Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

• Main Authors: Shaham Beg, Rohan Bareja, Kentaro Ohara, Kenneth Wha Eng, David C. Wilkes, David J. Pisapia, Wael Al Zoughbi, Sarah Kudman, Wei Zhang, Rema Rao, Jyothi Manohar, Troy Kane, Michael Sigouros, Jenny Zhaoying Xiang, Francesca Khani, Brian D. Robinson, Bishoy M. Faltas, Cora N. Sternberg, Andrea Sboner, Himisha Beltran, Olivier Elemento, Juan Miguel Mosquera
• Format: Article
• Language: English
• Published: Elsevier 2021-01-01
• Series: Translational Oncology
• Subjects: Anchored multiplex PCR-based next-generation sequencing; Whole-exome sequencing; RNA Sequencing; Novel fusion; Oncogenic
• Online Access: http://www.sciencedirect.com/science/article/pii/S1936523320304368

Background: Frequency of clinically relevant mutations in solid tumors by targeted and whole-exome sequencing is ∼30%. Transcriptome analysis complements detection of actionable gene fusions in advanced cancer patients. Goal of this study was to determine the added value of anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) assay to identify further potential drug targets, when coupled with whole-exome sequencing (WES). Methods: Selected series of fifty-six samples from 55 patients enrolled in our precision medicine study were interrogated by WES and AMP-based NGS. RNA-seq was performed in 19 cases. Clinically relevant and actionable alterations detected by three methods were integrated and analyzed. Results: AMP-based NGS detected 48 fusions in 31 samples (55.4%); 31.25% (15/48) were classified as targetable based on published literature. WES revealed 29 samples (51.8%) harbored targetable alterations. TMB-high and MSI-high status were observed in 12.7% and 1.8% of cases. RNA-seq from 19 samples identified 8 targetable fusions (42.1%), also captured by AMP-based NGS. When number of actionable fusions detected by AMP-based NGS were added to WES targetable alterations, 66.1% of samples had potential drug targets. When both WES and RNA-seq were analyzed, 57.8% of samples had targetable alterations. Conclusions: This study highlights importance of an integrative genomic approach for precision oncology, including use of different NGS platforms with complementary features. Integrating RNA data (whole transcriptome or AMP-based NGS) significantly enhances detection of potential targets in cancer patients. In absence of fresh frozen tissue, AMP-based NGS is a robust method to detect actionable fusions using low-input RNA from archival tissue.