Dual-molecular barcode sequencing detects rare variants in tumor and cell free DNA in plasma

Abstract

conventional next generation sequencing analysis has provided important insights into cancer genetics. However, the detection of rare (low allele fraction) variants remains difficult because of the error-prone nucleotide changes derived from sequencing/pcR errors. to eliminate the false-positive variants and detect genuine rare variants, sequencing technology combined with molecular barcodes will be useful. Here, we used the newly developed dual-molecular barcode technology (ion AmpliSeq HD) to analyze somatic mutations in 24 samples (12 tumor tissues and 12 plasma) from 12 patients with biliary-pancreatic and non-small cell lung cancers. We compared the results between next generation sequencing analysis with or without molecular barcode technologies. the variant allele fraction (VAf) between non-molecular barcode and molecular barcode sequencing was correlated in plasma DnA (R 2 = 0.956) and tumor (R 2 = 0.935). Both methods successfully detected high VAF mutations, however, rare variants were only identified by molecular barcode sequencing and not by non-molecular barcode sequencing. Some of these rare variants in tumors were annotated as pathogenic, and therefore subclonal driver mutations could be observed. Furthermore, the very low VAF down to 0.17% were identified in cell free DNA in plasma. These results demonstrate that the dual molecular barcode sequencing technologies can sensitively detect rare somatic mutations, and will be important in the investigation of the clonal and subclonal architectures of tumor heterogeneity. Cancer acquires somatic mutations during the evolution of a tumor. Subclonal mutants are considered to be associated with drug resistance in various cancers, including non-small cell lung, breast and colorectal cancers 1,2. Cell free DNA (cfDNA) in plasma contains a small fraction of tumor DNA with tumor-derived mutations, which is called circulating tumor DNA. Plasma cfDNA is useful for monitoring tumor recurrence, estimating treatment effects and identifying drug-resistant mutations 3. However, only low levels of mutated alleles are present in the overall cfDNA circulating in blood. Therefore, the development of highly sensitive methods to detect rare variants is required. Various sensitive and accurate methods have been developed for the detection and quantification of mutated alleles in low abundance among high amounts of the wild-type allele 4. These methods are important for medical oncology, cancer research, infectious disease and microbial studies. To investigate the tumor heterogeneity and cfDNA in liquid biopsy, highly sensitive assays are necessary for detecting somatic mutations with low variant allele fraction (VAF). Droplet digital PCR, chip-based digital PCR and beads, emulsion, amplification, magnetics and flow cytometry (BEAMing) assays can sensitively detect rare mutations present at 0.1% VAF 4. Digital PCR and BEAMing have been applied for well-known pathogenic variants and detect several types of variants simultaneously; however, these may not be suitable for target...

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Primary Driver Mutations in GTF2I Specific to the Development of Thymomas

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