Comprehensive Reproductive Male Genetic Screen

The Comprehensive Reproductive Male Genetic Screen utilizes next-generation sequencing (NGS) to examine 433 genes associated with autosomal recessive and X-linked genetic conditions. It is a targeted gene panel specifically designed to support accurate diagnosis, risk assessment, and prevention during family planning.

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Autosomal recessive and X-linked genetic conditions constitute a diverse group of inherited disorders that may affect multiple biological systems and developmental processes. These conditions typically arise when pathogenic variants disrupt essential cellular functions 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. However, when both partners carry variants in the same autosomal gene, there may be an increased probability of having an affected child. In the context of X-linked inheritance, risk assessment depends on the carrier status of the female partner, as well as gene-specific characteristics and inheritance patterns.

The genetic background of these conditions involves numerous genes associated with metabolic, neuromuscular, sensory, and developmental pathways. Representative examples include CFTR, associated with cystic fibrosis; PAH, involved in amino acid metabolism; and SMN1, which plays a role in motor neuron function. Additional genes such as GBA and HEXA are involved in lysosomal storage processes, while HBB and HBA1/HBA2 contribute to hemoglobin structure. Certain genes included in this panel, such as GLA and RPGR, are associated with X-linked conditions that may exhibit reduced penetrance or variable age of onset. The inclusion of a broad set of genes, such as ABCA3, CPT2, IDUA, and POLG, reflects the complexity and diversity of inherited disorders relevant to reproductive risk assessment.

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 such as hearing or vision loss, or dysfunction of specific organs. The severity and progression of disease may differ depending on the gene involved, the type of genetic alteration, and additional modifying factors. Even within the same condition, variability in clinical expression may be observed among affected individuals.

The Comprehensive Reproductive Male Genetic Screen is designed as a genetic carrier screening tool intended for use in healthy male individuals who wish to understand their likelihood of having a child affected by an autosomal recessive or selected X-linked condition. It is particularly intended for cases in which the female partner has already been tested and found negative for carrier status of X-linked conditions. The comprehensive reproductive male genetic screen does not constitute a diagnostic tool and is not intended to determine whether an individual has a genetic disorder. Instead, it evaluates carrier status and provides information related to reproductive risk, without implying certainty of outcome.

Within the broader genetic context, the likelihood of having an affected child depends on inheritance patterns, gene-specific characteristics, and the carrier status of both partners. The genes included in the comprehensive reproductive male genetic screen have been selected based on established clinical relevance and 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), with certain exclusions due to technical limitations or variability in clinical presentation. Risk classification is informed by scientific literature and established metrics, while interpretation of genetic findings follows internationally accepted standards, including ACMG/AMP guidelines. Only variants classified as pathogenic or likely pathogenic are reported.

The identification of carrier status in male individuals may contribute to a more comprehensive understanding of reproductive risk and support informed discussions within a clinical context. Such information may assist individuals or couples in considering 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 Male Genetic Screen)

Genes L-Z and Associated Phenotypes (Comprehensive Reproductive Male Genetic Screen)

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, 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.
• 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

Mitochondrial assay coverage metrics

Comprehensive clinical reports are delivered, designed to provide healthcare professionals with meaningful and actionable insights. Clinical interpretation requires a solid understanding of both clinical genetics and genetic principles. Reports are prepared by teams of molecular geneticists, medical experts, and other highly experienced professionals, who evaluate identified variants in the context of the patient’s phenotypic information provided in the requisition form.

The goal is to ensure that reports are clinically valuable and understandable to all healthcare providers, regardless of their level of training in genetics and genetics-related fields. Variant classification forms the foundation of clinical interpretation and guides patient management decisions. Classifications follow the ACMG 2015 guidelines. Sequence and copy number variants classified as pathogenic, likely pathogenic, or of uncertain significance (VUS) are confirmed using bidirectional Sanger sequencing or orthogonal methods such as qPCR/ddPCR whenever NGS quality metrics do not meet strict thresholds for a true positive call.

Each report includes tables for sequence and copy number variants, presenting essential information such as genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, phenotypic correlations, and variant classification. In addition, detailed descriptions are provided for the variant, the gene, and the related phenotypes, covering the gene’s role in human disease, mutation spectrum, variation in population cohorts, and links to associated conditions. References, abstracts, and variant databases are also cited, enabling healthcare providers to further evaluate reported findings if desired.

Reports are structured into two sections: primary findings and additional findings.

The primary findings consist of variants known to cause disease or rare variants that may explain the patient’s phenotype. The conclusion summarizes all available evidence and presents the rationale for classification.

Additional findings include variants that are not currently sufficient to explain the patient’s phenotype, based on existing knowledge. Examples include heterozygous variants in autosomal recessive genes, VUS in autosomal dominant genes (when a pathogenic or likely pathogenic variant already explains the phenotype), or risk alleles in genes included in the panel.

The identification of pathogenic or likely pathogenic variants in dominant disorders, or biallelic variants in recessive disorders, is considered molecular confirmation of the clinical diagnosis. In such cases, family testing may assist in risk assessment. Variants of uncertain significance are not recommended for patient management or family risk stratification. Genetic counseling is strongly advised.

Interpretation teams routinely analyze millions of variants across thousands of cases of rare diseases. With each case, internal knowledge of variant–phenotype relationships is enriched, enabling continuous refinement of classifications. As new evidence becomes available, previously reported variants may be reclassified. If a variant initially reported as a primary or secondary finding is later reclassified (for example, from VUS to pathogenic/likely pathogenic, or from pathogenic/likely pathogenic to VUS, likely benign, or benign), an updated statement is issued to the original ordering healthcare provider at no additional cost.