Diagnostic testing:
- Patient suspected for amyotrophic lateral sclerosis based on El Escorial criteria for probable or definitive diagnostic
Diagnostic testing for this analysis (symptomatic patients) can only be requested by neurologists and medical geneticists.
Predictive testing for this analysis (asymptomatic patients) can only be requested by medical geneticists.
This test consists in three separate analysis: a multigene panel for three genes associated with amyotrophic lateral sclerosis (ALS), a repeat expansion analysis in C9orf72, and a repeat expansion analysis in ATXN2. An individual report will be forwarded for each of the three analysis.
Multigene panel:
This test detects sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of SOD1 (NM_000454.5), FUS (NM_004960.4), and TARDBP (NM_007375.4).
C9orf72 repeat expansion:
This test detects expansion of a hexanucleotide repeat (GGGGCC) in the 5' region of C9orf72, which is the most common known hereditary cause of frontotemporal dementia (FTD), ALS and ALS-FTD (PMID: 20301623).
ATXN2 repeat expansion:
This test detects the pathogenic and intermediate expansions of the CAG repeat in exon 1 of ATXN2, which have been associated with several conditions, including spinocerebellar ataxia 2 (SCA2), and an increased risk of developing ALS (PMID: 20301452; 28017481).
Panel content
| Gene | Transcript |
|---|---|
| FUS | NM_004960.4 |
| SOD1 | NM_000454.5 |
| TARDBP | NM_007375.4 |
Multigene panel:
Targeted regions are enriched using hybridization probes (IDT) and sequencing libraries are prepared using the Illumina DNA Prep with Enrichment kit. Paired-end massively parallel sequencing of 150-bp fragments is performed with an Illumina instrument. Sequences are aligned and compared to reference genome GRCh37. Sample identity is confirmed in parallel using Applied Biosystems™ SNaPshot™ Multiplex Kit. Variants are interpreted as per standards and guidelines in the field (PMID: 25741868). Clinically relevant copy number variants are confirmed by an orthogonal method (gap-PCR, TaqMan, MLPA or microarray).
C9orf72 repeat expansion:
This test consists of determining the number of hexanucleotide repeats in C9orf72 by a combination of repeat primed PCR, gene-specific PCR, and capillary electrophoresis, as previously described (PMID: 30430876).
ATXN2 repeat expansion:
This test consists of determining the number of CAG repeats in ATXN2 by PCR and capillary electrophoresis, as previously described (PMID: 20740007).
Multigene panel:
Based on validation study results, this test achieves >99% analytical sensitivity and specificity for SNVs, indels and CNVs. A negative result does not rule out the possibility that a rare variant not detected by this assay is present in the individual. This test does not detect all possible variants in the genes tested. Unless explicitly specified, only coding exons and flanking intronic regions are covered by this assay. Furthermore, technically challenging variant types, such as large indels, small CNVs, complex rearrangements, low-complexity repeat associated, segmental duplication associated, and postzygotic variants, may not be detected (PMID: 34007000). Interpretation of results is highly dependent on the clinical and demographic information provided.
C9orf72 repeat expansion:
This test provides accurate sizing of alleles up to 145 repeats and identifies expanded alleles >145 repeats. In rare cases, insertions/deletions surrounding the hexanucleotide repeat region may compromise the accuracy of allele sizing. Due to somatic and germline instability, repeat size identified in the tissue tested may not reflect the repeat size in untested tissues such as the brain. In addition, a negative result does not definitively rule out the presence of an expansion in the mosaic state, as the current test is not validated to detect low-level mosaic repeats. Analysis is dependent on accurate clinical diagnosis of affected individuals and on correct reporting of family relationships. DNA variants located in primer binding sites and rare genotyping errors can result in inaccurate diagnosis.
ATXN2 repeat expansion:
This test is designed to detect intermediate ATXN2 CAG repeats (29, 30, 31, or 32) in individuals diagnosed with ALS. Analysis is dependent on accurate clinical diagnosis of affected individuals and on correct reporting of family relationships. DNA variants located in primer binding sites and rare genotyping errors can result in inaccurate analysis.
Multigene panel :
Only clinically relevant variants are reported. Benign/likely benign variants and variants of uncertain significance with limited evidence for pathogenicity are not reported.
C9orf72 repeat expansion:
Expansions of hundreds of repeats are known to be pathogenic (with age-dependent and incomplete penetrance), but there is currently no clear cutoff between benign and pathogenic alleles (PMID: 33575483). At present, alleles with 24 or fewer repeats are not considered disease-causing. Alleles with 61 or more repeats are considered pathogenic. Intermediate alleles with 25-60 repeats are thought to confer increased risk for disease, but their penetrance and expressivity remain poorly understood (PMID: 31315673).
ATXN2 repeat expansion:
Alleles with 28 or fewer repeats are not known to be disease-causing and generally segregate as a stable repeat. Although pathogenic expansions of >32 repeats are typically associated with SCA2, individuals with ALS and/or SCA2 have been reported in this range (PMID: 21562247; 28017481; 21670397; 21610160; 20740007). Intermediate expansion alleles within the range of 29, 30, 31, and 32 repeats are associated with an increased risk of developing ALS, though their penetrance and expressivity at the individual level remain incompletely understood, as expansions up to 31 repeats have also been reported in controls (PMID: 21562247; 21670397; 25285812; 28017481). Individuals who are homozygous for 31 repeats or who are heterozygous for 33 or more CAG repeats are at risk of developing SCA2 (PMID: 10735276; 30533529).
Turnaround time: 4-6 weeks
Specimens accepted:
- 2 x 4 mL blood in EDTA tubes (purple top tube)
- DNA: min 10 ug
- For any other sample type, contact the laboratory for testing availability
Submit your test request using our molecular genetics requisition.