A novel target enrichment strategy in next-generation sequencing through 7-deaza-dGTP-resistant enzymatic digestion

BMC Research Notes

Yanjuan Xu¹  Xiaofeng Fan²  Adrian M. Di Bisceglie²  Peng Peng³ 

[1] Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, 63104, St. Louis, MO, USA;Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, 63104, St. Louis, MO, USA;Saint Louis University Liver Center, Saint Louis University School of Medicine, 63104, St. Louis, MO, USA;Division of Gastroenterology & Hepatology, Department of Internal Medicine, Saint Louis University School of Medicine, 63104, St. Louis, MO, USA;Wuhan Pulmonary Hospital, 430030, Wuhan, Hubei, China;

关键词: Next-generation sequencing;    Target enrichment;    7-deaza-2′-deoxyguanosine 5′-triphosphate;    Hepatitis B virus;   

DOI  :  10.1186/s13104-020-05292-y

来源: Springer

【 摘 要 】

ObjectiveOwing to the overwhelming dominance of human and commensal microbe sequences, low efficiency is a major concern in clinical viral sequencing using next-generation sequencing. DNA composed of 7-deaza-2′-deoxyguanosine 5′-triphosphate (c7dGTP), an analog of deoxyguanosine triphosphate (dGTP), is resistant to selective restriction enzymes. This characteristic has been utilized to develop a novel strategy for target enrichment in next-generation sequencing.ResultsThe new enrichment strategy is named target enrichment via enzymatic digestion in next-generation sequencing (TEEDseq). It combined 7-deaza-2′-deoxyguanosine 5′-triphosphate (c7dGTP)-involved primer extension, splinter-assisted intracellular cyclization, c7dGTP)-resistant enzymatic digestion, and two-phase rolling cycle amplification. We first estimated c7dGTP for its efficiency in PCR amplification and its resistance to three restriction enzymes, AluI, HaeIII, and HpyCH4V. We then evaluated TEEDseq using a serum sample spiked with a 1311-bp hepatitis B virus (HBV) fragment. TEEDseq achieved an HBV on-target rate of 3.31 ± 0.39%, which was equivalent to 454× the enrichment of direct Illumina sequencing. Therefore, the current study has provided a concept proof for TEEDseq as an alternative option for clinical viral sequencing that requires an enrichment in next-generation sequencing.

【 授权许可】

CC BY