Saliva as a comparable-quality source of DNA for Whole Exome Sequencing on Ion platforms

Omar Ibrahim, Heidi G. Sutherland, Larisa M. Haupt, Lyn R. Griffiths

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Background: Whole Exome Sequencing (WES) utilises overlapping fragments prone to sequencing artefacts. Saliva, a non-invasive source of DNA, has been successfully used in WES studies on various platforms. This study explored the validity and quality of DNA sourced from saliva compared to whole blood on an Ion Platform. Methods: DNA was extracted from both sample types from four individuals. WES, performed on the Ion Proton platform was assessed for quality metrics (Depth, Genotyping Quality, etc.) and variant identification for the same source sample-pairs. Results: No significant differences in quality metrics were identified between data obtained from whole blood and saliva samples, with several saliva samples demonstrating higher coverage depth. Variants within the same sample, from the two genomic DNA sources, had an average concordance similar to other studies and platforms with different chemistry. Conclusion: Saliva-extracted DNA provides comparable sequencing quality to whole blood for WES on Ion Torrent Platforms.

Original languageEnglish
Pages (from-to)1437-1443
Number of pages7
JournalGenomics
Volume112
Issue number2
DOIs
Publication statusPublished - Mar 2020
Externally publishedYes

Keywords

  • DNA
  • Ion Torrent
  • NGS
  • Saliva
  • WES
  • Whole blood

Cite this