Abstract 5601: Oncomine™ dx express CE-IVD liquid biopsy assay for non-small cell lung cancer: Performance review and analytical validation

Introduction - Clinical diagnostics assays for oncology are becoming more readily available due to the advancement and democratization of Next-Generation Sequencing (NGS). Additionally, liquid biopsy can be used in NGS to detect genetic variants in circulating tumor DNA and RNA. Liquid biopsy is a less invasive option compared to traditional biopsy methods for early detection and continuous monitoring of cancer treatment outcomes. Here, we discuss screening of over 3,500 non-small cell lung cancer (NSCLC) samples, and the analytical validation of the Oncomine™ Dx Express Test (ODxET) and Genexus™ Dx Integrated Sequencer for detection of clinically significant variants in liquid biopsy samples.

Methods - Our team screened over 3,500 NSCLC liquid biopsy samples in search of high priority clinical variants. Variants selected for analytical validation studies included ERBB2 exon 20 insertion, EGFR exon 20 insertion, EGFR exon 19 deletion, EGFR T790M, KRAS G12C, BRAF V600E, and RNA fusion isoforms including ALK, NTRK1/2/3, RET, and ROS1 oncogenic drivers. Over 550 screened samples were found to be positive for these variants of interest. This screening was performed on the Genexus™ Dx Integrated Sequencer according to the user guide.

Results - The Genexus™ Dx Integrated Sequencer automates library preparation, sequencing, analysis, and reporting QC metrics and variant calls. Sequencing run setup is quick and straightforward, taking less than 15 minutes to start a run and just over 24 hours to go from nucleic acid to report. Limit of detection (LoD) for DNA SNVs, insertions, and deletions at 5 ng DNA input level ranged from 0.65% to 1.82% allelic frequency (AF), depending on the variant. The higher DNA input of 30 ng resulted in a lower LoD range, from 0.31% to 0.42% AF. RNA fusion and splice variant LoD at 5 ng sample input ranged from 9.9 to 19.6 molecular counts. The higher 30 ng input resulted in a lower LoD range for RNA variants as well, ranging from 6.4 to 8.0 molecular counts. In the analytical accuracy study, the false positive rate was found to be 0.2% for SNVs, 0% for insertions/deletions, and 0% for fusion targets. In the analytical reproducibility study, the average with-in run repeatability call rate (No Calls excluded) was 99.64% for DNA variants and 98.75% for RNA variants.

Conclusion - Here, we demonstrated that the ODxET workflow on Genexus™ Dx Integrated Sequencer is a fast and efficient tool for testing clinical NSCLC liquid biopsy samples with high sensitivity and specificity.

For in vitro diagnostic use. Not available in all regions including the United States.

Citation Format: Nicholas Siepert, Jeoffrey Schageman, Jian Gu, Thilanka Jayaweera, Madhu Jasti, Luming He, Stephen Wunch, Emilia Ostrowska, Tasha Delacour, Diarra Hassell, Thomas Bowden, Daniela Garcia, Stephanie Tong, Swasti Raut, Nader Ezzedine, Elliott Martinez, Kelli Bramlett. Oncomine™ dx express CE-IVD liquid biopsy assay for non-small cell lung cancer: Performance review and analytical validation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5601.

Abstract 78: Detection of gene fusions and exon skipping events in lung FFPE samples with Oncomine Precision Assay on Ion Torrent Genexus࣪ System

Introduction: Gene fusions and exon skipping events play an important oncogenic role in non-small cell lung cancer (NSCLC). Here we employed the Oncomine Precision Assay (OPA) for sequencing of 998 clinical research FFPE (Formalin-Fixed Paraffin-Embedded) lung samples using the Genexus࣪ integrated sequencing platform. The RNA assay strategy is aimed at providing a wide scope for studying known oncogenic fusions and exon skip variants, as well as a method for detection of novel fusion combinations and detection of fusions in a partner agnostic manner. We summarize the findings that include detected samples with oncogenic fusions in tyrosine kinase genes ALK, RET, ROS1 as well as MET exon14 skipping, and demonstrate the novel fusion detection capabilities of the panel.

