Abstract 3863: Analytical performance of a novel next generation sequencing assay for myeloid cancers

Title: Analytical performance of a novel next generation sequencing assay for myeloid cancers

Nick Khazanov, Wally Zhang, Dinesh Cyanam, Scott P. Myrand, Denis Kaznadzey, Paul Williams, Vinay Mittal, Dan Mazur, Sihong Chen, Jason Wustman, Efren Ballesteros-Villagrana, Goutam Nistala, Jon Sherlock, Michael Hogan, Jim Veitch, John Bishop, Seth Sadis

Introduction: Myeloid malignancies contain a diverse and heterogeneous set of genomic alterations that include recurrent somatic mutations in key driver genes as well as frequent and diagnostic chromosomal rearrangements that generate a wide array of gene fusion products. To support clinical and translational research into precision oncology strategies for myeloid cancers, a next-generation sequencing (NGS) assay was generated to detect common and relevant somatic alterations.

Methods: To define gene targets that were recurrently altered in myeloid cancers and relevant for clinical and translational research, an extensive survey of investigators at hematology oncology research labs was performed. The gene targets identified by researchers were complemented by a comprehensive survey of literature and genomic databases. Clinical guidelines for myeloid diseases in the US and in Europe were reviewed to ensure representation of relevant alterations. A targeted Ion AmpliSeq panel was generated to support the detection of recurrent single-nucleotide variants, insertions/deletions, and gene fusions from blood or bone marrow samples. The panel was developed for manual or automated library preparation and sequencing on the Ion Torrent PGM or Ion S5 instruments.

Results: The Oncomine™ Myeloid Research Assay gene panel included 58 genes and generated an average read depth of >2,000 reads per targeted amplicon with an average uniformity of >95%. Important GC-rich targets such as CEBPA generated sufficient balanced read depth to support variant detection. A cohort of samples positive for FLT3 alterations was analyzed and successful detection of FLT3-internal tandem repeat variants was demonstrated. Several gene fusion transcripts common to myeloid cancers were detected. Comparable results were observed on Ion Torrent PGM and Ion S5 instruments.

Conclusions: A novel myeloid specific NGS assay capable of detecting relevant DNA and RNA alterations from the same sample was developed. The assay is useful for characterizing relevant alterations in a range of myeloid diseases including acute myeloid leukemia, myelodysplastic syndrome, myeloproliferative neoplasms, chronic myelogenous leukemia, chronic myelomonocytic leukemia, and juvenile myelomonocytic leukemia. A review of the analytical studies will be presented.

Citation Format: Nickolay Khazanov, Wally Zhang, Dinesh Cyanam, Scott P. Myrand, Denis Kaznadzey, Paul D. Williams, Vinay Mittal, Daniel J. Mazur, Sihong Chen, Jason Wustman, Efren Ballesteros-Villagrana, Goutam Nistala, Santhoshi Bandla, Jim Veitch, Jon Sherlock, John Bishop, Seth Sadis. Analytical performance of a novel next generation sequencing assay for myeloid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3863.

Abstract 5396: An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers

Noninvasive detection of rare mutations in blood could allow tumor monitoring for research purposes. Research studies have suggested that cfDNA contains DNA from tumor cells with somatic mutations that could inform on tumor progression and therapeutic resistance. Here, we demonstrate a complete workflow from a single tube of blood through data analysis for research samples down to a 0.1% allelic frequency.

The low abundance tumor mutations found in cfDNA requires sensitive and accurate mutation detection. We have developed two panels that utilize an amplification-based assay that generates tagged DNA copies, which allows detection of low abundance tumor mutations found in cfDNA. The two panels allow multiplex interrogation of primary driver and resistance mutations specific to ctDNA from breast and colon cancer. The Oncomine Colon cfDNA panel targets 236 hotspots within 14 genes while the Oncomine Breast cfDNA panel covers 157 hotspot mutations in 10 genes. This workflow was validated from matched single blood tubes, Streck and K2EDTA. Additionally, the utility for cancer research was demonstrated with concordance studies using matched FFPE and plasma from oncology samples.

To further characterize these panels we have developed an oncology control for cfDNA with nucleosome fragment sizing and minimal sonication damage. This engineered control contains SNPs and indels at 0.1% allelic frequencies, orthogonally confirmed with TaqMan based Rare Mutation assays. With this control, the Oncomine Breast cfDNA panel had over 81% sensitivity and 99.9% specificity. The Oncomine Colon cfDNA panel had over 85% sensitivity and 100% specificity. The Oncomine Breast cfDNA panel and Oncomine Colon cfDNA panel integrated into a complete workflow starting from a single tube of blood can advance oncology research with the ability to detect blood based cancer biomarkers present at 0.1%.

