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Laboratory considerations for prenatal genetic testing.

Karen Wou1, Wendy K Chung1, Ronald J Wapner2

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Summary

New genetic tests like cell-free DNA (cfDNA) screening and chromosomal microarray are entering clinical practice. Consistent reporting of predictive values, fetal fraction, and variants of uncertain significance (VUS) is crucial for accurate genetic testing.

Keywords:
Genetic testingMaternal-fetal medicinePrenatal diagnosisPrenatal genetics

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Area of Science:

  • Clinical Genetics
  • Molecular Diagnostics
  • Prenatal Testing

Background:

  • Rapid integration of novel genetic tests into clinical care lacks standardization in laboratory practices and reporting.
  • Emerging genetic technologies, including non-invasive prenatal screening (NIPS) and chromosomal microarray (CMA), offer advanced diagnostic capabilities but present unique challenges.
  • Whole-exome and whole-genome sequencing are on the cusp of clinical adoption, necessitating thorough investigation of associated complexities.

Purpose of the Study:

  • To highlight the inconsistencies in laboratory testing and reporting for new genetic technologies.
  • To emphasize the importance of reporting key performance metrics for genetic tests.
  • To address the challenges and considerations for the clinical implementation of advanced genetic sequencing techniques.

Main Methods:

  • Review of current practices and limitations in genetic testing, including cell-free DNA (cfDNA) screening, chromosomal microarray (CMA), whole-exome sequencing (WES), and whole-genome sequencing (WGS).
  • Analysis of critical reporting parameters such as positive and negative predictive values, fetal fraction, and variants of uncertain significance (VUS).
  • Discussion of the advantages and disadvantages of various laboratory platforms and their implications for clinical decision-making.

Main Results:

  • cfDNA screening tests for aneuploidies and microdeletions require reporting of predictive values and fetal fraction due to inherent false positives and negatives.
  • Chromosomal microarray analysis can identify clinically relevant information beyond karyotyping but may yield variants of uncertain significance (VUS) in a small percentage of cases, necessitating clear reporting policies.
  • Whole-exome and whole-genome sequencing require further investigation into VUS, incidental findings, and genotype-phenotype correlations before routine clinical use.

Conclusions:

  • Standardization of laboratory testing and reporting is essential for the reliable clinical application of new genetic technologies.
  • Clear communication of test performance metrics and potential limitations, such as VUS, is critical for informed clinical interpretation and patient management.
  • Further research and guideline development are needed to ensure the safe and effective integration of advanced sequencing technologies into routine healthcare.