Methods: The Oncomine Precision Assay panel developed using the Ion AmpliSeq HD technology for use on both tissue and liquid biopsy samples to detect fusions with high sensitivity in low input RNA. The panel features 981 known fusion isoforms in 16 oncogenic drivers as well as assays for exon skipping and deletion in MET and EGFR. The amplicons are strategically designed around known fusion breakpoints and generate reads only if the variant is present. Results are assessed bioinformatically with a framework that includes detailed genomic annotations of the fusion breakpoint, and generates interpretable fusion calls and report in the Genxus࣪ software. In addition, the panel contains an algorithm for novel fusion detection, and 78 exon-junction amplicons for partner agnostic fusion detection in ALK, RET, NTRK1,2,3 and FGFR1,2,3 with an exon tiling expression imbalance assay. We used the Genexus࣪ instrument to sequence 998 unique lung FFPE samples and analyzed the results with the Genexus࣪ fusion analysis workflow.

Results: A total of 998 unique lung FFPEs were sequenced, of which 906 (91%) resulted with >5000 aligned reads and at least 5 of the 7 RNA expression controls at the assay threshold. A total of 25 samples with ALK fusions were detected by either the targeted fusions or the expression imbalance assays. In addition, we detected 10 samples with RET fusions, 4 with FGFR3 fusions, 3 with ROS1 fusions, and additional single observations of NRG1, RSPO3 and FGFR1 fusions. Exon 14 skipping in MET was detected in 14 samples, of which we were able to detect a likely splice site variant SNV or indel at, or near the boundaries of exon 14, with the DNA assays of the panel. These variants were observed in a mutually exclusive set of 59 total samples (6.5% of the samples).

Conclusions: We used the OPA panel for fusions and intragenic rearrangements that retains the simple workflow and fast turn-around time of previous Oncomine fusion, and demonstrated known and novel fusion detection as well exon skip variant detection capabilities in a research cohort of lung FFPE samples. For research use only. Not for use in diagnostic procedures.

Citation Format: Amir Marcovitz, Jeoffrey Schageman, Jian Gu, Stephen Wunsch, David Chi, Paul D. williams, Scott P. Myrand, Fiona C. Hyland, Seth Sadis, Kelli S. Bramlett. Detection of gene fusions and exon skipping events in lung FFPE samples with Oncomine Precision Assay on Ion Torrent Genexus࣪ System [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 78.

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

Liquid Biopsy Enables Quantification of the Abundance and Interindividual Variability of Hepatic Enzymes and Transporters

Variability in individual capacity for hepatic elimination of therapeutic drugs is well recognized and is associated with variable expression and activity of liver enzymes and transporters. Although genotyping offers some degree of stratification, there is often large variability within the same genotype. Direct measurement of protein expression is impractical due to limited access to tissue biopsies. Hence, determination of variability in hepatic drug metabolism and disposition using liquid biopsy (blood samples) is an attractive proposition during drug development and in clinical practice. This study used a multi-"omic" strategy to establish a liquid biopsy technology intended to assess hepatic capacity for metabolism and disposition in individual patients. Plasma exosomal analysis (n = 29) revealed expression of 533 pharmacologically relevant genes at the RNA level, with 147 genes showing evidence of expression at the protein level in matching liver tissue. Correction of exosomal RNA expression using a novel shedding factor improved correlation against liver protein expression for 97 liver-enriched genes. Strong correlation was demonstrated for 12 key drug-metabolizing enzymes and 4 drug transporters. The developed test allowed reliable patient stratification, and in silico trials demonstrated utility in adjusting drug dose to achieve similar drug exposure between patients with variable hepatic elimination. Accordingly, this approach can be applied in characterization of volunteers prior to enrollment in clinical trials and for patient stratification in clinical practice to achieve more precise individual dosing.

