Validation of a Targeted Next-Generation Sequencing Panel for Tumor Mutation Burden Analysis: Results from the Onconetwork Immuno-Oncology Consortium

Tumor mutation burden (TMB) is evaluated as a biomarker of response to immunotherapy. We present the efforts of the Onconetwork Immuno-Oncology Consortium to validate a commercial targeted sequencing test for TMB calculation. A three-phase study was designed to validate the Oncomine Tumor Mutational Load (OTML) assay at nine European laboratories. Phase 1 evaluated reproducibility and accuracy on seven control samples. In phase 2, six formalin-fixed, paraffin-embedded samples tested with FoundationOne were reanalyzed with the OTML panel to evaluate concordance and reproducibility. Phase 3 involved analysis of 90 colorectal cancer samples with known microsatellite instability (MSI) status to evaluate TMB and MSI association. High reproducibility of TMB was demonstrated among the sites in the first and second phases. Strong correlation was also detected between mean and expected TMB in phase 1 (r² = 0.998) and phase 2 (r² = 0.96). Detection of actionable mutations was also confirmed. In colorectal cancer samples, the expected pattern of MSI-high/high-TMB and microsatellite stability/low-TMB was present, and gene signatures produced by the panel suggested the presence of a POLE mutation in two samples. The OTML panel demonstrated robustness and reproducibility for TMB evaluation. Results also suggest the possibility of using the panel for mutational signatures and variant detection. Collaborative efforts between academia and companies are crucial to accelerate the translation of new biomarkers into clinical research.

Abstract 5472: Development of customizable targeted RNA fusion panels using a novel automated high-multiplexing primer design strategy

Introduction

Gene fusions play an important role in oncogenesis and the progression of cancer. As important biomarkers, sensitive identification of gene fusions is critical to future oncology research. Next generation sequencing with Ion Ampliseq targeted enrichment enables simple, accurate and specific detection of relevant fusion isoforms. Here we introduce a novel automatic high-multiplexing primer design strategy that has the flexibility to develop customized Ampliseq fusion panels for any combination of fusion isoforms, scaling to panels that can detect thousands of isoforms in a single primer pool, which increases the sensitivity of fusion detection while decreasing the sample input required to as low as 10 ng.

Methods

The automated primer design pipeline takes a Gene-Transcript-Exon (GTE) file as input. Each record in the GTE file represents a unique RNA fusion isoform to establish an easy-parsing format for the pipeline. The pipeline locates the fusion breakpoint position, extracts gene sequences of every candidate fusion target and builds the fusion reference. Candidate amplicons are generated against the fusion reference. According to the design requirements of pool number and the conflicts among primer pairs, the pipeline performs pooling to minimize primer interactions. Finally, the pipeline generates an optimal set of amplicons strategically targeted for fusion junctions. The output files are used for downstream analysis with a fully automated analysis pipeline.

Results

The pipeline has been used extensively to develop high performing multiplex RNA fusion panels. The pipeline generates 175-base amplicons for use on formalin-fixed, paraffin-embedded (FFPE) samples or 120-base amplicons for use on cfRNA from blood samples. A single panel can include thousands of known fusion variants. This pipeline has been used to design the fusion assays contained in Oncomine Focus and Comprehensive assays, Oncomine Precision Assay, and others. Oncomine Comprehensive Assay v3 fusion panel was tested using the Ion GeneStudio S5 Sequencer; for example, testing on SeraCare fusion control confirms that all 14 fusion isoforms were detected with 100% accuracy. Testing on FFPE samples with known positive fusions confirms that the expected fusions including NTRK1, ERG, ETV1 and MET driver genes were also detected with 100% accuracy.

Conclusions

In summary, we have developed an automatic pipeline that can generate robust, comprehensive customized multiplex RNA fusion assays for targeted next-generation sequencing.

For research use only. Not for use in diagnostic procedures.

Citation Format: NA LI, Antonio Martinez-Alcantara, Aren Ewing, Rajesh Gottimukkala, Fiona Hyland, Seth Sadis. Development of customizable targeted RNA fusion panels using a novel automated high-multiplexing primer design strategy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5472.

