New insights into the performance of human whole-exome capture platforms

Meienberg, Janine; Zerjavic, Katja; Keller, Irene; Okoniewski, Michał; Patrignani, Andrea; Ludin, Katja; Xu, Zhenyu; Steinmann, Beat; Carrel, Thierry; Röthlisberger, Benno; Schlapbach, Ralph; Bruggmann, Rémy; Mátyás, Gábor

doi:10.1093/nar/gkv216

Cited by 110 publications

(98 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The critical difference between panel sequencing and WES is coverage. Under standard conditions, WES aims for a mean read depth of around 100×2930, while panel sequencing generally targets a range of 200–1000×142731. Assuming a “standard run” for both approaches, our study clearly demonstrates that the number of target region bases not reaching C30 is much higher in WES than in panel sequencing.…”

Section: Discussionmentioning

confidence: 99%

Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer

Feliubadaló

Tonda

Gausachs

et al. 2017

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 99%

Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer

Feliubadaló

Tonda

Gausachs

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Differences in hybridization efficiency during capture, due to GC content variation in the genome, account for the poor coverage of some target exon regions. DNA regions with nucleotide repeats may also result in coverage problems (19, 20). Pseudogenes, as for IKBKG and NCF1 , also hamper correct data generation.…”

Section: Generating Next Generation Sequencing Datamentioning

confidence: 99%

Exome and genome sequencing for inborn errors of immunity

Meyts

Bosch

Bolze

et al. 2016

Journal of Allergy and Clinical Immunology

166

148

View full text Add to dashboard Cite

The advent of next generation sequencing (NGS) in 2010 has transformed medicine and particularly the growing field of monogenic inborn errors of immunity, including primary immunodeficiencies (PID). NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with PID. Whole-exome sequencing (WES) is presently the most cost-effective approach for PID research and diagnostics, though whole genome sequencing (WGS) offers several advantages. The scientific or diagnostic challenge consists in selecting one or two candidate variants among thousands of NGS calls. Variant- and gene-level computational methods as well as immunological hypotheses can help to narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on three key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and the frequency cut-offs for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches, in order not to assign PID to false positives. Finding the needle in the haystack takes patience, prudence, and discernment.

show abstract

“…Targeted capture of genomic regions by oligonucleotide (oligo) 1 probes, followed by massively parallel sequencing (MPS) enables consistent sequencing reactions (1 ). However, some regions of interest have poor depth of coverage (DOC) (defined as Ͻ50ϫ in our laboratory) to no DOC after capture, leading to incomplete analysis of genes and, possibly, false negative test results (2 ).…”

Section: To the Editormentioning

confidence: 99%