DNA-pools targeted-sequencing as a robust cost-effective method to detect rare variants: application to dilated cardiomyopathy genetic diagnosis
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 G...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
30 October 2023
|
| Edition: | Online version of record before inclusion in an issue |
| In: |
Clinical genetics
Year: 2023, Pages: 1-5 |
| ISSN: | 1399-0004 |
| DOI: | 10.1111/cge.14427 |
| Online Access: | Verlag, kostenfrei, Volltext: https://doi.org/10.1111/cge.14427 Verlag, kostenfrei, Volltext: https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.14427 
|
| Author Notes: | Claire Perret, Carole Proust, Ulrike Esslinger, Flavie Ader, Jan Haas, Jean-François Pruny, Richard Isnard, Pascale Richard, David-Alexandre Trégouët, Philippe Charron, François Cambien, Eric Villard |
| Summary: | 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. |
|---|---|
| Item Description: | Gesehen am 08.12.2023 |
| Physical Description: | Online Resource |
| ISSN: | 1399-0004 |
| DOI: | 10.1111/cge.14427 |