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

Meienberg, Janine; Zerjavic, Katja; Keller, Irene; Okoniewski, Michal; Patrignani, Andrea; Ludin, Katja; Xu, Zhenyu; Steinmann, Beat; Carrel, Thierry; Röthlisberger, Benno; Schlapbach, Ralph; Bruggmann, Rémy; Matyas, Gabor (2015). New insights into the performance of human whole-exome capture platforms. Nucleic acids research, 43(11), e76. Oxford University Press 10.1093/nar/gkv216

[img]
Preview
Text
gkv216.pdf - Published Version
Available under License Creative Commons: Attribution (CC-BY).

Download (1MB) | Preview

Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most recent standard exome enrichment platforms from Agilent, NimbleGen and Illumina applied to six different DNA samples by two sequencing vendors per platform. Our results suggest that both Agilent and NimbleGen overall perform better than Illumina and that the high enrichment performance of Agilent is stable among samples and between vendors, whereas NimbleGen is only able to achieve vendor- and sample-specific best exome coverage. Moreover, the recent Agilent platform overall captures more coding exons with sufficient read depth than NimbleGen and Illumina. Due to considerable gaps in effective exome coverage, however, the three platforms cannot capture all known coding exons alone or in combination, requiring improvement. Our data emphasize the importance of evaluation of updated platform versions and suggest that enrichment-free whole genome sequencing can overcome the limitations of WES in sufficiently covering coding exons, especially GC-rich regions, and in characterizing structural variants.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > DCR Services > Genomics
04 Faculty of Medicine > Department of Cardiovascular Disorders (DHGE) > Clinic of Cardiovascular Surgery

UniBE Contributor:

Carrel, Thierry and Bruggmann, Rémy

Subjects:

600 Technology > 610 Medicine & health

ISSN:

0305-1048

Publisher:

Oxford University Press

Language:

English

Submitter:

Daniela Huber

Date Deposited:

03 Feb 2016 15:41

Last Modified:

26 Jun 2018 08:46

Publisher DOI:

10.1093/nar/gkv216

PubMed ID:

25820422

BORIS DOI:

10.7892/boris.75025

URI:

https://boris.unibe.ch/id/eprint/75025

Actions (login required)

Edit item Edit item
Provide Feedback