Core Reproductive Screen Duo with FMR1 repeat expansion

The Blueprint Genetics Core Reproductive Screen Duo with FMR1 repeat expansion (test code CS0104):

Read about our accreditations, certifications and CE-marked IVD medical devices here.

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 noncoding disease-causing variants in our clinical grade NGS assay for panels (please see ‘Noncoding 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

• 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.

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 noncoding disease-causing variants in our clinical grade NGS assay for panels (please see ‘Noncoding 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

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
• Our Nucleus online portal provides transparent and easy access to quality and performance data at the patient level
• Our publicly available analytic validation demonstrates complete details of test performance
• ~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 test’)
• Our rigorous variant classification scheme
• Our systematic clinical interpretation workflow using proprietary software enables accurate and traceable processing of NGS data
• Our comprehensive clinical statements

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
-Noncoding 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.

CFTR: The 5T and associated TG repeat variants are not reported as their relevance in relation to classical cystic fibrosis is unclear and this test is not intended to screen for risk of congenital bilateral absence of the vas deferens (CBAVD) or CFTR-related pancreatitis risk.

CYP21A2 (NM_000500.9): only the following variants are reported:

c.955C>T p.(Gln319*)

c.844G>T p.(Val282Leu)

c.293-13C>G

c.1360C>T p.(Pro454Ser)

c.518T>A p.(Ile173Asn)

c.1447C>T p.(Pro483Ser)

c.92C>T p.(Pro31Leu)

FMR1: Repeat expansion reporting includes findings consistent with intermediate CGG repeat length (45-54), premutation (55-200) and full mutation (>200 repeats) (PMID: 23765048). Indication of AGG interruptions is reported for female carriers of premutations but specific nature of the repeat (presence and number of AGG interruptions) will require confirmation using additional methods.

HBA1 and HBA2 genes have identical sequences at coding region and their mapping rely purely on differences at intronic/UTR regions. This reduces sensitivity for detecting variants in this region by using standard NGS diagnostics. However, Blueprint Genetics custom assay has good coverage (>20x) with improved mapping rates (mapping quality >40) within the target regions of these genes:  HBA1 80.7% and HBA2 59.4%. Our validation showed high mean coverage of 604x for HBA1 gene and 463x for HBA2. We have been able to detect sequence variants and the common disease-causing deletions using our assay but some limitations in sensitivity is expected to exist at the moment.

SMN1: Analysis includes only SMN1 copy number analysis, sequence variants are not included in this test. “Silent” carriers of SMA (individuals with two copies of SMN1 on one allele, and zero copies on the other allele) is not detected with this test. We do not include SMN1 c.*3+80T>G as this is mostly uninformative in the general population. This variant is common in African American individuals (27% carrier frequency) where it poorly predicts SMN1 2+0 allele status and it is rare in Ashkenazi Jewish individuals (3.5% carrier frequency) where it reliably predicts SMN1 2+0 allele status (PMID: 23788250).

TYR: The c.1205G>A, p.(Arg402Gln) (NM_000372.5) hypomorphic variant is typically associated with mild skin/hair/eye pigmentation changes and is therefore not reported as this test is intended to identify variants that cause severe TYR-related oculocutaneous albinism.

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.