Abstract 3118: Next generation sequencing assay for detection of gene fusions and exon deletion events in tissue and liquid biopsy samples at very low frequency

Introduction: Gene fusions caused by chromosomal rearrangements and the exon deletion events caused by aberrant RNA splicing events play a key role in oncogenesis and the progression of cancer. Next generation sequencing using molecular tagged AmpliSeq HD chemistry enables highly sensitive variant detection down to <=0.1% mutant allele fractions. Here we present the Oncomine Precision RNA Assay developed using the Ion AmpliSeq HD Technology for use on both tissue and liquid biopsy samples to detect fusion and exon deletions with very high sensitivity. The assay also includes capabilities for novel fusion detection in driver genes via exon level expression measurements.

Methods: The Oncomine Precision RNA assay can detect >900 known fusion isoforms including those of ALK, ROS1, RET, NTRK1,2,3, FGFR1,2,3, and BRAF and exon deletion events in MET and EGFR genes. The assay also includes amplicons in 8 key driver genes like NTRK1,2,3 to detect novel gene fusions in a partner agnostic manner based on the expression imbalance. The amplicons to detect targeted isoforms are designed strategically around the known break-points of the targeted fusions and exon skipping events. These amplicons generate reads when the target variant is present in the sample and provide complete information of the fusion event including the precise break-point with annotations such as cosmic ID. The unique molecular tags attached on both ends of the reads are used for error correction and this enables us to detect fusions at a very low frequency with high accuracy which is critical in liquid biopsy samples . The assay also includes amplicons to measure the wild-type expression of MET and EGFR genes and the exon deletion events are detected by comparing the expression of the exon-deletion transcript to that of the wild-type transcript.

Results: To test the panel, we used the GenexusTM sequencer to sequence ALK, ROS1, RET,FGFR3 and NTRK1 fusion positive cell lines and correctly identified all the targeted fusions and concordant results with expression imbalance. We sequenced cell-free total nucleic acid(cfTNA) control samples and identified the expected fusions in ALK, RET and ROS1 genes and the MET Exon 14 skipping event. We sequenced 16 FFPE samples with known truth and correctly identified all the 11 ALK and 5 ROS1 fusion isoforms and observed highly concordant results with the expression imbalance in the samples positive for ALK fusion. We sequenced the ALK, RET, NTRK1 and FGFR3 cell lines diluted to 2%, 2%, 5% and 20% respectively with the background of wild-type RNA and detected the expected fusions and observed concordant results with the expression imbalance.

Conclusions: This targeted sequencing assay enables researchers to detect gene fusions and exon deletions in both FFPE and blood samples with >99% sensitivity and high specificity.

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

Citation Format: Rajesh K. Gottimukkala, Fiona C. Hyland, Amir Marcovitz, Jeoffrey Schageman, Varun Bagai, Ru Cao, Paul D. Williams, Scott P. Myrand, Jian Gu, Seth Sadis, Kelli S. Bramlett. Next generation sequencing assay for detection of gene fusions and exon deletion events in tissue and liquid biopsy samples at very low frequency [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 3118.

Analytical validation of the Oncomine Pan-Cancer Cell-Free Assay in a CLIA- and CAP-regulated laboratory for detection of solid tumor-derived variants in blood plasma

