Comprehensive Reproductive Genetic Screen with FMR1 Repeat Expansion

The Comprehensive Reproductive Genetic Screen with FMR1 Repeat Expansion utilizes next-generation sequencing (NGS) to examine 461 genes associated with autosomal recessive and X-linked genetic conditions, as well as fragile X syndrome. It is a targeted gene panel specifically designed to support accurate diagnosis, risk assessment, and prevention during family planning.

More Information

Autosomal recessive and X-linked genetic conditions comprise a broad group of inherited disorders that may affect multiple biological systems and developmental pathways. These conditions typically arise when pathogenic variants disrupt essential cellular processes such as enzymatic activity, metabolic pathways, protein transport, or structural integrity of tissues. In many cases, individuals carrying a single altered copy of a gene remain clinically unaffected, as one functional copy is sufficient to maintain normal physiological function. However, when both alleles are affected or when X-linked inheritance is involved, there may be an increased probability of having an affected child. In addition, certain conditions may result from dynamic mutations, such as repeat expansions, which can influence gene expression and disease risk.

The genetic background of these disorders involves numerous genes associated with metabolic, neuromuscular, hematological, and developmental functions. Representative examples include CFTR, associated with cystic fibrosis; PAH, involved in amino acid metabolism; and SMN1, which plays a role in motor neuron survival. Additional genes such as GBA and HEXA are involved in lysosomal storage pathways, while HBB and HBA1/HBA2 contribute to hemoglobin structure. The FMR1 gene is associated with fragile X-related conditions, in which expansion of CGG trinucleotide repeats in the 5′ untranslated region may alter gene expression. The inclusion of a wide range of genes, such as ABCA3, CPT2, IDUA, and POLG, reflects the complexity and diversity of inherited genetic disorders.

The clinical and phenotypic spectrum associated with these conditions is highly variable. Manifestations may range from severe, early-onset disorders presenting in infancy or childhood to milder or later-onset forms. Clinical features may include metabolic abnormalities, neurological impairment, developmental delay, sensory deficits, or organ-specific dysfunction. In the case of repeat expansion disorders such as those involving FMR1, phenotypic expression may depend on the number of repeats and may vary across individuals and generations. The severity and progression of disease may differ significantly depending on the gene involved, the type of genetic alteration, and additional modifying factors.

The Comprehensive Reproductive Genetic Screen with FMR1 Repeat Expansion is designed as a carrier screening tool intended for use in healthy individuals who wish to understand their genetic likelihood of having a child affected by an autosomal recessive or X-linked condition. It does not constitute a diagnostic test and is not intended to determine whether an individual currently has a genetic disorder. Instead, it evaluates carrier status by identifying pathogenic variants and, in the case of FMR1, assessing CGG repeat length associated with fragile X-related conditions. The comprehensive reproductive genetic screen with FMR1 repeat expansion is intended for asymptomatic individuals and provides information related to reproductive risk without implying certainty of outcome.

Within the broader genetic context, the likelihood of having an affected child varies depending on inheritance patterns, gene-specific characteristics, and the presence of pathogenic variants in one or both parents. For FMR1, classification is based on CGG repeat size categories, including intermediate, premutation, and full mutation ranges, which are associated with different biological implications. The genes included in the comprehensive reproductive genetic screen have been selected based on established clinical relevance, including alignment with recommendations from professional organizations such as the American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics and Genomics (ACMG). However, variability exists in disease frequency, severity, and penetrance across different conditions. Interpretation of genetic findings follows internationally accepted standards, including ACMG/AMP guidelines, and only variants classified as pathogenic or likely pathogenic are reported.

The identification of carrier status and repeat expansion categories may contribute to increased awareness of reproductive risk and support informed discussions in a clinical context. Such information may assist individuals or couples in understanding potential genetic implications when planning a family. However, genetic results are intended to complement, and not replace, professional medical consultation and individualized clinical evaluation.

The test is performed in a clinical laboratory accredited to ISO 15189 and certified by CLIA and CAP, ensuring the validity, accuracy and international recognition of the results.

