Spastic Paraplegia Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: NE0501

The Blueprint Genetics Spastic Paraplegia Panel is a 35 gene test for genetic diagnostics of patients with clinical suspicion of spastic paraplegia.

The panel covers genes for the nonsyndromic and syndromic hereditary spastic paraplegia (HSP), which is inherited in an autosomal recessive, autosomal dominant or X-linked manner. For patients with suspected amyotrophic lateral sclerosis, we offer Amyotrophic Lateral Sclerosis Panel.

About Spastic Paraplegia

HSP is a group of clinically and genetically heterogeneous neurodegenerative disorders characterized by lower extremity spasticity and weakness. If symptoms begin in very early childhood, they may be non-progressive and resemble spastic diplegic cerebral palsy. If symptoms begin later, they usually progress slowly and steadily. HSP is classified clinically as nonsyndromic (uncomplicated) or syndromic (complicated). Nonsyndromic HSPs are characterized by slowly progressive lower extremity spasticity and weakness, often associated with hypertonic urinary disturbances, mild reduction of lower extremity vibration sense and, occasionally, of joint position sensation. Syndromic HSP forms are characterized by the presence of additional neurological or non-neurological features. The prevalence of HSP is estimated to be 1-9 / 100 000.

Availability

Results in 3-4 weeks.

Genes in the Spastic Paraplegia Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
AFG3L2*Spastic ataxia, Spinocerebellar ataxiaAD/AR1925
ALS2Amyotrophic lateral sclerosis, Spastic paralysisAR2354
ATL1Spastic paraplegia, Neuropathy, hereditary sensoryAD2270
B4GALNT1Spastic paraplegiaAR513
BSCL2Lipodystrophy, congenital generalized, Encephalopathy, progressiveAR2043
C12ORF65Spastic paraplegia, Combined oxidative phosphorylation deficiencyAR9
C19ORF12Spastic Paraplegia, Neurodegeneration with brain iron accumulationAR12
CYP7B1Bile acid synthesis defectAR1341
DDHD1Spastic paraplegiaAR48
DDHD2Spastic paraplegiaAR911
FA2HSpastic paraplegiaAR1339
FXN*Friedreich ataxiaAR1165
GALCKrabbe diseaseAR35210
GBA2Cerebellar ataxia with spasticityAR913
GJC2Spastic paraplegia, Lymphedema, hereditary, Leukodystrophy, hypomyelinatingAD/AR1553
HSPD1*Spastic paraplegia, Leukodystrophy, hypomyelinatingAD/AR44
KDM5CMental retardation, syndromic, Claes-JensenXL2144
KIAA0196Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome)AD/AR714
KIF1ASpastic paraplegia, Neuropathy, hereditary sensory, Mental retardationAD/AR3527
KIF5ASpastic paraplegiaAD1035
L1CAMMental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesisXL37286
MARS2Combined oxidative phosphorylation deficiencyAR65
NIPA1Spastic paraplegiaAD416
PLP1Spastic paraplegia, Pelizaeus-Merzbacher diseaseXL41266
PNPLA6Laurence-Moon syndrome, Boucher-Neuhauser syndromeAR1649
REEP1Spastic paraplegia, Distal hereditary motor neuronopathyAD1154
SACSSpastic ataxia, Charlevoix-SaguenayAR34220
SETXAtaxia with oculomotor apraxia, Amyotrophic lateral sclerosis, juvenile, Spinocerebellar ataxiaAD/AR25185
SLC16A2Allan-Herndon-Dudley syndromeXL2879
SLC33A1*Congenital cataracts, hearing loss, and neurodegenerationAR67
SPASTSpastic paraplegiaAD90648
SPG7Spastic paraplegiaAR42104
SPG11Spastic paraplegia, Amyotrophic lateral sclerosis, Charcot-Marie-Tooth diseaseAR107239
SPG20Spastic paraplegia (Troyer syndrome)AR43
SPRDystonia, Dopa-responsive, due to sepiapterin reductase deficiencyAR919
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.

Blueprint Genetics offers a comprehensive spastic paraplegia panel that covers classical genes associated with spastic paraplegia. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

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. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes

SEQ81479
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Spastic Paraplegia Panel

ICD-10Disease
G11.4Spastic paraplegia

Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • 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.