Journal
SCIENTIFIC REPORTS
Volume 7, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/srep37984
Keywords
-
Categories
Funding
- Instituto de Salud Carlos III (ISCIII, MINECO) [PI13/00285, RD12/0036/0008, PIE13/00022, RD12/0036/0031]
- FEDER funds/European Regional Development Fund (ERDF) - a way to Build Europe-// FONDOS FEDER una manera de hacer Europa
- Generalitat de Catalunya (Government of Catalonia) [2014SGR338]
- Asociacion Espanola Contra el Cancer
- Spanish Society of Medical Oncology grant
- ISCIII Ministerio de Economia y Competitividad [PT13/0001/0044]
Ask authors/readers for more resources
Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c. 255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available