Comprehensive Reproductive Screen DUO with FMR1
Is a 461 gene test for couples who want information about their chances of having a child with an autosomal recessive or X-linked genetic condition. This type of test is sometimes called carrier screening.
Duo report will combine results of the two tested individuals, to provide reproductive risk assessment for a couple in one test.
Please note that for DUO testing we must receive the samples from both individuals in order to start the analysis.
- PLUS
Summary
The Blueprint Genetics Comprehensive Reproductive Screen DUO with FMR1 (test code CS0002):
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
- 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
Sample Requirements
- 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 Comprehensive Reproductive Screen test is intended for healthy couples interested in carrier screening. Carrier screening gives individuals and/or couples an estimate of their chances of having a child affected with an autosomal recessive or X-linked condition. With this information, individuals or couples can discuss with their healthcare provider to make informed decisions about their reproductive options with medical advice. This might include choosing prenatal diagnosis, preimplantation genetic testing, use of a donor gamete/embryo, adoption, no testing, etc.
In a DUO report results of the two tested individuals are combined, to provide reproductive risk assessment for a couple in one test.
Comprehensive Reproductive Screen test includes screening for:
- 105 out of 113 disorders recommended by the American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics (ACMG) (PMID: 34285390)
- The following disorders are not included due to limitations in variant detection by short-read NGS methods: alpha-methylacetoacetic aciduria (ACAT1), Fragile XE syndrome (AFF2), congenital adrenal insufficiency (CYP11A1), hemophilia A (F8), fragile X syndrome (FMR1), Friedreich ataxia (FXN), Schindler disease (NAGA), Ehlers-Danlos syndrome, classic-like (TNXB)
- Some serious childhood-onset conditions
Only variants classified as pathogenic or likely pathogenic based on an ACMG/AMP classification scheme will be reported.
Genes in the Comprehensive Reproductive Screen DUO with FMR1 and their clinical significance
To view complete table content, scroll horizontally.
| Gene | Associated phenotypes | Inheritance | ClinVar | HGMD |
|---|
Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), 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 Mitomap databases.
Non-coding variants covered by Comprehensive Reproductive Screen DUO with FMR1
To view complete table content, scroll horizontally.
| Gene | Genomic location HG19 | HGVS | RefSeq | RS-number |
|---|
Test Strengths
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
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
Test Limitations
This test does not detect the following:
• 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:
• 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 a 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) |
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.
Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.
| Sensitivity % (TP/(TP+FN) | Specificity % | |
|---|---|---|
| Single nucleotide variants | 99.89% (99,153/99,266) | >99.9999% |
| Insertions, deletions and indels by sequence analysis | ||
| 1-10 bps | 99.2% (7,745/7,806) | >99.9999% |
| 11-50 bps | 99.13% (2,524/2,546) | >99.9999% |
| Copy number variants (exon level dels/dups) | ||
| 1 exon level deletion (heterozygous) | 100% (20/20) | NA |
| 1 exon level deletion (homozygous) | 100% (5/5) | NA |
| 1 exon level deletion (het or homo) | 100% (25/25) | NA |
| 2-7 exon level deletion (het or homo) | 100% (44/44) | NA |
| 1-9 exon level duplication (het or homo) | 75% (6/8) | NA |
| Simulated CNV detection | ||
| 5 exons level deletion/duplication | 98.7% | 100.00% |
| Microdeletion/-duplication sdrs (large CNVs, n=37)) | ||
| Size range (0.1-47 Mb) | 100% (25/25) | |
| The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics | ||
| Mean sequencing depth | 143X | |
| Nucleotides with >20x sequencing coverage (%) | 99.86% |
Performance of Blueprint Genetics Mitochondrial Sequencing Assay.