Abstract 179: Comprehensive genomic profiling of solid tumors for key targeted and immuno-oncology biomarkers using Ion Torrent NGS technology on the Oncomine Comprehensive Assay Plus (OCA Plus)

Comprehensive genomic profiling (CGP) of tumor samples by next-generation sequencing is used to support clinical and translational research into the genetic variants that serve as biomarkers for diagnosis, prognosis and potential therapeutic response. However, as these assays grow in size to meet the expanding demands of users, it is challenging to maintain performance in the face of limited sample input necessitated by small sample volumes and to provide a simple and fast sample to report workflow with limited hands-on time. We, therefore, developed OCA Plus to meet user needs for a large CGP assay with excellent performance.

Gene content was prioritized based on potential clinical relevance and variant prevalence in solid tumors. Over 500 genes were selected including genes in the indication statements of approved drug labels, clinical guidelines, and in the enrollment criteria of clinical trials. In addition, driver genes were selected in key pathways including DNA repair and immune checkpoint response. Amplicon design strategies were optimized accordingly for key hotspots, full coding sequences or copy number variation (CNV). The assay used Ion AmpliSeq™ technology with manual library preparation or automated templating on the Ion Chef™ System and sequencing on the Ion GeneStudio™ S5 platform. Twenty ng of purified DNA was routinely used as input. An automated tumor-only workflow for variant calling and sample quality reporting was provided within Ion Reporter™ Software. Streamlined access to reporting of variant relevance was enabled by Oncomine™ Reporter.

In development studies of cancer cell line and formaldehyde-fixed, paraffin-embedded (FFPE) tumor samples, the assay displayed excellent uniformity (98% and 94%, respectively). Detection of single nucleotide variants and indels in cell lines and FFPE samples showed >95% sensitivity and PPV. Detection of CNV gain and loss in cell lines and FFPE samples showed >95% sensitivity and PPV. Assessment of tumor mutational burden (TMB) using publicly available whole-exome cancer sequencing data as well as test cell lines and FFPE samples showed high concordance with whole exome sequencing (R2 > 0.90). MSI sensitivity and specificity was >95% as tested using a diverse set of tumor samples. Targeted fusions were reported with 100% sensitivity and specificity when tested with commercially available controls. Total time from purified DNA to end of sequencing was < 2 days with < 3 hours of hands-on time and the time from post-sequencing to report generation was < 2 hours.

Oncomine Comprehensive Assay (OCA Plus) was developed to support CGP and routine clinical research in oncology. The assay design and informatics workflow were optimized to support low input and rapid sample-to-report turn-around time, which will accelerate clinical and translational research.

Citation Format: Vinay Mittal, Jennifer Kilzer, Dinesh Cyanam, Janice Au-Young, Santhoshi Bandla, Gary Bee, Sameh El-Difrawy, Aren Ewing, Rajesh Gottimukkala, Mohit Gupta, Nickolay Khazanov, Anelia Kraltcheva, Amir Marcovitz, Scott Myrand, Rose Putler, Yu-Ting Tseng, Warren Tom, Cristina Van Loy, James Veitch, Paul Williams, Elaine Wong-Ho, Huimin Xie, Chenchen Yang, Zheng Zang, Seth Sadis. Comprehensive genomic profiling of solid tumors for key targeted and immuno-oncology biomarkers using Ion Torrent NGS technology on the Oncomine Comprehensive Assay Plus (OCA Plus) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 179.

Profiling molecular regulators of recurrence in chemorefractory triple-negative breast cancers

Background

Approximately two thirds of patients with localized triple-negative breast cancer (TNBC) harbor residual disease (RD) after neoadjuvant chemotherapy (NAC) and have a high risk-of-recurrence. Targeted therapeutic development for TNBC is of primary significance as no targeted therapies are clinically indicated for this aggressive subset. In view of this, we conducted a comprehensive molecular analysis and correlated molecular features of chemorefractory RD tumors with recurrence for the purpose of guiding downstream therapeutic development.

