Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods. Issue 7 (July 2018)

• Record Type: Journal Article
• Authors: Sloan, Daniel B.; Broz, Amanda K.; Sharbrough, Joel; Wu, Zhiqiang
• Is Part Of: Trends in biotechnology. Volume 36:Issue 7(2018)
• Page Start: 729
• Page End: 740
• Publication Date: 2018-07
• Subjects: high-fidelity DNA sequencing -- oxidative damage -- rare variants -- subclonal mutations; Biotechnology -- Periodicals; Biochemical engineering -- Periodicals; Genetic engineering -- Periodicals; Industrial microbiology -- Periodicals; 660.605
• DOI: 10.1016/j.tibtech.2018.02.009
• Languages: English
• ISSNs: 0167-7799

Abstract

Abstract : There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologies are error prone, resulting in high noise thresholds. Most DNA sequencing methods are also generally incapable of identifying chemically modified bases arising from DNA damage. In recent years, numerous specialized modifications to sequencing methods have been developed to address these shortcomings. Here, we review this landscape of emerging techniques, highlighting their respective strengths, weaknesses, and target applications. Highlights: Detection of rare mutations and site-specific modifications/damage in DNA is now plausible because of advances in high-throughput sequencing technologies, but sequencing error rates have remained a major impediment and set undesirably high noise thresholds for detection. Numerous modified library construction methods have recently been developed to generate redundant sequences from each original DNA fragment and thereby suppress error rates. Further elaborations such as circle sequencing, duplex sequencing, and locus-specific targeting have made improvements to yield and/or accuracy and broadened the range of applications. Additional sequencing methods have been developed to identify low-frequency chemical modifications to bases and nucleotides at a site-specific level.