| Sensitivity % | Specificity % | |
|---|---|---|
| ANALYTIC VALIDATION (NA samples; n=4) | ||
| Single nucleotide variants | ||
| Heteroplasmic (45-100%) | 100.0% (50/50) | 100.0% |
| Heteroplasmic (35-45%) | 100.0% (87/87) | 100.0% |
| Heteroplasmic (25-35%) | 100.0% (73/73) | 100.0% |
| Heteroplasmic (15-25%) | 100.0% (77/77) | 100.0% |
| Heteroplasmic (10-15%) | 100.0% (74/74) | 100.0% |
| Heteroplasmic (5-10%) | 100.0% (3/3) | 100.0% |
| Heteroplasmic (<5%) | 50.0% (2/4) | 100.0% |
| CLINICAL VALIDATION (n=76 samples) | ||
| All types | ||
| Single nucleotide variants n=2026 SNVs | ||
| Heteroplasmic (45-100%) | 100.0% (1940/1940) | 100.0% |
| Heteroplasmic (35-45%) | 100.0% (4/4) | 100.0% |
| Heteroplasmic (25-35%) | 100.0% (3/3) | 100.0% |
| Heteroplasmic (15-25%) | 100.0% (3/3) | 100.0% |
| Heteroplasmic (10-15%) | 100.0% (9/9) | 100.0% |
| Heteroplasmic (5-10%) | 92.3% (12/13) | 99.98% |
| Heteroplasmic (<5%) | 88.9% (48/54) | 99.93% |
| Insertions and deletions by sequence analysis n=40 indels | ||
| Heteroplasmic (45-100%) 1-10bp | 100.0% (32/32) | 100.0% |
| Heteroplasmic (5-45%) 1-10bp | 100.0% (3/3) | 100.0% |
| Heteroplasmic (<5%) 1-10bp | 100.0% (5/5) | 99,997% |
| SIMULATION DATA /(mitomap mutations) | ||
| Insertions, and deletions 1-24 bps by sequence analysis; n=17 | ||
| Homoplasmic (100%) 1-24bp | 100.0% (17/17) | 99.98% |
| Heteroplasmic (50%) | 100.0% (17/17) | 99.99% |
| Heteroplasmic (25%) | 100.0% (17/17) | 100.0% |
| Heteroplasmic (20%) | 100.0% (17/17) | 100.0% |
| Heteroplasmic (15%) | 100.0% (17/17) | 100.0% |
| Heteroplasmic (10%) | 94.1% (16/17) | 100.0% |
| Heteroplasmic (5%) | 94.1% (16/17) | 100.0% |
| Copy number variants (separate artifical mutations; n=1500) | ||
| Homoplasmic (100%) 500 bp, 1kb, 5 kb | 100.0% | 100.0% |
| Heteroplasmic (50%) 500 bp, 1kb, 5 kb | 100.0% | 100.0% |
| Heteroplasmic (30%) 500 bp, 1kb, 5 kb | 100.0% | 100.0% |
| Heteroplasmic (20%) 500 bp, 1kb, 5 kb | 99.7% | 100.0% |
| Heteroplasmic (10%) 500 bp, 1kb, 5 kb | 99.0% | 100.0% |
| The performance presented above reached by following coverage metrics at assay level (n=66) | ||
| Mean of medians | Median of medians | |
| Mean sequencing depth MQ0 (clinical) | 18224X | 17366X |
| Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical) | 100% | |
| rho zero cell line (=no mtDNA), mean sequencing depth | 12X |
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 and regulatory 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 including, 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, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.
We provide customers with the most comprehensive report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists prepare the report by assessing the pathogenicity of the identified variants. Our goal is to provide clinically meaningful reports that are understandable for all medical professionals regardless of whether they have formal training in genetics.
Variant classification is the cornerstone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015. Only variants classified as pathogenic or likely pathogenic based on an ACMG/AMP classification scheme will be reported.
Our screening panel report 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 report includes descriptions of the variant and its association with disease. We also provide links to the references, abstracts, and variant databases used to help ordering providers further evaluate the reported findings if desired.
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, or in proactive testing, to confer a risk of developing an inherited disease. In reproductive screening, identification of single pathogenic or likely pathogenic variants in genes related to recessive disorders is considered as a carriership. Disease risk of potential offspring depends on whether both parents have a pathogenic or likely pathogenic variant in the same gene. Reproductive risk related to X-linked disorders may be difficult to estimate due to the possibility of skewed X-chromosome inactivation. Genetic counseling is recommended whenever pathogenic or likely pathogenic variants are reported.
Reporting focuses on high-quality variants that meet our stringent NGS quality metrics for a true positive call but they are not confirmed with alternative methods. Ordering healthcare professionals should consider further confirmation of the reported variants using a diagnostic test.