Performance comparison of four commercial human whole-exome capture platforms

Daichi Shigemizu, Yukihide Momozawa, Testuo Abe, Takashi Morizono, Keith A. Boroevich, Sadaaki Takata, Kyota Ashikawa, Michiaki Kubo, Tatsuhiko Tsunoda

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

Whole exome sequencing (WXS) is widely used to identify causative genetic mutations of diseases. However, not only have several commercial human exome capture platforms been developed, but substantial updates have been released in the past few years. We report a performance comparison for the latest release of four commercial platforms, Roche/NimbleGen's SeqCap EZ Human Exome Library v3.0, Illumina's Nextera Rapid Capture Exome (v1.2), Agilent's SureSelect XT Human All Exon v5 and Agilent's SureSelect QXT, using the same DNA samples. Agilent XT showed the highest target enrichment efficiency and the best SNV and short indel detection sensitivity in coding regions with the least amount of sequencing. Agilent QXT had slightly inferior target enrichment than Agilent XT. Illumina, with additional sequencing, detected SNVs and short indels at the same quality as Agilent XT, and showed the best performance in coverage of medically interesting mutations. NimbleGen detected more SNVs and indels in untranslated regions than the others. We also found that the platforms, which enzymatically fragment the genomic DNA (gDNA), detected more homozygous SNVs than those using sonicated gDNA. We believe that our analysis will help investigators when selecting a suitable exome capture platform for their particular research.

Original languageEnglish
Article number12742
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 03-08-2015

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Exome
DNA
Untranslated Regions
Mutation
Inborn Genetic Diseases
Exons
Research Personnel
Research

All Science Journal Classification (ASJC) codes

  • General

Cite this

Shigemizu, D., Momozawa, Y., Abe, T., Morizono, T., Boroevich, K. A., Takata, S., ... Tsunoda, T. (2015). Performance comparison of four commercial human whole-exome capture platforms. Scientific Reports, 5, [12742]. https://doi.org/10.1038/srep12742
Shigemizu, Daichi ; Momozawa, Yukihide ; Abe, Testuo ; Morizono, Takashi ; Boroevich, Keith A. ; Takata, Sadaaki ; Ashikawa, Kyota ; Kubo, Michiaki ; Tsunoda, Tatsuhiko. / Performance comparison of four commercial human whole-exome capture platforms. In: Scientific Reports. 2015 ; Vol. 5.
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Shigemizu, D, Momozawa, Y, Abe, T, Morizono, T, Boroevich, KA, Takata, S, Ashikawa, K, Kubo, M & Tsunoda, T 2015, 'Performance comparison of four commercial human whole-exome capture platforms', Scientific Reports, vol. 5, 12742. https://doi.org/10.1038/srep12742

Performance comparison of four commercial human whole-exome capture platforms. / Shigemizu, Daichi; Momozawa, Yukihide; Abe, Testuo; Morizono, Takashi; Boroevich, Keith A.; Takata, Sadaaki; Ashikawa, Kyota; Kubo, Michiaki; Tsunoda, Tatsuhiko.

In: Scientific Reports, Vol. 5, 12742, 03.08.2015.

Research output: Contribution to journalArticle

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Shigemizu D, Momozawa Y, Abe T, Morizono T, Boroevich KA, Takata S et al. Performance comparison of four commercial human whole-exome capture platforms. Scientific Reports. 2015 Aug 3;5. 12742. https://doi.org/10.1038/srep12742