Amyotrophic Lateral Sclerosis Panel

Last modified: Jun 12, 2018

Summary

  • Is a 32 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion or diagnosis of amyotrophic lateral sclerosis (ALS).

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

32

Test code

NE2201

CPT codes

SEQ 81404
SEQ 81406
SEQ 81407
DEL/DUP 81479

Summary

The Blueprint Genetics Amyotrophic Lateral Sclerosis Panel (test code NE2201):

  • Is a 32 gene panel that includes assessment of selected non-coding disease-causing variants
  • This panel covers genes implicated in patients with ALS and frontotemporal dementia, *BSCL2*-related neurologic disorders, *DCTN1*-related distal hereditary motor neuronopathy type VIIB, *GBE1*-related adult polyglucosan body disease, and inclusion body myopathy associated with Paget disease of bone and/or frontotemporal dementia (IBMPFD).

  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

Test Specific Strength

This panel covers genes implicated in patients with ALS and frontotemporal dementia, *BSCL2*-related neurologic disorders, *DCTN1*-related distal hereditary motor neuronopathy type VIIB, *GBE1*-related adult polyglucosan body disease, and inclusion body myopathy associated with Paget disease of bone and/or frontotemporal dementia (IBMPFD).

ICD codes

Commonly used ICD-10 code(s) when ordering the Amyotrophic Lateral Sclerosis Panel

ICD-10 Disease
G12.21 Amyotrophic lateral sclerosis

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease characterized by the selective loss of motor neurons in the motor cortex, brain stem, and spinal cord. The dysfunction and loss of these neurons results in muscle weakness, atrophy and eventually paralysis of limb, bulbar and respiratory muscles. The prevalence of ALS is 1-9 per 100,000. A majority of ALS occurs in individuals with no family history of ALS. Familial ALS is most frequently inherited in an autosomal dominant disorder. Less frequently, it can be inherited in an autosomal recessive or X-linked fashion.

Genes in the Amyotrophic Lateral Sclerosis Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ALS2 Amyotrophic lateral sclerosis, Spastic paralysis AR 31 64
ANG Amyotrophic lateral sclerosis AD 8 37
ATL1 Spastic paraplegia, Neuropathy, hereditary sensory AD 28 79
BSCL2 Lipodystrophy, congenital generalized, Encephalopathy, progressive, Neuropathy, distal hereditary motor, type VA, Charcot-Marie-Tooth disease type 2, Silver syndrome, Silver spastic paraplegia syndrome, Spastic paraplegia 17 AR 32 47
CHCHD10 Myopathy, isolated mitochondrial, Frontotemporal dementia and/or amyotrophic lateral sclerosis 2, Spinal muscular atrophy, Jokela type AD 4 20
CHMP2B Amyotrophic lateral sclerosis, CHMP2B-related, Frontotemporal dementia AD 6 21
DCTN1 Perry syndrome, Neuropathy, distal hereditary motor AD 10 45
FIG4 Amyotrophic lateral sclerosis, Polymicrogyria, bilateral occipital, Yunis-Varon syndrome, Charcot-Marie-Tooth disease AD/AR 29 60
FUS Amyotrophic lateral sclerosis, Essential tremor AD/AR 22 108
GBE1 Glycogen storage disease AR 34 70
GRN Frontotemporal lobar degeneration with TDP43 inclusions, GRN-related, Neuronal ceroid lipofuscinosis AD/AR 36 175
HEXA Tay-Sachs disease, GM2-gangliosidosis, Hexosaminidase A deficiency AR 112 184
HNRNPA1* Amyotrophic lateral sclerosis, Inclusion body myopathy with early-onset Paget disease AD 20 7
HSPD1* Spastic paraplegia, Leukodystrophy, hypomyelinating AD/AR 4 4
KIAA0196 Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome) AD/AR 10 16
KIF5A Spastic paraplegia AD 18 40
OPTN Glaucoma, open angle, Glaucoma, normal tension, Amyotrophic lateral sclerosis 12 AD 9 56
PRF1 Lymphoma, non-Hodgkin, Aplastic anemia, adult-onset, Hemophagocytic lymphohistiocytosis AR 22 172
REEP1 Spastic paraplegia, Distal hereditary motor neuronopathy AD 16 59
SETX Ataxia with oculomotor apraxia, Amyotrophic lateral sclerosis, juvenile, Spinocerebellar ataxia AD/AR 35 194
SLC52A2 Brown-Vialetto-Van Laere syndrome AR 26 22
SLC52A3 Fazio-Londe disease, Brown-Vialetto-Van Laere syndrome AR 34 40
SOD1 Amyotrophic lateral sclerosis, Keratoconus AD/AR 37 209
SPAST Spastic paraplegia AD 163 682
SPG11 Spastic paraplegia, Amyotrophic lateral sclerosis, Charcot-Marie-Tooth disease AR 146 262
SPG20 Spastic paraplegia (Troyer syndrome) AR 6 6
SQSTM1 Paget disease of bone, Frontotemporal dementia and/or amyotrophic lateral sclerosis 3, Myopathy, distal, with rimmed vacuoles, Neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset AD 13 90
TARDBP* Amyotrophic lateral sclerosis AD 20 66
TUBA4A Amyotrophic lateral sclerosis 22 AD 6 12
UBQLN2 Amyotrophic lateral sclerosis XL 6 30
VAPB Amyotrophic lateral sclerosis, Spinal muscular atrophy, late-onset, Finkel AD 2 9
VCP Amyotrophic lateral sclerosis, Inclusion body myopathy with early-onset Paget disease, Charcot-Marie-Tooth disease AD 18 57

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
BSCL2 Chr11:62470032 c.405-11A>G NM_001122955.3
FUS Chr16:31202867 c.*108C>T NM_004960.3 rs780606789
FUS Chr16:31202869 c.*110G>A NM_004960.3
FUS Chr16:31202891 c.*132C>A NM_004960.3 rs565540429
FUS Chr16:31202949 c.*190C>A NM_004960.3
FUS Chr16:31202807 c.*48G>A NM_004960.3 rs376510148
FUS Chr16:31202818 c.*59G>A NM_004960.3
GBE1 Chr3:81542963 c.2053-3358_2053-3350delGTGTGGTGGinsTGTTTTTTACATGACAGGT NM_000158.3
GRN Chr17:42422705 c.-8+3A>T NM_002087.2 rs63751020
GRN Chr17:42422707 c.-8+5G>C NM_002087.2 rs63750313
GRN Chr17:42422701 c.-9A>G NM_002087.2
SOD1 Chr21:33038893 c.239+62T>C NM_000454.4
SOD1 Chr21:33040773 c.358-11A>G NM_000454.4 rs369600566
SOD1 Chr21:33040480 c.358-304C>G NM_000454.4
TARDBP Chr1:11083408 c.*697G>A NM_007375.3 rs387906334
TARDBP Chr1:11082794 c.*83T>C NM_007375.3 rs80356744
VCP Chr9:35072710 c.-360G>C NM_007126.3

Added and removed genes from the panel

Genes added Genes removed
TUBA4A

Test strength

This panel covers genes implicated in patients with ALS and frontotemporal dementia, *BSCL2*-related neurologic disorders, *DCTN1*-related distal hereditary motor neuronopathy type VIIB, *GBE1*-related adult polyglucosan body disease, and inclusion body myopathy associated with Paget disease of bone and/or frontotemporal dementia (IBMPFD).

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

This panel does not cover the expansion of a hexanucleotide repeat in a non-coding region of *C9orf72*. Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics amyotrophic lateral sclerosis panel covers classical genes associated with amyotrophic lateral sclerosis. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.