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Background: Assessing tumor-derived somatic variants from blood plasma provides minimally invasive tumor profiling, decreased cost relative to traditional tissue biopsy and rapid turn-around-time. We describe here the analytical validation of the Oncomine Pan-Cancer Cell-Free assay in a CAP-accredited, CLIA-certified laboratory. The assay is designed to detect somatic DNA single-nucleotide variants (SNV), insertions/deletions (INDEL), copy number variants (CNV), and gene fusions in cell-free total nucleic acid (cfTNA) across 52 genes. For research use only. Not for use in diagnostic procedures. Methods: We assessed the sensitivity, specificity, accuracy, and precision of the assay. Pre-characterized reference materials with alterations at known allelic frequencies (AF) were used to establish performance characteristics for each variant class followed by verification on clinical specimens. Whole blood (n = 73) from healthy (10), breast cancer (9), colorectal cancer (32), and lung cancer (22) donors were collected in K2EDTA tubes and plasma was separated within 8 hours of collection. cfTNA was isolated using the MagMAX Cell-Free Total Nucleic Acid Isolation Kit on the KingFisher Flex. Libraries were prepared following kit instructions. Templating and sequencing were performed using the Ion 550 Kit on the Ion Chef and S5 XL systems. Alignment to hg19 and variant calling were performed using Torrent Suite and Ion Reporter software. Results: We observed a sensitivity of 80% at 0.1% AF and > 99.9% at 0.5% AF for SNV/INDEL. Sensitivity was > 99.9% at 1.34 fold-change for CNV, and > 99.9% at 0.4% fusion fraction. Specificity and accuracy were > 99% for all variant classes. Precision was 98% for SNV/INDEL and > 99.9% for CNV/fusions. Analysis of donor plasma demonstrated clinical feasibility; on average, we detected 1 hotspot SNV/INDEL (range 0-4) across the 3 cancer types. For SNV/INDEL in plasma where matched tissue genotyping was available (n = 17), we observed > 99% concordance (AF range 0.09%-52%). Conclusions: We have demonstrated that this assay is a sensitive method for evaluating tumor-derived somatic variants in blood plasma. It may provide an alternative and minimally invasive method for mutation profiling.

Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project

INTRODUCTION

The reported prevalence of ALK receptor tyrosine kinase gene (ALK) rearrangement in NSCLC ranges from 2% to 7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proved to be a reproducible and sensitive technique. Reverse-transcriptase polymerase chain reaction (RT-PCR) has also been advocated, and most recently, the advent of targeted next-generation sequencing (NGS) for ALK and other fusions has become possible. This study compares anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape cohort.

METHODS

A total of 96 cases from the European Thoracic Oncology Platform Lungscape iBiobank, with any ALK immunoreactivity were examined by FISH, central RT-PCR, and NGS. An H-score higher than 120 defines IHC positivity. RNA was extracted from the same formalin-fixed, paraffin-embedded tissues. For RT-PCR, primers covered the most frequent ALK translocations. For NGS, the Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific, Waltham, MA) was used. The concordance was assessed using the Cohen κ coefficient (two-sided α ≤ 5%).

RESULTS

NGS provided results for 77 of the 95 cases tested (81.1%), whereas RT-PCR provided results for 77 of 96 (80.2%). Concordance occurred in 55 cases of the 60 cases tested with all four methods (43 ALK negative and 12 ALK positive). Using ALK copositivity for IHC and FISH as the criterion standard, we derived a sensitivity for RT-PCR/NGS of 70.0%/85.0%, with a specificity of 87.1%/79.0%. When either RT-PCR or NGS was combined with IHC, the sensitivity remained the same, whereas the specificity increased to 88.7% and 83.9% respectively.

CONCLUSION

NGS evaluation with the Oncomine Solid Tumour Fusion transcript kit and RT-PCR proved to have high sensitivity and specificity, advocating their use in routine practice. For maximal sensitivity and specificity, ALK status should be assessed by using two techniques and a third one in discordant cases. We therefore propose a customizable testing algorithm. These findings significantly influence existing testing paradigms and have clear clinical and economic impact.

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

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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.)

