Arthrogryposes Panel

The Blueprint Genetics Arthrogryposes Panel (test code MA0501):

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All exons of the *GBA* gene have segmentally duplicated pseudogenes that reduce sensitivity of NGS diagnostics in general. However, Blueprint Genetics custom assay has good coverage (>20x) with high mapping rates (mapping quality >40) for 100.0% of the target regions in *GBA* gene. Our validation showed high mean coverage of 184X for the *GBA* gene. Thus, our NGS Panel is not expected to have major limitations in detecting variants in *GBA* gene although clinical validation has not been performed at large scale for Gaucher disease.

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. In individuals identified to have homozygous *SMN1* deletions, we include reporting of *SMN2* copy number.

Refer to the most current version of ICD-10-CM manual for a complete list of ICD-10 codes.

• Blood (min. 1ml) in an EDTA tube
• Extracted DNA, min. 2 μg in TE buffer or equivalent
• Saliva (Please see Sample Requirements for accepted saliva kits)

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

We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.

Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.

Read more about our sample requirements here.

All exons of the *GBA* gene have segmentally duplicated pseudogenes that reduce sensitivity of NGS diagnostics in general. However, Blueprint Genetics custom assay has good coverage (>20x) with high mapping rates (mapping quality >40) for 100.0% of the target regions in *GBA* gene. Our validation showed high mean coverage of 184X for the *GBA* gene. Thus, our NGS Panel is not expected to have major limitations in detecting variants in *GBA* gene although clinical validation has not been performed at large scale for Gaucher disease.

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. In individuals identified to have homozygous *SMN1* deletions, we include reporting of *SMN2* copy number.

The strengths of this test include:

• CAP accredited laboratory
• 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
• Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
• Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
• ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
• Our rigorous variant classification scheme
• Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
• Our comprehensive clinical statements

Due to high sequence homology between *SMN1* and *SMN2*, this panel has not been validated to detect single nucleotide variants or small insertions and deletions in *SMN1* which are associated with spinal muscular atrophy in a small number of patients (<5%). The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *SELENON* (NM_020451:3), *TK2* (NM_001271934:3), *TSEN2* (NM_001321278:12). Genes with suboptimal coverage in our assay are marked with number sign (#) and 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. Gene is considered to have suboptimal coverage when >90% of the gene’s target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. 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
• Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
• 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
• Stretches of mononucleotide repeats
• Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
• Indels larger than 50bp
• Single exon deletions or duplications
• Variants within pseudogene regions/duplicated segments
• Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.

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.

The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

The performance metrics listed below are from an initial validation performed at our main laboratory in Finland. The performance metrics of our laboratory in Marlborough, MA, are equivalent.