Methods

We assembled DNA and RNA sequencing data from RD tumors as well as pre-operative biopsies, lymphocytic infiltrate, and survival data as part of a molecular correlative to a phase II post-neoadjuvant clinical trial. Matched somatic mutation, gene expression, and lymphocytic infiltrate were assessed before and after chemotherapy to understand how tumors evolve during chemotherapy. Kaplan-Meier survival analyses were conducted categorizing cancers with TP53 mutations by the degree of loss as well as by the copy number of a locus of 18q corresponding to the SMAD2, SMAD4, and SMAD7 genes.

Results

Analysis of matched somatic genomes pre-/post-NAC revealed chaotic acquisition of copy gains and losses including amplification of prominent oncogenes. In contrast, significant gains in deleterious point mutations and insertion/deletions were not observed. No trends between clonal evolution and recurrence were identified. Gene expression data from paired biopsies revealed enrichment of actionable regulators of stem cell-like behavior and depletion of immune signaling, which was corroborated by total lymphocytic infiltrate, but was not associated with recurrence. Novel characterization of TP53 mutation revealed prognostically relevant subgroups, which were linked to MYC-driven transcriptional amplification. Finally, somatic gains in 18q were associated with poor prognosis, likely driven by putative upregulation of TGFß signaling through the signal transducer SMAD2.

Conclusions

We conclude TNBCs are dynamic during chemotherapy, demonstrating complex plasticity in subclonal diversity, stem-like qualities, and immune depletion, but somatic alterations of TP53/MYC and TGFß signaling in RD samples are prominent drivers of recurrence, representing high-yield targets for additional interrogation.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1171-7) contains supplementary material, which is available to authorized users.

Abstract P2-07-04: Molecular regulators of resistance and relapse in chemorefractory triple-negative breast cancers

Triple-Negative Breast Cancer (TNBC) accounts for approximately one-fifth of breast cancer incidence but disproportionately high mortality. Two-thirds of early-stage TNBCs are resistant to pre-surgical chemotherapy and highly prone to relapse within 3 years. Morever, no advanced therapies are indicated for patients with these cancers. We have embarked on a comprehensive genomic analysis of chemoresistant TNBC to gain an in-depth understanding of molecular entities driving chemoresistance and relapse. By collecting somatic mutation and copy number, RNA-sequencing, and outcome data in the context of a phase II post-neoadjuvant clinical trial, we have uncovered several molecular mechanisms behind these aggressive cancers. Through the analysis of matched pairs sampled before and after chemotherapy, we have discovered multiple means by which tumors are able to overcome the effects of chemotherapy including clonal evolution of high-level oncogene amplification, repression of the in situ immune system, and upregulation of the stem cell-related MEK-ERK and JAK-STAT pathways. Investigation into factors related to prognosis revealed important correlations between relapse and immune and JAK-STAT signaling. Finally, using a novel method of demarcating loss-of-function of p53, which we have termed graduated inactivation, we discovered additional associations between p53 loss and relapse, mortality, and MYC signalling.

Citation Format: Hancock BA, Chen Y-H, Solzak JP, Ahmad MN, Wedge DC, Brinza D, Scafe C, Veitch J, Gottimukkala R, Short W, Atale RV, Ivan M, Badve SS, Schneider BP, Miller KD, Radovich M. Molecular regulators of resistance and relapse in chemorefractory triple-negative breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-04.

Somatic mutation burden in cancer samples determined by targeted next generation sequencing

