Title:
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Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer
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Author:
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Feliubadaló i Elorza, Maria Lídia; Tonda, Raúl; Gausachs, Mireia; Trotta, Jean Rémi; Castellanos, Elisabeth; López Dóriga Guerra, Adriana; Teulé-Vega, Àlex; Tornero, Eva; Valle, Jesús del; Gel, Bernat; Gut, Marta; Pineda Riu, Marta; González, Sara; Menéndez Vilà, Mireia; Navarro, Matilde; Capellá, G. (Gabriel); Gut, Ivo; Serra, Eduard; Brunet, Joan; Beltran, Sergi; Lázaro García, Conxi
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Abstract:
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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. Eightythree 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. |
Subject(s):
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-Càncer -Malalties hereditàries -Diagnòstic -Cribratge genètic -Cancer -Genetic diseases -Diagnosis -Genetic screening |
Rights:
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cc-by (c) Feliubadaló i Elorza, Maria Lídia et al., 2017
http://creativecommons.org/licenses/by/3.0/es |
Document type:
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Article Article - Published version |
Published by:
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Nature Publishing Group
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