Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq

Markham, John; Fellowes, Andrew; Green, Thomas; Leal, José Luis; Legaie, Roxane; Cullerne, Darren; Morris, Tessa Altair; John, Thomas; Solomon, Ben; Fox, Stephen B.

doi:10.1038/s41416-022-02105-w

Cited by 3 publications

(2 citation statements)

References 44 publications

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“…Currently, in many clinical laboratories, DNA‐based targeted NGS analysis has become a routine approach for mutation detection instead of multiple different traditional molecular assays, such as Sanger sequencing and qPCR. Recently, several studies demonstrated that RNA NGS was a valuable addition to identify fusions and exon‐skipping events, especially for novel or unusual gene fusions 25,28,35–37 . A study by Benayed et al.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, several studies demonstrated that RNA NGS was a valuable addition to identify fusions and exon-skipping events, especially for novel or unusual gene fusions. 25,28,[35][36][37] A study by Benayed et an RNA-based approach detected a higher proportion of MET exon 14 skipping cases than did DNA-based analysis (4.2% versus 1.3%). 17 Another study showed that treatment options were changed by adding RNA NGS analysis in 5% of all NSCLC patients, in which 22% never smoked.…”

Section: Performance Of the Drcc-seq Approach In Real-world Clinical ...mentioning

confidence: 98%

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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

Chen,

Wang,

Zhang

et al. 2023

Clinical Laboratory Analysis

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BackgroundTargeted 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.MethodsA 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.ResultsThe 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.ConclusionsThe 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.

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Section: Discussionmentioning

confidence: 99%

Section: Performance Of the Drcc-seq Approach In Real-world Clinical ...mentioning

confidence: 98%

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

Chen,

Wang,

Zhang

et al. 2023

Clinical Laboratory Analysis

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Tumour mutational burden: clinical utility, challenges and emerging improvements

Budczies,

Kazdal,

Menzel

et al. 2024

Nat Rev Clin Oncol

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Adaptation and Experimental Validation of Clinical RNA Sequencing Protocol Oncobox for MGI DNBSEQ-G50 Platform

Khilal,

Suntsova,

Knyazev

et al. 2023

Biochem. Moscow Suppl. Ser. B

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Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq

Cited by 3 publications

References 44 publications

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

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

Tumour mutational burden: clinical utility, challenges and emerging improvements

Adaptation and Experimental Validation of Clinical RNA Sequencing Protocol Oncobox for MGI DNBSEQ-G50 Platform

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