Interest of exome sequencing trio‐like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases

• Published in: Molecular genetics & genomic medicine Vol. 9; no. 12; pp. e1836 - n/a
• Main Authors: Tran Mau‐Them, Frederic, Duffourd, Yannis, Vitobello, Antonio, Bruel, Ange‐Line, Denommé‐Pichon, Anne‐Sophie, Nambot, Sophie, Delanne, Julian, Moutton, Sebastien, Sorlin, Arthur, Couturier, Victor, Bourgeois, Valentin, Chevarin, Martin, Poe, Charlotte, Mosca‐Boidron, Anne‐Laure, Callier, Patrick, Safraou, Hana, Faivre, Laurence, Philippe, Christophe, Thauvin‐Robinet, Christel
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.12.2021; John Wiley and Sons Inc; Wiley
• Subjects: cost effectiveness; Deoxyribonucleic acid; Diabetes; Diagnosis; Disease; DNA; DNA sequencing; exome sequencing; Genetic Markers; Genetic Predisposition to Disease; Genetic Testing; Genome-Wide Association Study; Humans; Inflammatory bowel disease; Intellectual disabilities; Laboratories; Original; Parents & parenting; Rare diseases; Rare Diseases - diagnosis; Rare Diseases - genetics; Reproducibility of Results; Research Design; Segregations; Sensitivity and Specificity; Sequence Analysis, DNA; Translation; Translational Research, Biomedical - methods; Translational Research, Biomedical - standards; trio‐like strategy; parental‐pool strategy; Whole Exome Sequencing - methods; Whole Exome Sequencing - standards; Workflow; rare diseases; exome sequencing; trio-like strategy; parental-pool strategy; cost effectiveness
• ISSN: 2324-9269; 2324-9269
• DOI: 10.1002/mgg3.1836

Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders. Conclusions Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.