Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer Article Swipe
Lídia Feliubadaló
,
Raúl Tonda
,
Mireia Gausachs
,
Jean-Rémi Trotta
,
Elisabeth Castellanos
,
Adriana López‐Doriga
,
Àlex Teulé
,
Eva Tornero
,
Jesús Del Valle
,
Bernat Gel
,
Marta Gut
,
Marta Pineda
,
Sara González
,
Mireia Menéndez
,
Matilde Navarro
,
Gabriel Capellá
,
Marta Gut
,
Eduard Serra
,
Joan Brunet
,
Sergi Beltrán
,
Conxi Lázaro
·
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1038/srep37984
YOU?
·
· 2017
· Open Access
·
· DOI: https://doi.org/10.1038/srep37984
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.
Related Topics
Concepts
Exome sequencing
Exome
Genetics
MSH6
Computational biology
Biology
DNA sequencing
Genetic testing
Mutation
Gene
Germline mutation
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/srep37984
- https://www.nature.com/articles/srep37984.pdf
- OA Status
- gold
- Cited By
- 50
- References
- 40
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2568054806
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2568054806Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1038/srep37984Digital Object Identifier
- Title
-
Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary CancerWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2017Year of publication
- Publication date
-
2017-01-04Full publication date if available
- Authors
-
Lídia Feliubadaló, Raúl Tonda, Mireia Gausachs, Jean-Rémi Trotta, Elisabeth Castellanos, Adriana López‐Doriga, Àlex Teulé, Eva Tornero, Jesús Del Valle, Bernat Gel, Marta Gut, Marta Pineda, Sara González, Mireia Menéndez, Matilde Navarro, Gabriel Capellá, Marta Gut, Eduard Serra, Joan Brunet, Sergi Beltrán, Conxi LázaroList of authors in order
- Landing page
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https://doi.org/10.1038/srep37984Publisher landing page
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https://www.nature.com/articles/srep37984.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.nature.com/articles/srep37984.pdfDirect OA link when available
- Concepts
-
Exome sequencing, Exome, Genetics, MSH6, Computational biology, Biology, DNA sequencing, Genetic testing, Mutation, Gene, Germline mutationTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
50Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 4, 2024: 7, 2023: 2, 2022: 3, 2021: 7Per-year citation counts (last 5 years)
- References (count)
-
40Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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