An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

Scolnick, Jonathan; Dimon, Michelle; Wang, I‐Ching; Huelga, Stephanie C.; Amorese, D.

doi:10.1371/journal.pone.0128916

Cited by 44 publications

(37 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As intron 8 of BRAF is captured in the FoundationOne assay, it can identify novel rearrangements of BRAF involving this region. Other targeted approaches to identify fusion proteins include target enrichment based RNA-seq analysis, where target enrichment can be accomplished by hybrid capture, single primer-extension technology, or the anchored multiplex polymerase chain reaction (PCR) approach (22,23).…”

Section: Discussionmentioning

confidence: 99%

BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma

Kulkarni

Al-Hraishawi

Simhadri

et al. 2017

Clinical Cancer Research

View full text Add to dashboard Cite

Purpose: Many patients with BRAF V600E mutant melanoma treated with BRAF inhibitors experience a rapid response, but ultimately develop resistance. Insight into the mechanism of resistance is critical for development of more effective treatment strategies.Experimental Design: Comprehensive genomic profiling of serial biopsies was performed in a patient with a BRAF V600E mutant metastatic melanoma who developed resistance to vemurafenib. An AGAP3-BRAF fusion gene, identified in the vemurafenib-resistant tumor, was expressed in BRAF V600E melanoma cell lines, and its effect on drug sensitivity was evaluated.Results: Clinical resistance to vemurafenib in a melanoma harboring a BRAF V600E mutation was associated with acquisition of an AGAP3-BRAF fusion gene. Expression of the AGAP3-BRAF fusion in BRAF V600E mutant melanoma cells induced vemurafenib resistance; however, these cells remained relatively sensitive to MEK inhibitors. The patient experienced clinical benefit following treatment with the combination of a BRAF and a MEK inhibitor. Rebiopsy of the tumor at a later time point, after BRAF and MEK inhibitors had been discontinued, showed loss of the AGAP3-BRAF fusion gene. Mixing experiments suggest that cells harboring both BRAF V600E and AGAP3-BRAF only have a fitness advantage over parental BRAF V600E cells during active treatment with a BRAF inhibitor.Conclusions: We report acquisition of a BRAF fusion as a novel mechanism of acquired resistance to vemurafenib in a patient with melanoma harboring a BRAF V600E mutation. The acquisition and regression of clones harboring this fusion during the presence and absence of a BRAF inhibitor are consistent with rapidly evolving clonal dynamics in melanoma.

show abstract

Section: Discussionmentioning

confidence: 99%

BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma

Kulkarni

Al-Hraishawi

Simhadri

et al. 2017

Clinical Cancer Research

View full text Add to dashboard Cite

show abstract

“…Other enrichment methods have also been described recently, including anchored multiplex PCR 26 and single-primer enrichment technology. 50 These methods are based on the strategy used in rapid amplification of cDNA ends, in which universal adapters are ligated to doublestranded cDNA, and amplification is performed using a universal primer along with a gene-specific primer. These methods have the distinct advantage of requiring knowledge only of one partner in the fusion and are thus able to identify novel gene fusions with previously unknown partners.…”

Section: Discussionmentioning

confidence: 99%

A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing

Beadling

Wald

Warrick

et al. 2016

The Journal of Molecular Diagnostics

View full text Add to dashboard Cite

Chromosomal rearrangements that result in oncogenic gene fusions are clinically important drivers of many cancer types. Rapid and sensitive methods are therefore needed to detect a broad range of gene fusions in clinical specimens that are often of limited quantity and quality. We describe a next-generation sequencing approach that uses a multiplex PCR-based amplicon panel to interrogate fusion transcripts that involve 19 driver genes and 94 partners implicated in solid tumors. The panel also includes control assays that evaluate the 3'/5' expression ratios of 12 oncogenic kinases, which might be used to infer gene fusion events when the partner is unknown or not included on the panel. There was good concordance between the solid tumor fusion gene panel and other methods, including fluorescence in situ hybridization, real-time PCR, Sanger sequencing, and other next-generation sequencing panels, because 40 specimens known to harbor gene fusions were correctly identified. No specific fusion reads were observed in 59 fusion-negative specimens. The 3'/5' expression ratio was informative for fusions that involved ALK, RET, and NTRK1 but not for BRAF or ROS1 fusions. However, among 37 ALK or RET fusion-negative specimens, four exhibited elevated 3'/5' expression ratios, indicating that fusions predicted solely by 3'/5' read ratios require confirmatory testing.

show abstract

“…Targeted and deep DNA sequencing provides an in-depth evaluation of clinically relevant and low-frequency genetic variations (72,73). Targeted RNA sequencing allows the analysis of complex transcriptomes and gene fusions (74,75). Long-read and linked-read sequencing is able to identify complex genetic aberrations, such as the haplotype of genetic aberrations and genomic rearrangements (76,77).…”

Section: Discussionmentioning

confidence: 99%

The context of prostate cancer genomics in personalized medicine

Liu

2017

Oncology Letters

View full text Add to dashboard Cite

Abstract. Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring. There is a requirement for novel genetic biomarkers in order to understand the oncogenic heterogeneity in a patient-personalized clinical setting and to improve the efficacy of risk prognosis and treatment choice. A number of biomarkers and gene panels have been established from patient sample cohort studies. These previous studies have provided distinct information to the investigation of heterogeneous malignancy in prostate cancer, which aids in clinical decision-making. Biomarker-guided therapies may facilitate the effective selection of drugs during early treatment; therefore, are beneficial to the individual patient. A non-invasive approach allows for convenient and repeated sampling to screen for cancer and monitor treatment response without the requirement for invasive tissue biopsies. With the current availability of numerous advanced technologies, reliable detection of the minimal tumor residues present following treatment may become clinical practice and, therefore, inform further in the field of personalized medicine.

show abstract

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

Cited by 44 publications

References 15 publications

BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma

BRAF Fusion as a Novel Mechanism of Acquired Resistance to Vemurafenib in BRAFV600E Mutant Melanoma

A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing

The context of prostate cancer genomics in personalized medicine

Contact Info

Product

Resources

About