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Background: High somatic mutation burden in tumor tissues is associated with the presentation of neoantigens that promote immune responses particularly in the context of immune checkpoint therapies. Herein, we characterize the ability of targeted cancer research panels to generate estimates of somatic mutation burden. Methods: Somatic mutation data from > 8000 cancer samples obtained from The Cancer Genome Atlas (TCGA) was curated and standardized, and the number of single nucleotide variants (SNVs) in exonic regions of each sample determined. Next, the number of SNVs associated with target regions of two Ion AmpliSeq cancer panels (Oncomine Comprehensive Assay [OCA, 146 genes, 0.35 MB]; Comprehensive Cancer Panel [CCP, 409 genes, 1.7 MB]) was likewise determined and the frequency of mutation counts in the exome and the panel target regions was compared. Mutation counts of samples containing truncating mutations in mismatch repair (MMR) and other DNA repair genes were characterized. A facile workflow with less than 60 minutes of hands-on time was developed to estimate mutation counts for a batch of 8 samples using the Ion Chef for automated library preparation and templating followed by sequencing on the Ion S5. Results: The sensitivity of targeted panels in estimating somatic mutation burden was positively correlated with panel size. The area under the Receiver Operating Characteristic (ROC) curve showed that CCP had > 90% sensitivity and > 95% specificity to differentiate high and low mutation burden based on informatics analysis of TCGA data. As expected, truncating mutations in MMR genes were associated with higher somatic mutation counts in colorectal tumor tissue. Using data generated from OCA and CCP, we characterized a set of filters that provided a good estimate of somatic mutation counts when applied to a tumor-only workflow. Conclusions: A simple workflow was developed on the Ion Torrent sequencing platform to estimate somatic mutation burden in cancer samples. The methods described herein will help advance research in immuo-oncology.

Abstract 5272: Cloud-based informatics enables the design and analysis of massively multiplex custom gene fusion panels for next-generation sequencing on FFPE RNA samples

Gene fusions, a combination of two genes, comprising their coding and/or regulatory sequences, are caused by structural rearrangements in DNA or in RNA transcripts. Many gene fusions are strong driver mutations in neoplasia, and are important in understanding basic biology, interaction with targeted therapy, and research into risk stratification and outcomes.

Next-generation sequencing enables sensitive, specific and precise detection of particular fusion isoforms for defined gene pairs. Massively multiplex Ampliseq gene fusion assays enable enrichment of fusion transcripts using as little as 10 ng of RNA extracted from FFPE samples. Sequencing on Ion Torrent instruments reveals the full sequence of the gene fusion, for precise definition of the breakpoint and the expressed exons or promoter regions of both genes.

We developed cloud-based software to support the design of a custom Ampliseq gene fusion panel, comprising 1 to 1,000 fusion isoform assays and any gene expression assays for normalization.

We extensively mined the scientific literature on fusions and the COSMIC database to identify over 1000 fusion isoforms. We rigorously curated this data using automated and manual methods, including mapping, confirmation and correction of reported sequence to obtain genomic coordinates, identification of breakpoints, annotation of exon junctions, and selected wet lab testing. We created a database containing over 1000 high quality curated and annotated fusion isoforms, including 70 ALK, 60 RET, 26 ROS1, and 21 NTRK1 fusions. We designed Ampliseq primer pairs for each of these fusions using advanced assay design and pooling algorithms, such that all fusion and gene expression assays can be multiplexed into 1 or 2 compatible pools.

Assays can be selected by gene or gene pair; detailed information about each assay selected includes isoform, genes, exon numbers, and links to COSMIC and to relevant publications.

We developed cloud-based analysis software to analyze the BAM file resulting from amplification and sequencing of custom Ampliseq fusion panels on an Ion Torrent sequencer. This analysis leverages the rich annotation information from the assay design. The reads are mapped to a custom reference sequence tailored to the custom Ampliseq fusion assay, and applying an optimized algorithm to select confidently mapped reads based on read length and overlap with each gene of the gene pair based on the reference and annotated breakpoint. Gene fusions are detected based on the total number of fusion reads and optionally frequency, and on the properties of those reads. Software QC steps for total number of mapped reads, number of reads for gene expression controls, and elimination of cross-talk artifacts result in a highly sensitive and specific detection of fusions, with LOD below 1%. Fusion results for any or all samples can be viewed, annotated, filtered, and visualized, and exported.

Citation Format: Fiona Hyland, Rajesh Gottimukkala, Efren Ballesteros, Heinz Breu, Yuandan Lou, Scott Myrand, Michael Hogan, Kelli Bramlett, Guoying Liu, Seth Sadis. Cloud-based informatics enables the design and analysis of massively multiplex custom gene fusion panels for next-generation sequencing on FFPE RNA samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5272.

Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with < 20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.