Disease Predisposition, Comprehensive Genetic Screening

The Comprehensive Genetic Test for Disease Predisposition utilizes next-generation sequencing (NGS) to examine 181 genes associated with hereditary disease predisposition and genetic risk syndromes. It is a targeted gene panel specifically designed to support accurate diagnosis, risk assessment, and prevention.

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A wide range of complex, potentially life-threatening diseases, including cancer, cardiovascular, pulmonary, metabolic, and hematological disorders, may arise from underlying genetic susceptibility in combination with environmental and lifestyle factors. At the biological level, these conditions are often associated with disruptions in essential cellular processes, including DNA repair, cell cycle regulation, signal transduction, ion transport, connective tissue integrity, and metabolic homeostasis. Inherited genetic variants affecting these pathways may alter normal cellular function and regulatory mechanisms. Although such variants may remain clinically silent for extended periods, they can contribute to an increased long-term predisposition to disease before the onset of observable symptoms.

The genetic background of these conditions is highly heterogeneous, involving numerous genes with diverse biological functions. Representative examples include BRCA1, BRCA2, and PALB2, which are involved in DNA repair; TP53, a key regulator of cell cycle control and apoptosis; and MLH1, MSH2, MSH6, and PMS2, which participate in mismatch repair pathways. Additional genes such as MYH7, MYBPC3, and TTN are associated with cardiac muscle structure, while SCN5A, KCNQ1, and RYR2 are involved in cardiac electrophysiology. Genes such as LDLR, APOB, and PCSK9 are involved in lipid metabolism, whereas F5, PROC, and PROS1 are involved in coagulation pathways. The inclusion of a comprehensive set of genes, including APC, PTEN, RET, SDHB, TGFBR1, TERT, and VHL, reflects the wide spectrum of biological mechanisms underlying disease susceptibility.

The clinical and phenotypic spectrum associated with inherited predisposition to these disorders is broad and variable. Individuals carrying similar genetic variants may present with a wide range of outcomes, from remaining asymptomatic throughout life to developing clinically significant disease. Manifestations may include malignancies, cardiovascular abnormalities, pulmonary conditions, endocrine or metabolic disorders, and hematological abnormalities. The age of onset, severity, and progression of disease may differ substantially between individuals. This variability reflects the influence of additional genetic modifiers, environmental exposures, and lifestyle-related factors, contributing to a heterogeneous and individualized clinical presentation.

The Comprehensive Genetic Test for Disease Predisposition is a genetic risk assessment tool designed for asymptomatic adults seeking information about their inherited predisposition to a wide range of serious health conditions. It does not constitute a diagnostic test and is not intended to confirm or exclude the presence of disease. Instead, it evaluates genetic variants associated with increased susceptibility, providing insight into potential risk. The comprehensive genetic test for disease predisposition is specifically designed for individuals without symptoms and excludes genes primarily associated with childhood-onset conditions or clearly recognizable phenotypes. The results are intended to support awareness of genetic predisposition without implying certainty of disease development.

Within the broader genetic context, the level of risk associated with different genes varies and is generally categorized as low, moderate, or high based on current scientific evidence. The comprehensive genetic test for disease predisposition includes genes with well-established clinical relevance, including all genes recommended for reporting as secondary findings by the American College of Medical Genetics and Genomics (ACMG, version 3.1), as well as additional genes associated with cancer, cardiovascular, pulmonary, metabolic, and hematological conditions. Risk classification is informed by peer-reviewed literature and quantitative metrics such as odds ratios, although these thresholds are not absolute and may vary across studies. Interpretation of genetic variants follows internationally accepted standards, including ACMG/AMP guidelines, and only variants classified as pathogenic or likely pathogenic are reported.

The identification of clinically significant genetic variants may increase awareness of individual susceptibility and support long-term monitoring strategies. Such findings may provide a framework for understanding potential risks and facilitate informed discussions within a clinical context. However, genetic results are intended to complement, and not replace, comprehensive medical evaluation and clinical judgment.

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 and Associated Phenotypes (Comprehensive Genetic Testing for Disease Predisposition)

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:

• Special Reporting Policies: HFE: Only the homozygous c.845G>A, p.(Cys282Tyr) (NM_000410.4) variant is reported. TTN: Missense variants and in-frame insertions/deletions are not included in the report. MT-RNR1: Only the m.1555A>G (NC_012920.1) variant is reported.
• 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.
• The following exons are excluded from the panel due to insufficient coverage by high-quality sequencing reads: CHEK2 NM_001005735.2:3, PDGFRA NM_001347828.2:2, PKP2 NM_004572.4:6, PMS2 NM_000535.7:13-15, SDHD NM_001276506.2:4.
• 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.