Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification

• Published in: Clinical chemistry (Baltimore, Md.) Vol. 64; no. 7; pp. 1063 - 1073
• Main Authors: Hogan, Gregory J, Vysotskaia, Valentina S, Beauchamp, Kyle A, Seisenberger, Stefanie, Grauman, Peter V, Haas, Kevin R, Hong, Sun Hae, Jeon, Diana, Kash, Shera, Lai, Henry H, Melroy, Laura M, Theilmann, Mark R, Chu, Clement S, Iori, Kevin, Maguire, Jared R, Evans, Eric A, Haque, Imran S, Mar-Heyming, Rebecca, Kang, Hyunseok P, Muzzey, Dale
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-07-2018
• Subjects: Bioinformatics; Complexity; Congenital diseases; Copy number; Cystic fibrosis; Disease; Fetuses; FMR1 protein; Gene sequencing; Genes; Genetic screening; Genetics; Genomes; Genomics; Haplotypes; Hyperplasia; Identification; Laboratories; Mathematical analysis; Molecular chains; Parents; Pregnancy; Risk assessment; Saliva; Screening; Sensitivity analysis
• ISSN: 0009-9147; 1530-8561
• DOI: 10.1373/clinchem.2018.286823

By identifying pathogenic variants across hundreds of genes, expanded carrier screening (ECS) enables prospective parents to assess the risk of transmitting an autosomal recessive or X-linked condition. Detection of at-risk couples depends on the number of conditions tested, the prevalence of the respective diseases, and the screen's analytical sensitivity for identifying disease-causing variants. Disease-level analytical sensitivity is often <100% in ECS tests because copy number variants (CNVs) are typically not interrogated because of their technical complexity.
We present an analytical validation and preliminary clinical characterization of a 235-gene sequencing-based ECS with full coverage across coding regions, targeted assessment of pathogenic noncoding variants, panel-wide CNV calling, and specialized assays for technically challenging genes. Next-generation sequencing, customized bioinformatics, and expert manual call review were used to identify single-nucleotide variants, short insertions and deletions, and CNVs for all genes except
and those whose low disease incidence or high technical complexity precluded novel variant identification or interpretation.
Screening of 36859 patients' blood or saliva samples revealed the substantial impact on fetal disease-risk detection attributable to novel CNVs (9.19% of risk) and technically challenging conditions (20.2% of risk), such as congenital adrenal hyperplasia. Of the 7498 couples screened, 335 were identified as at risk for an affected pregnancy, underscoring the clinical importance of the test. Validation of our ECS demonstrated >99% analytical sensitivity and >99% analytical specificity.
Validated high-fidelity identification of different variant types-especially for diseases with complicated molecular genetics-maximizes at-risk couple detection.