Genes A-K and Associated Phenotypes (Comprehensive Reproductive Genetic Screen with FMR1 Repeat Expansion)

Genes L-Z and Associated Phenotypes (Comprehensive Reproductive Genetic Screen with FMR1 Repeat Expansion)

Genetic testing is performed by taking a blood sample or by taking genetic material from inside the cheeks (with a swab), and can be done:

• By taking the sample at Diagnostiki Athinon. Book your appointment in real-time and purchase the test online
• By taking the sample at home. We send you all the necessary collection materials to your home via courier. The courier also returns the sample to the laboratory. Purchase the test online

Test Strengths

The test is characterized by the following strengths:

• Analysis is performed in a CAP-accredited laboratory with the participation of CLIA-certified personnel.
• Advanced sequencing technologies, high-performance target enrichment methods, and precise bioinformatics pipelines ensure superior analytical performance.
• Gene panels are carefully designed to be clinically effective and scientifically validated.
• In some panels, the entire mitochondrial genome is included (see Panel Content section).
• Approximately 2,000 non-coding disease-causing variants are covered in the clinical-grade NGS assay (see Non-coding disease-causing variants covered by this panel in the Panel Content section).
• A rigorous variant classification system is applied.
• A systematic interpretation workflow, supported by proprietary software, enables accurate and traceable processing of NGS data.
• Comprehensive and clinically meaningful reports are provided.

Test Limitations

Specific technical and biological limitations apply:

• The following exons are excluded from the panel due to insufficient coverage by high-quality sequencing reads:  ADAMTS2 NM_021599.4:11, CHM NM_001145414.4:5, KIAA0586 NM_001244189.2:6,33, MCPH1 NM_001322042.2:14, PCCB NM_001178014.2:4, RPGRIP1L NM_015272.5:23, TSEN2 NM_001321278.2:12, TSFM NM_001172696.2:5, VPS45 NM_001279353.2:13, ZNHIT3 NM_001281432.2:5.
• The coding regions of HBA1 and HBA2 are identical, which complicates accurate mapping of short reads generated by next-generation sequencing (NGS). In these cases, alignment depends mainly on differences in intronic and untranslated regions (UTRs), potentially reducing sensitivity for variant detection with standard NGS approaches. The present custom assay addresses this challenge by providing high coverage (>20x) and improved mapping quality (MQ >40) across the targeted regions. Validation studies have also demonstrated a high mean depth of coverage. This assay enables detection of sequence variants and certain known disease-associated deletions; however, some limitations remain, including reduced sensitivity for specific variant types such as gene fusions and certain deletions.
• Special Reporting Policies: CFTR: The 5T variant and associated TG repeat variants are not reported, as their clinical relevance to classical cystic fibrosis remains uncertain. This test is not intended for the assessment of risk for congenital bilateral absence of the vas deferens (CBAVD) or CFTR-related pancreatitis. CYP21A2 (NM_000500.9): Reporting is limited to the following variants: 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). SMN1: Analysis includes only copy number determination of SMN1. Sequence variants are not assessed. Silent carriers (individuals with two copies on one allele and none on the other) cannot be detected. The c.*3+80T>G variant is not included, as it has limited clinical utility in the general population and variable predictive value across different ethnic groups (PMID: 23788250). TYR: The hypomorphic variant c.1205G>A, p.(Arg402Gln) (NM_000372.5), typically associated with mild pigmentation changes, is not reported. This test focuses on variants causing severe TYR-related oculocutaneous albinism.
• Repeat Expansion Reporting Policy: The number of CGG repeats is reported when an allele falls within the intermediate range (45–54 repeats) or the premutation range (55–200 repeats). If a heterozygous premutation allele is identified, the presence or absence of AGG interruptions is reported. However, the exact number of AGG interruptions is not provided, as this cannot be determined by the current testing method. If further characterization is required, additional testing at a specialized laboratory is recommended when AGG interruptions are detected. Full mutation alleles (>200 repeats) are reported as “>200 CGG repeats,” without specifying an exact repeat count. Methylation analysis is not performed as part of this test. Repeat numbers are not reported for alleles within the normal range (5–44 repeats). If both alleles fall within this range, no specific comment or repeat count is included in the report.
• Genes with suboptimal coverage are marked with a number sign (#), while those with partial or complete segmental duplications overlapping UCSC pseudogene regions are marked with an asterisk (*).
• A gene is considered to have suboptimal coverage when more than 90% of its target nucleotides are not covered at a depth of greater than 20x with mapping quality score (MQ > 20) reads. In such cases, detection of variants may be limited.

