Spinal Muscular Atrophy Panel

Last modified: Jun 12, 2018

Summary

  • Is a 30 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of distal hereditary motor neuropathy or spinal muscular atrophy.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

4 weeks

Number of genes

30

Test code

NE1801

Panel size

Large

CPT codes

SEQ 81400
SEQ 81401
SEQ 81405
DEL/DUP 81479

Summary

The Blueprint Genetics Spinal Muscular Atrophy Panel (test code NE1801):

  • Is a 30 gene panel that includes assessment of selected non-coding disease-causing variants
  • Deletion / duplication analysis (either in isolation or as part of Plus analysis including sequencing) testing can detect the copy number of SMN1 exon 7, which is commonly used as a marker for copy number of the SMN1 gene.

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

Test Specific Strength

Deletion / duplication analysis (either in isolation or as part of Plus analysis including sequencing) testing can detect the copy number of SMN1 exon 7, which is commonly used as a marker for copy number of the SMN1 gene.

ICD codes

Commonly used ICD-10 code(s) when ordering the Spinal Muscular Atrophy Panel

ICD-10 Disease
G12.1 Spinal muscular atrophy

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.

Spinal muscular atrophies (SMAs) are a genetically and clinically heterogeneous group of rare debilitating disorders characterized by the degeneration of lower motor neurons and subsequent atrophy of various muscle groups in the body. While some SMAs lead to death in infancy, other types can present with mild weakness in an otherwise healthy adult. Based on the type of muscles affected, spinal muscular atrophies can be divided into proximal and distal SMAs. The distal SMAs significantly overlap with distal hereditary motor neuropathies and this has been taken into account in the panel design. While the presence of several symptoms may point towards a particular genetic disorder, an accurate diagnosis can only be established with certainty by genetic testing.

Genes in the Spinal Muscular Atrophy Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
AARS Epileptic encephalopathy, early infantile, Charcot-Marie-Tooth disease AD/AR 6 16
ASAH1 Spinal muscular atrophy with progressive myoclonic epilepsy, Farber lipogranulomatosis AR 13 71
ATP7A Menkes disease, Occipital horn syndrome, Spinal muscular atrophy, distal, X-linked 3 XL 113 354
BICD2 Childhood-onset proximal spinal muscular atrophy with contractures AD 12 25
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
DCTN1 Perry syndrome, Neuropathy, distal hereditary motor AD 10 45
DNAJB2 Spinal muscular atrophy, distal, Charcot-Marie-Tooth disease AR 9 5
DYNC1H1 Spinal muscular atrophy, Charcot-Marie-Tooth disease, Mental retardation AD 57 64
EXOSC3 Pontocerebellar hypoplasia AR 12 19
EXOSC8 Pontocerebellar hypoplasia AR 1 3
FBXO38 Neuronopathy, distal hereditary motor AD 1 3
GARS Neuropathy, distal hereditary motor, Charcot-Marie-Tooth disease AD 18 37
HEXA Tay-Sachs disease, GM2-gangliosidosis, Hexosaminidase A deficiency AR 112 184
HSPB1 Neuropathy, distal hereditary motor, Charcot-Marie-Tooth disease AD 19 43
HSPB3 Neuronopathy, distal hereditary motor AD 1
HSPB8 Charcot-Marie-Tooth disease, Distal hereditary motor neuronopathy AD 3 10
IGHMBP2 Spinal muscular atrophy, distal, Charcot-Marie-Tooth disease AR 43 126
LAS1L* Spinal muscular atrophy with respiratory distress XL 5 4
PLEKHG5 Spinal muscular atrophy, Charcot-Marie-Tooth disease AR 13 8
REEP1 Spastic paraplegia, Distal hereditary motor neuronopathy AD 16 59
SCO2 Leigh syndrome, Hypertrophic cardiomyopathy (HCM), Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency, Myopia AR 42 33
SLC5A7 Neuronopathy, distal hereditary motor, Myasthenic syndrome, congenital, Neuronopathy, distal hereditary motor, type VIIA AD/AR 5 16
SMN1*,# Spinal muscular atrophy AR 27 111
SMN2*,# Spinal muscular atrophy AD 1 9
TBCE Progressive encephalopathy with amyotrophy and optic atrophy (PEAMO) AR 11 7
TRPV4 Metatropic dysplasia, Spondyloepiphyseal dysplasia Maroteaux type, Parastremmatic dwarfism, Hereditary motor and sensory neuropathy, Spondylometaphyseal dysplasia Kozlowski type, Spinal muscular atrophy, Charcot-Marie-Tooth disease, Brachyolmia (autosomal dominant type), Familial Digital arthropathy with brachydactyly AD 60 76
UBA1 Spinal muscular atrophy, infantile XL 3 4
VAPB Amyotrophic lateral sclerosis, Spinal muscular atrophy, late-onset, Finkel AD 2 9
VRK1 Pontocerebellar hypoplasia AR 6 9

* 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
ATP7A ChrX:77279056 c.2916+2480T>G NM_000052.5
ATP7A ChrX:77287843 c.3294+763C>G NM_000052.5
BSCL2 Chr11:62470032 c.405-11A>G NM_001122955.3
EXOSC3 Chr9:37782146 c.475-12A>G NM_016042.3 rs370087266
HSPB1 Chr7:75931813 c.-217T>C NM_001540.3 rs545738637

Test strength

Deletion / duplication analysis (either in isolation or as part of Plus analysis including sequencing) testing can detect the copy number of SMN1 exon 7, which is commonly used as a marker for copy number of the SMN1 gene.

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

Deletion / duplication analysis (either in isolation or as part of Plus analysis including sequencing) testing can detect the copy number of SMN1 exon 7, which is commonly used as a marker for copy number of the SMN1 gene.

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 (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • 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 spinal muscular atrophy panel covers classical genes associated with spinal muscular atrophy and distal hereditary motor neuropathy. 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.

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.