Next Generation Sequencing for FHM, EA1, EA2, SCA6, CADASIL, CARASIL, … see more Next Generation Sequencing for FHM, EA1, EA2, SCA6, CADASIL, CARASIL, COL4A1/2, Fabry Disease, Small Vessel Disease, Epilepsy  see less
GTR Test Accession: Help GTR000530677.3
INHERITED DISEASENERVOUS SYSTEMCARDIOVASCULAR ... View more
Last updated in GTR: 2024-02-27
Last annual review date for the lab: 2024-02-27 LinkOut
At a Glance
Diagnosis; Predictive; Prognostic
Migraine, familial hemiplegic, 1; Alternating hemiplegia of childhood; CARASIL syndrome; ...
ATP1A2 (1q23.2), ATP1A3 (19q13.2), CACNA1A (19p13.13), COL4A1 (13q34), COL4A2 (13q34), ...
Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Patients with symptoms of CADASIL, CARASIL, Fabry Disease, COL4A1/2 related …
Not provided
Not provided
Ordering Information
Offered by: Help
Genomics Research Centre Diagnostics Clinic
View lab's test page
Test short name: Help
NGS-Panel
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
Lab contact: Help
Robert Smith, PhD, Quality Manager
r157.Smith@qut.edu.au
+61 7 31380970
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
Testing submission form can be found on website or following contact with lab. Samples of purified DNA or blood in EDTA or heparin for testing can be sent along with request form to:

GENOMICS RESEARCH CENTRE (GRC) Clinic
Institute for Health and Biomedical Innovation
Queensland University of Technology
5 …
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Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
    Comment: Next Generation Sequencing test for Familial Hemiplegic Migraine Types 1-3, Episodic Ataxia types 1 and 2, Spinocerebellar Ataxia Type 6, Epilepsy, Alternating Hemiplegia of Childhood, CADASIL, CARASIL, Fabry Disease, COL4A1/2 related encephalopathy, and small vessel disease.
Clinical Testing/Confirmation of Mutations Identified Previously
    Comment: Sanger sequencing of known mutation site for confirmaiton of family carrier status
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Decline to answer
Test strategy: Help
If symptoms present but no likely causative variant identified, exome testing and potentially research testing are available.
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 18
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 12
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 1
Method Category Help
Test method Help
Instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Ion Torrent S5 Sequencer
Clinical Information
Test purpose: Help
Diagnosis; Predictive; Prognostic
Target population: Help
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.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
VUS are interpreted according to ACMG guidelines.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Not provided.
Research:
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.
Recommended fields not provided:
Technical Information
Test Procedure: Help
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.
View citations (1)
  • Maksemous N, Roy B, Smith RA, Griffiths LR. Next-generation sequencing identifies novel CACNA1A gene mutations in episodic ataxia type 2. Mol Genet Genomic Med. 2016;4(2):211-22. doi:10.1002/mgg3.196. Epub 2016 Jan 20. PMID: 27066515.
Test Platform:
Ion Torrent Proton OR Ion Torrent S5
Test Confirmation: Help
Positive mutations confirmed by direct Sanger Sequencing.
Availability: Help
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: Help
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.
Assay limitations: Help
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 … View more
Proficiency testing (PT):
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.
VUS:
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.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: Not Applicable
Additional Information

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