Citation Format: Dalia Dhingra, Richard Chien, Jian Gu, Dumitru Brinza, Ruchi Chaudhary, Kunal Banjara, Yanchun Li, Efren Ballesteros-Villagrana, Kelli Bramlett. An NGS workflow to detect down to 0.1% allelic frequency in cfDNA for breast and colon cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5396. doi:10.1158/1538-7445.AM2017-5396

Comprehensive detection of ctDNA variants at 0.1% allelic frequency using a broad targeted NGS panel for liquid biopsy research

e23065

Background: Advances in non-invasive tumor biomarker research have shown that tumor cells release fragments of DNA called circulating tumor DNA (ctDNA) into peripheral blood. Somatic mutations representing the tumors could be successfully detected from isolated ctDNA, providing new potential for tumor sample assessment in addition to traditional tissue biopsy methods. However, the low amount of ctDNA in the blood, which can be less than 1% allelic frequency, presents significant challenges for reliable variant detection with NGS assays. Improvement of sequencing accuracy at low allelic frequency is a critical factor in the implementation of NGS in ctDNA liquid biopsy research. Methods: We demonstrate the technical feasibility for a sample-to-variant NGS workflow that utilizes a broad multi-gene panel to survey a comprehensive list of variants relevant to multiple tumor types for liquid biopsy research. The method includes novel library preparation and analysis reporting for Ion Torrent™ sequencing platforms. 20ng of input cell-free DNA was subjected to the library generation protocol. Prepared libraries were templated on Ion Chef™ and sequenced on Ion S5™. Results: We successfully optimized an NGS workflow that enables the simultaneous examination of more than 360 driver and resistance hotspot mutations in a single-pool assay panel, achieving high sensitivity and specificity with limit of detection at 0.1% allelic frequency. The targeted regions span genes and variants relevant to multiple tumor types for comprehensive variant detection across high-value content reviewed by industry experts and researchers. Sequencing on the Ion S5™ delivered > 95% on-target reads and uniform amplification across targeted regions with deep sequencing depth ( > 40,000x). The workflow is compatible with single or multiple pooled samples on Ion Torrent™ sequencing chips. Conclusions: We demonstrate the ability to accurately detect high-value variants implicated in multiple tumors at 0.1% allelic frequency on Ion Torrent™ NGS. (For Research Use Only. Not for use in diagnostic procedures.)

Abstract 5267: Gene fusion database to create custom panels: Enabling detection of fusion transcripts and gene expression assays

Gene fusions play an important role in tumorigenesis and are increasingly recognized as important entities for the diagnosis and treatment of hematological malignancies and solid tumors. Fusion events generate a hybrid mRNA transcript comprising sequence from multiple otherwise distinct genes. Oncogenic fusion events often involve tyrosine kinases or transcription factors, leading to aberrant growth signaling, making these events potentially attractive drug targets. For instance, targeted therapies such as known tyrosine kinase inhibitors are currently approved to treat ALK fusion positive Non-Small Cell Lung Carcinoma (NSCLC) patients. Detection of known gene fusion events is an important part of genomic characterization which can inform patient diagnosis. Current methods for fusion detection include chromosome banding analysis (CBA), fluorescence in situ hybridization (FISH), and reverse transcription polymerase chain reaction (RT-PCR). New developments in next-generation sequencing (NGS) enable the efficient and simultaneous assessment of multiple gene fusion targets with high sensitivity. To enable researchers to design their own custom panels and assess a set of gene fusions of interest, we developed a comprehensive RNA gene fusion database. Oncology researchers now have the capability to create custom panels from this comprehensive database which includes over 1,000 well annotated and optimized gene fusion assays and over 20,000 gene expressions assays.

To build this comprehensive gene fusion database, we identified breakpoint information for 1,178 well annotated fusions described in publications and in the COSMIC and NCBI databases. We prepared a target RNA sequence for each breakpoint using transcript sequences from the Ensembl database. We used a proprietary primer designer to generate candidates for each fusion target amenable to the AmpliSeq™ product line requirements. Quality control was performed throughout the design process to identify the best primer set for each target, to avoid primers overlapping common germline SNPs, potential primer/primer or primer/amplicon interactions, or off-target or wild-type amplifications.

With this comprehensive database we provide a complete range of solutions available on ampliseq.com. Making use of the AmpliSeq™ technology, researchers now have the capability to create their own custom fusion panel and place the order within an hour. These custom panels are used with AmpliSeq™ Library reagents and Ion Torrent™ sequencing platforms for targeting next-generation sequencing. The analysis solution is provided through the Ion Reporter™ (IR) software package. Custom fusion panel workflows in IR are used to analyze sequencing data coming from the custom panels, which includes visualization of fusion transcripts and gene expression levels in a heat map feature.

Citation Format: Efren Ballesteros-Villagrana, Jeoffrey Schageman, Kelli Bramlett, Paul Williams, Scott Myrand, Guoying Liu, Fiona Hyland, Seth Sadis. Gene fusion database to create custom panels: Enabling detection of fusion transcripts and gene expression assays. [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 5267.

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.

DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies

SUMMARY

Systematic studies of drug repositioning require the integration of multi-level drug data, including basic chemical information (such as SMILES), drug targets, target-related signaling pathways, clinical trial information and Food and Drug Administration (FDA)-approval information, to predict new potential indications of existing drugs. Currently available databases, however, lack query support for multi-level drug information and thus are not designed to support drug repositioning studies. DrugMap Central (DMC), an online tool, is developed to help fill the gap. DMC enables the users to integrate, query, visualize, interrogate, and download multi-level data of known drugs or compounds quickly for drug repositioning studies all within one system.

AVAILABILITY

DMC is accessible at http://r2d2drug.org/DMC.aspx.

CONTACT

STWong@tmhs.org.