – Exons 1-3, 5’UTR, 3’UTR (complete coverage) View more

Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
European Molecular Genetics Quality Network, EMQN

Description of PT method: Help
Sequencing performed on test DNA according to established laboratory protocol. Results compiled and sent to EMQN for analysis of genotyping accuracy. QAP testing is undertaken for both next generation sequencing and Sanger sequencing annually.

Description of internal test validation method: Help
Internal test validation is performed by crosschecking of sequences within batches for sequencing bias and all potential positive mutations are subject to Sanger sequencing.

Software used to interpret novel variations Help
SIFT, Poly-Phen, Mutation Taster, REVEL, reference to publication and mutation databases.

Laboratory's policy on reporting novel variations Help
Novel variations are reported to clinician with an estimate of effect based on prediction software and any additional information available from research publications for mutations in the region.