Molecular Basis of Disease

Representing Normal Human Variation or Benign Genetic Variants

  • Importance of understanding genetic variants in healthcare

    • Growing prevalence of genetic testing in healthcare and direct-to-consumer testing

    • Essential for healthcare professionals, including genetic counselors, to determine if a genetic variant is disease-associated

Background on Genetic Variants

  • Establishing gene-disease relationships

    • Importance of confirming that a gene is associated with a genetic disorder before making a diagnosis

    • Variants found in numerous protein-coding genes; redundancy in biological systems complicates associations

    • Ongoing research influences gene-disease associations over time

    • Challenges include:

    • Reliance on publicly available data (which can be flawed)

    • Some genes are implicated in multiple diseases, complicating diagnostics

  • Considerations for genetic testing

    • Ethical considerations regarding testing for genes with weak or poorly established disease associations

    • The risk of discovering variants that are not disease-causing (e.g., benign variants)

Classifications of Genetic Variants on Test Reports

  • Various classifications of genetic variants:

    • Benign or Likely Benign

    • Common human variants, typically seen in the general population

    • Example: synonymous or missense mutations that do not impact gene function

    • Not reported on test results; indicated as "negative" or "normal"

    • Pathogenic or Likely Pathogenic

    • Variants with strong evidence of disease association and functional impact on the gene

    • Clinically treated as positive results, leading to diagnoses or carrier status

    • Variants of Uncertain Significance (VUS)

    • Represents a major challenge in clinical genetics

    • Insufficient evidence to classify as benign or pathogenic; may cause anxiety and unnecessary healthcare costs

    • As testing increases, the frequency of VUS findings also rises

Factors Considered in Variant Classification

  • Questions genetics providers ask regarding variants:

    • Does the variant alter the amino acid sequence, and what is the nature of that alteration?

    • What is the evolutionary conservation of the variant site across species?

    • Is the variant predicted to be damaging to the protein?

    • Is the variant located in a functional domain of the gene?

    • Has the variant been previously reported in healthy individuals or diseased populations?

  • In Silico Predictors

    • Computer programs that estimate the potential impact of genetic variants on protein function

    • Consider evolutionary conservation, location, and expected biochemical consequences

    • Limitations due to variability in predictions from different programs

  • Functional and Segregation Data

    • Family studies help understand whether a variant segregates with disease in affected individuals

  • De Novo Variants

    • Variants that occur spontaneously and are not inherited from parents

    • Can strongly indicate potential pathogenicity if present in a child but absent in parents

Confidence Levels in Variant Classification

  • Consensus Criteria and Point System

    • Points are assigned based on evidence from different categories (population data, computational data, functional studies, etc.)

    • Strong evidence for a variant being pathogenic includes high frequency in patients versus general population

    • Strong evidence for a benign classification includes high frequency in healthy individuals for a penetrant disease

    • Specific criteria designations (e.g., PS4 for pathogenic evidence, BS2 for benign evidence)

    • Final designation of variants includes classifications of Pathogenic, Likely Pathogenic, Benign, or Likely Benign

  • Variants with insufficient or contradictory evidence are categorized as VUS

Real-World Example: TTN Gene Variant

  • A case of an individual with a variant in the TTN gene associated with multiple disorders

    • Initial symptoms included weakness in skeletal muscles and respiratory insufficiency

    • Analysis of the variant c.1396C>T leading to a premature stop signal

    • The interpretation indicated a loss-of-function variant, but wasn’t linked to the presenting symptoms

    • Follow-up recommendations included checking for heart conditions associated with the variant rather than confirming the suspected skeletal muscle disease

Variants of Uncertain Significance (VUS)

  • Common occurrence in genetic testing, especially in pediatric cohorts

  • Study shows very high frequency of VUS (36% in a pediatric epilepsy cohort)

  • Underrepresented ethnic groups show a disproportionate frequency of VUS due to historical lack of representation in genetic databases

  • Calls for better representation in genetic research to alleviate uncertainty in test results

Risks of Over-Classification of Variants

  • Pressure on healthcare providers to provide definitive answers can lead to over-classification of variants

    • Importance of adhering to strict criteria to avoid misclassification, which can lead to harmful outcomes for patients

  • Real-world implications include patients undergoing unnecessary preventative procedures based on misclassified variants

  • Genetic counselors must not only classify variants accurately but also provide clinical interpretation based on the individual patient's context

  • The need for ongoing updates to classifications based on new evidence as more data becomes available

Conclusion

  • Understanding genetic variant interpretation is crucial for healthcare professionals.

  • Distinguishing between benign, pathogenic, and uncertain variants requires comprehensive analysis and established guidelines.

  • Awareness and consideration of ethical implications, population diversity, and societal impacts are essential in genetics practice.