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

Abstract

PurposeMedical 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.MethodsAnalytical 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).ResultsAnalytical 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.ConclusionModern 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.

Clinical experience with carrier screening in a general population: support for a comprehensive pan-ethnic approach

“…17 Our results show NGS-based CS is particularly advantageous for CF screening in East and South East Asians and African Americans because some of the most common variants in these groups are not included in the CF23 panel. 25,26 Likewise, our approach to SMA screening also allows for the identification of considerably more at-risk pregnancies, particularly among African Americans where identification of the g.27134T>G variant (linked to two copies of SMN1) facilitates identification of those at risk to be silent (2 + 0) carriers. We screened for disorders typically associated with AJ ancestry in non-AJ ethnicities, and for variants in genes with frequent disease occurrence but without standard panels, such as for DMD-related dystrophinopathies and hemoglobinopathies.…”

Bradykinin-Mediated Angioedema: An Update of the Genetic Causes and the Impact of Genomics

“…This is because heterozygous variants are technically more difficult to detect and analyze. A recent analytical validation of an NGS-based carrier screen for cystic fibrosis demonstrated that NGS enabled accurate detection of the causal variants, achieving high sensitivity and specificity compared to the established genetic screening methods (Beauchamp et al, 2019). According to the experience of the International Rare Diseases Research Consortium (IRDiRC), the utility of WES for rare disease gene identification is beyond any doubt (Boycott et al, 2017).…”

Expanded universal carrier screening and its implementation within a publicly funded healthcare service

“…These vary from using allele-specific testing such as genotyping arrays for a limited number of variants associated with a single AR disease gene (Picci et al 2010), to GWS to test all variants found in any number of AR genes (Punj et al 2018). A targeted approach simplifies variant interpretation and avoids variants of uncertain significance (VUS) but risks missing carriers if only a limited number of causative variants are genotyped (Stafler et al 2016;Beauchamp et al 2019a) and would require regular reviewing and updating. Additionally, there is wide variability between laboratories regarding which variants to report (Hoffman et al 2014), potentially resulting in substantial health disparities.…”