DNA-pools targeted-sequencing as a robust cost-effective method to detect rare variants: Application to dilated cardiomyopathy genetic diagnosis.

Autor: Perret C; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France., Proust C; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France., Esslinger U; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France., Ader F; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France.; APHP, UF Cardiogénétique et Myogénétique, Service de Biochimie Métabolique, Hôpital Universitaire Pitié-Salpêtrière, Paris, France., Haas J; Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany.; DZHK (German Centre for Cardiovascular Research), Berlin, Germany., Pruny JF; APHP, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France., Isnard R; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France.; APHP, Cardiology Department, Pitié-Salpêtrière Hospital, Paris, France., Richard P; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France.; APHP, UF Cardiogénétique et Myogénétique, Service de Biochimie Métabolique, Hôpital Universitaire Pitié-Salpêtrière, Paris, France., Trégouët DA; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France., Charron P; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France.; APHP, Centre de Référence Maladies Cardiaques Héréditaires, Hôpital Pitié-Salpêtrière, Paris, France.; APHP, Cardiology Department, Pitié-Salpêtrière Hospital, Paris, France., Cambien F; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France., Villard E; Sorbonne Université, INSERM, UMR-S1166, Research Unit on Cardiovascular and Metabolic Diseases, Paris, France.; ICAN Institute for Cardiometabolism and Nutrition, Paris, France.
Jazyk: angličtina
Zdroj: Clinical genetics [Clin Genet] 2024 Feb; Vol. 105 (2), pp. 185-189. Date of Electronic Publication: 2023 Oct 30.
DOI: 10.1111/cge.14427
Abstrakt: Dilated cardiomyopathy (DCM) is a heart disease characterized by left ventricular dilatation and systolic dysfunction. In 30% of cases, pathogenic variants, essentially private to each patient, are identified in at least one of almost 50 reported genes. Thus, while costly, exons capture-based Next Generation Sequencing (NGS) of a targeted gene panel appears as the best strategy to genetically diagnose DCM. Here, we report a NGS strategy applied to pools of 8 DNAs from DCM patients and validate its robustness for rare variants detection at 4-fold reduced cost. Our pipeline uses Freebayes to detect variants with the expected 1/16 allele frequency. From the whole set of detected rare variants in 96 pools we set the variants quality parameters optimizing true positives calling. When compared to simplex DNA sequencing in a shared subset of 50 DNAs, 96% of SNVs/InsDel were accurately identified in pools. Extended to the 384 DNAs included in the study, we detected 100 variants (ACMG class 4 and 5), mostly in well-known morbid gene causing DCM such as TTN, MYH7, FLNC, and TNNT2. To conclude, we report an original pool-sequencing NGS method accurately detecting rare variants. This innovative approach is cost-effective for genetic diagnostic in rare diseases.
(© 2023 The Authors. Clinical Genetics published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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