A unified DNA‐ and RNA‐based NGS strategy for the analysis of multiple types of variants at the dual nucleic acid level in solid tumors

Abstract

Background

Targeted next‐generation sequencing (NGS) is a powerful and suitable approach to comprehensively identify multiple types of variants in tumors. RNA‐based NGS is increasingly playing an important role in precision oncology. Both parallel and sequential DNA‐ and RNA‐based approaches are expensive, burdensome, and have long turnaround times, which can be impractical in clinical practice. A streamlined, unified DNA‐ and RNA‐based NGS approach is urgently needed in clinical practice.

Methods

A DNA/RNA co‐hybrid capture sequencing (DRCC‐Seq) approach was designed to capture pre‐capture DNA and RNA libraries in a single tube and convert them into one NGS library. The performance of the DRCC‐Seq approach was evaluated by a panel of reference standards and clinical samples.

Results

The average depth, DNA data ratio, capture ratio, and target coverage 250 (×) of the DNA panel data had a negative correlation with an increase in the proportion of RNA probes. The SNVs, indels, fusions, and MSI status were not affected by the proportion of RNA probes, but the copy numbers of the target genes were higher than expected in the standard materials, and many unexpected gene amplifications were found using D:R (1:2) and D:R (1:4) probe panels. The optimal ratio of DNA and RNA probes in the combined probe panel was 1:1 using the DRCC‐Seq approach. The DRCC‐Seq approach was feasible and reliable for detecting multiple types of variants in reference standards and real‐world clinical samples.

Conclusions

The DRCC‐Seq approach is more cost‐effective, with a shorter turnaround time and lower labor requirements than either parallel or sequential targeted DNA NGS and RNA NGS. It is feasible to identify multiple genetic variations at the DNA and RNA levels simultaneously in clinical practice.

Abstract

Genomic DNA was processed to pre‐capture the DNA NGS library through fragmentation, adaptor ligation, and PCR amplification. The total RNA was subjected to fragmentation and reverse transcription to generate the double‐stranded, fragmented cDNA. The pre‐capture RNA library was prepared through adaptor ligation and PCR amplification. The different indexes or barcodes were used during the DNA and RNA library preparation process to identify the DNA and RNA data from the same sample. The pre‐capture DNA and RNA libraries were mixed. Then, the library mixture was captured using the combined custom DNA and RNA panel probes in a single tube and converted to one sequencing library.