Non‐invasive prenatal testing (NIPT): Combination of copy number variant and gene analyses using an “in‐house” target enrichment next generation sequencing—Solution for non‐centralized NIPT laboratory?

• Published in: Prenatal diagnosis Vol. 43; no. 10; pp. 1320 - 1332
• Main Authors: Faldynová, Lucie, Walczysková, Sylwia, Černá, Dita, Kudrejová, Monika, Hilscherová, Šárka, Kaniová, Romana, Širůčková, Simona
• Format: Journal Article
• Language: English
• Published: Charlottesville Wiley Subscription Services, Inc 01.09.2023
• Subjects: Chromosomes; Copy number; Deoxyribonucleic acid; DNA; Enrichment; Fetuses; Genetics; Genomic analysis; Laboratories; Next-generation sequencing; Sensitivity analysis
• ISSN: 0197-3851; 1097-0223
• DOI: 10.1002/pd.6421

Abstract Objective Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non‐invasive prenatal testing (NIPT) facilities. Method From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell‐free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods. Results The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (‐/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell‐free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant. Conclusion The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data. Key points What is already known about this topic? Non‐invasive prenatal testing (NIPT) using a whole‐genome approach via next generation sequencing (NGS) to detect the fetal genome is currently standard practice. Copy number variant and gene analyses using targeted enrichment have previously been integrated with NIPT, but only in studies of cohorts of pregnant women from large prenatal care centers with sufficient positive and negative controls, and a strong bioinformatics background. What does this study add? Our team developed an unconventional NIPT method using a target enrichment design covering 135 genes associated with severe monogenic diseases combined with a backbone enabling detection of clinically significant chromosomal aberrations. We attempted to transfer the integrated NIPT platform to the environment of a regular genetics laboratory (not a specialized NIPT center) and to assess the informative value of the data for inclusion in the method in clinical practice.