Sequencing as a first-line methodology for cystic fibrosis carrier screening

Genet Med. 2019 Nov;21(11):2569-2576. doi: 10.1038/s41436-019-0525-y. Epub 2019 Apr 30.

Abstract

Purpose: Medical society guidelines recommend offering genotyping-based cystic fibrosis (CF) carrier screening to pregnant women or women considering pregnancy. We assessed the performance of sequencing-based CF screening relative to genotyping, in terms of analytical validity, clinical validity, clinical impact, and clinical utility.

Methods: Analytical validity was assessed using orthogonal confirmation and reference samples. Clinical validity was evaluated using the CFTR2 database. Clinical impact was assessed using ~100,000 screened patients. Three screening strategies were compared: genotyping 23 guideline-recommended variants ("CF23"), sequencing all coding bases in CFTR ("NGS"), and sequencing with large copy-number variant (CNV) identification ("NGS + CNV"). Clinical utility was determined via self-reported actions of at-risk couples (ARCs).

Results: Analytical accuracy of NGS + CNV was 100% for SNVs, indels, and CNVs; interpretive clinical specificity relative to CFTR2 was 99.5%. NGS + CNV detected 58 ARCs, 18 of whom would have gone undetected with CF23 alone. Most ARCs (89% screened preconceptionally, 56% prenatally) altered pregnancy management, and no significant differences were observed between ARCs with or without at least one non-CF23 variant.

Conclusion: Modern NGS and variant interpretation enable accurate sequencing-based CF screening. Limiting screening to 23 variants does not improve analytical validity, clinical validity, or clinical utility, but does fail to detect approximately 30% (18/58) of ARCs.

Keywords: carrier screening; cystic fibrosis; sequencing.

MeSH terms

  • Adult
  • Cystic Fibrosis / diagnosis*
  • Cystic Fibrosis / genetics*
  • DNA Copy Number Variations / genetics
  • Female
  • Genetic Testing / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • INDEL Mutation / genetics
  • Mutation / genetics
  • Pregnancy
  • Sensitivity and Specificity