Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings.Duplex sequencing technology is t...Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings.Duplex sequencing technology is the most commonly used approach in liquid biopsies.Unique molecular identifiers are attached to each double-stranded DNA template,followed by production of low-error consensus sequences to detect low frequency variants.However,high sequencing costs have hindered application of this approach in clinical practice.Here,we have developed an improved duplex sequencing approach called Sino Duplex,which utilizes a pool of adapters containing pre-defined barcode sequences to generate far fewer barcode combinations than with random sequences,and implemented a novel computational analysis algorithm to generate duplex consensus sequences more precisely.Sino Duplex increased the output of duplex sequencing technology,making it more cost-effective.We evaluated our approach using reference standard samples and cell-free DNA samples from lung cancer patients.Our results showed that Sino Duplex has high sensitivity and specificity in detecting very low allele frequency mutations.The source code for Sino Duplex is freely available at https://github.com/Sin Oncology/sinoduplex.展开更多
基金financed by Grant-in-aid for scientific research from the Guangzhou Science and Technology Plan projects of China(Grant No.201802020004)
文摘Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings.Duplex sequencing technology is the most commonly used approach in liquid biopsies.Unique molecular identifiers are attached to each double-stranded DNA template,followed by production of low-error consensus sequences to detect low frequency variants.However,high sequencing costs have hindered application of this approach in clinical practice.Here,we have developed an improved duplex sequencing approach called Sino Duplex,which utilizes a pool of adapters containing pre-defined barcode sequences to generate far fewer barcode combinations than with random sequences,and implemented a novel computational analysis algorithm to generate duplex consensus sequences more precisely.Sino Duplex increased the output of duplex sequencing technology,making it more cost-effective.We evaluated our approach using reference standard samples and cell-free DNA samples from lung cancer patients.Our results showed that Sino Duplex has high sensitivity and specificity in detecting very low allele frequency mutations.The source code for Sino Duplex is freely available at https://github.com/Sin Oncology/sinoduplex.
