LGMD and Congenital Muscular Dystrophy 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: NE0801

The Blueprint Genetics LGMD and Congenital Muscular Dystrophy Panel is a 33 gene test for genetic diagnostics of patients with clinical suspicion of congenital muscular dystrophy or limb-girdle muscular dystrophy.

Limb-girdle muscular dystrophy (LGMD) is inherited in an autosomal dominant or recessive manner. More than 50 loci have been associated to different forms of LGMD, making accurate diagnosis and genetic counseling a challenge. The DMD gene causing Duchenne muscular dystrophy and Becker muscular dystrophy is also included to the panel. We offer two panels for other muscular dystrophies: Emery Dreifuss Muscular Dystrophy Panel and Collagen Type VI-Related Disorders Panel. For differential diagnostics, also Comprehensive Muscular Dystrophy / Myopathy Panel including all of these genes is availabe.

About LGMD and Congenital Muscular Dystrophy

LGMD is a group of disorders with atrophy and weakness of proximal limb girdle muscles, typically sparing the heart and bulbar muscles. However, cardiac and respiratory impairment may be observed in certain forms of LGMD. In congenital muscular dystrophy (CMD), the muscle weakness typically presents from birth to early infancy. Clinical severity, age of onset, and disease progression are highly variable among the different forms of LGMD/CMD. Phenotypes overlap both within CMD subtypes and among the congenital muscular dystrophies, congenital myopathies, and limb-girdle muscular dystrophies

Availability

Results in 3-4 weeks.

Genes in the LGMD and Congenital Muscular Dystrophy Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ANO5Gnathodiaphyseal dysplasiaAR42106
CAPN3Muscular dystrophy, limb-girdle, Eosinophilic myositisAR102400
CAV3Creatine phosphokinase, elevated serum, Hypertrophic cardiomyopathy (HCM), Long QT syndromeAD/Digenic2347
COL4A1Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel diseaseAD2788
COL4A2Hemorrhage, intracerebralAD512
DESDilated cardiomyopathy (DCM), Myopathy, myofibrillarAD/AR5195
DMDBecker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy (DCM)XL4893390
DNAJB6Muscular dystrophy, limb-girdleAD913
DYSFMiyoshi muscular dystrophy, Muscular dystrophy, limb-girdle, Myopathy, distal, with anterior tibial onsetAD/AR145507
FKRPMuscular dystrophy-dystroglycanopathyAR3199
FKTNMuscular dystrophy-dystroglycanopathy, Dilated cardiomyopathy (DCM), Muscular dystrophy-dystroglycanopathy (limb-girdle)AD/AR2851
GMPPBMuscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), Limb-girdle muscular dystrophy-dystroglycanopathyAR1326
ISPDMuscular dystrophy-dystroglycanopathyAR2042
LAMA2Muscular dystrophy, congenital merosin-deficient, SchizophreniaAD/AR72225
LARGEMuscular dystrophy-dystroglycanopathyAR1522
LIMS2Muscular dystrophy, limb-girdleAR23
LMNAHeart-hand syndrome, Slovenian, Limb-girdle muscular dystrophy, Muscular dystrophy, congenital, LMNA-related, Lipodystrophy (Dunnigan), Emery-Dreiffus muscular dystrophy, Malouf syndrome, Dilated cardiomyopathy (DCM)AD/AR183458
MYOTMyopathy, myofibrillarAD813
PNPLA2Neutral lipid storage disease with myopathyAR1143
POMGNT1Muscular dystrophy-dystroglycanopathyAR5573
POMT1Muscular dystrophy-dystroglycanopathyAR3181
POMT2Muscular dystrophy-dystroglycanopathyAR2848
SGCAMuscular dystrophy, limb-girdleAR2589
SGCBMuscular dystrophy, limb-girdleAR1556
SGCDMuscular dystrophy, limb-girdle, Dilated cardiomyopathy (DCM)AR1219
SGCGMuscular dystrophy, limb-girdleAR1855
SMCHD1Facioscapulohumeral muscular dystrophyDigenic (involving a SMCHD1 mutation and permissive D4Z4 haplotype)1647
TCAPMuscular dystrophy, limb-girdle, Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD/AR1024
TNPO3Muscular dystrophy, limb-girdleAD33
TOR1AIP1Muscular dystrophy with progressive weakness, distal contractures and rigid spineAD/AR15
TRAPPC11Limb-girdle muscular dystrophyAR43
TRIM32Bardet-Biedl syndrome, Muscular dystrophy, limb-girdleAR715
TTN*Hypertrophic cardiomyopathy (HCM), Dilated cardiomyopathy (DCM)AD437226
  • * 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 LGMD and congenital muscular dystrophy panel that covers classical genes associated with congenital muscular dystrophy, Fukuyama congenital muscular dystrophy, limb-girdle muscular dystrophy, muscle-eye-brain disease and walker-Warburg syndrome. 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 LGMD and Congenital Muscular Dystrophy Panel

ICD-10Disease
G71.0Limb-girdle muscular dystrophy
G71.2Congenital muscular dystrophy

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.