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A comprehensive strategy for exome-based preconception carrier screening.

Suzanne C E H Sallevelt1, Bart de Koning1,2, Radek Szklarczyk2

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Whole-exome sequencing (WES) enables genome-wide preconception carrier screening (PCS). A novel filter strategy efficiently identifies pathogenic mutations in couples, making WES practical for clinical use.

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Area of Science:

  • Genetics
  • Genomic Medicine
  • Reproductive Health

Background:

  • Whole-exome sequencing (WES) offers potential for comprehensive preconception carrier screening (PCS).
  • Developing efficient methods to analyze WES data for PCS is crucial for clinical application.

Purpose of the Study:

  • To propose and validate a filter strategy for rapidly identifying pathogenic mutations from WES data for preconception carrier screening.
  • To assess the applicability of WES-based PCS for both consanguineous and nonconsanguineous couples.

Main Methods:

  • Developed a filter strategy using WES data from consanguineous and nonconsanguineous couples.
  • Selected presumably pathogenic variants based on frequency, database annotations, and mutation type in shared genes and the female's X-chromosome.
  • Applied the strategy to additional couples and manually verified remaining variants.

Main Results:

  • The strategy yielded an average of 29 variants for consanguineous couples and 15 for nonconsanguineous couples in shared genes.
  • X-linked variant numbers were 3 per female for consanguineous and 1 for nonconsanguineous couples.
  • Manual verification quickly discarded most variants, leaving true pathogenic ones.

Conclusions:

  • Whole-exome sequencing is a viable tool for preconception carrier screening in both consanguineous and nonconsanguineous couples.
  • The proposed filter strategy effectively reduces the variant load to a manageable level for clinical settings.
  • Continuous curation of pathogenic mutation databases is essential to enhance WES-based PCS sensitivity; gene panels were unfavorable for filtering.