This test does not detect:

• Complex inversions
• Gene conversions
• Balanced translocations
• Repeat expansion disorders, unless otherwise specified
• Non-coding variants beyond ±20 base pairs from the exon–intron boundary, unless otherwise indicated
• The complete mitochondrial genome in all panels (see Panel Content section

This test may not reliably detect:

• Low-level mosaicism in nuclear genes (variants with a minor allele fraction of ~14.6% are detected with 90% probability)
• Stretches of mononucleotide repeats
• Low-level heteroplasmy in mtDNA (>90% detected at 5% level)
• Insertions or deletions larger than 50 bp
• Single-exon deletions or duplications
• Variants within pseudogene regions or duplicated genomic segments
• Disease-causing mtDNA variants not present in blood; in such cases, post-mitotic tissue (e.g., skeletal muscle) may be required to establish a molecular diagnosis

For further details, please refer to the Bioinformatics & Performance section.

Bioinformatics

The target region for each gene encompasses the coding exons as well as ±20 base pairs from the exon–intron boundaries. In addition, the panel may include non-coding and regulatory variants, as listed in the “Non-coding variants covered by the panel” section. Specific regions of certain gene(s) may be excluded from analysis if noted in the “Test limitations” section. When the test includes the mitochondrial genome, the target region also comprises the complete set of mitochondrial genes.

Sequencing data is processed through a proprietary analysis and annotation pipeline that integrates state-of-the-art algorithms and industry-standard software solutions. Multiple quality control steps are embedded throughout the workflow to ensure the accuracy, validity, and consistency of the results. The pipeline is optimized to maximize sensitivity without compromising specificity.

For variant interpretation, the system incorporates data from multiple reference populations and mutation databases, including (but not limited to) the 1000 Genomes Project, gnomAD, ClinVar, and HGMD. In silico tools such as SIFT, PolyPhen, and MutationTaster are also applied to support the classification of missense variants.

All findings are summarized in a clear and detailed clinical report. This report includes sequencing quality metrics, gene-level coverage information, and highlights any regions where coverage is limited (<20x for nuclear genes and <1000x for mtDNA, when applicable). This ensures transparency and supports accurate clinical decision-making.

Test Performace

The genes included in this panel have been carefully selected based on evidence from scientific literature, mutation databases, and accumulated clinical expertise.

All panels are derived from a high-quality, clinical-grade NGS assay. Details regarding the detection of different types of genetic alterations are provided in the sequencing and detection performance table (see Table).

The assay has been validated for several sample types, including EDTA blood, isolated DNA (excluding DNA from formalin-fixed paraffin-embedded tissue), saliva, and dried blood spots (filter cards). These sample types were chosen to maximize the probability of obtaining high-quality DNA. The diagnostic yield may vary depending on the assay performed, the referring healthcare professional, the hospital, and the country in which the test is conducted. The Plus Analysis further enhances the chance of reaching a genetic diagnosis, as large deletions and duplications cannot be detected by sequencing alone. This approach integrates both sequencing and deletion/duplication (copy number variant, CNV) analysis.

The performance metrics shown below are based on initial validation studies at an accredited clinical laboratory, with equivalent results confirmed across additional laboratory sites.

Performance of a high-quality, clinical-grade NGS sequencing assay for panels

Coverage metrics

Performance of Mitochondrial Sequencing Assay