Development of a breast and lung cancer research panel to target therapeutically relevant copy number and gene fusion variants from blood

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Background: With recent advances in next-generation sequencing (NGS) technologies, it is now possible to detect somatic mutations with allele frequencies in blood samples as low as 0.1% from circulating tumor DNA. A natural extension to this achievement is adding the ability to simultaneously detect copy number variants and gene fusions. A panel such as this addresses a full repertoire of variant classes found to be linked with certain tumors and would enable researchers additional tools to profile cancer samples more dynamically thus enriching current diagnostic tool sets. Here, we present progress on such an approach and apply current NGS technology to achieve our goals. Methods: Samples were sequecned using the Ion S5™ system. Results: Using control samples, we can reproducibly demonstrate detection of ERBB2 (HER2/neu) gene amplifications with high statistical significance and as low as a 2 fold difference versus non-amplified loci in titration experiments. In addition, this ERBB2 gene amplification was detected in the context of a validated breast cancer somatic mutation panel in which no negative impact was exhibited and mutation detection specificity and sensitivity were both greater than 90%. Lastly, we developed an additional panel to detect gene fusions relevant to lung cancer. Using the titration approach above, the EML4-ALK fusion variant was shown to have a limit of detection near 1% with no negative impact on detection sensitivity and specificity when combined with the validated lung cfDNA somatic mutation panel. Conclusions: From the outcomes of these experiments, we have shown the ability to reproducibly and simultaneously detect copy number and gene fusion variants as well as somatic mutations at very low limits of detection in a cell free DNA background derived from blood samples.

Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium

The cancer community understands the value of blood profiling measurements in assessing and monitoring cancer. We describe an effort among academic, government, biotechnology, diagnostic, and pharmaceutical companies called the Blood Profiling Atlas in Cancer (BloodPAC) Project. BloodPAC will aggregate, make freely available, and harmonize for further analyses, raw datasets, relevant associated clinical data (e.g., clinical diagnosis, treatment history, and outcomes), and sample preparation and handling protocols to accelerate the development of blood profiling assays.

Abstract 1836: Global gene expression profiles from bladder tumor FFPE samples

Cancer is a disease characterized by uncontrolled cell growth and proliferation. Recent advances in molecular medicine and cancer biology have changed the way clinicians evaluate and consider treatment. Selected tumor biomarkers have been utilized as targets for drug therapy leading to better more effective treatment. Gene expression profiling has been used for identifying new biomarkers for tumor classification and driving decision making for better patient outcome in different tumor types. DNA microarrays have become a key method to acquire a comparative snapshot of the gene expression profile from test samples in a high throughput manner. Quantitative PCR and newer sequencing techniques are popular alternatives offering highly accurate gene expression measurements, but with limitations due to cost, complex instrumentation and analysis needs. RNA extracted from formalin fixed paraffin embedded tissue (FFPE) creates considerable additional challenges in acquiring accurate gene expression measurements due to the highly fragmented and compromised integrity of FFPE RNA due to the fixation process.

To address the challenges of current sequencing based methods and take advantage of the simplicity of analysis that comes with using technologies such as microarrays; we have tested the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit using RNA isolated from bladder tumor FFPE specimens. This targeted RNA sequencing approach allows profiling the global mRNA expression of human RNA in a highly multiplexed fashion using the Ion AmpliSeq™ technology. 10ng of total RNA extracted from FFPE tissue was reverse transcribed followed by automated library preparation on the Ion Chef™ system using the new Ion AmpliSeq™ Kit for Chef and the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel. Eight pooled libraries were then sequenced on the Ion S5™XL System with Ion 540™ Chip. Libraries were also prepared with well characterized control RNAs, Universal Human Reference RNA (UHR) and First Choice Human Brain Reference RNA (HBR) using both the manual and automated library generation protocol for validation and comparison studies.

The results show detection of more genes than popular microarray platforms with comparable differential gene expression measurements to quantitative PCR (r = 0.96) and RNA-Seq methods (r = 0.94). Gene expression values correlated with R>0.99 for all technical replicates and R>0.95 between manual and automated library preparation methods using well characterized samples. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit is a simple method to measure global gene expression profiles from human RNA samples in a timely, cost effective, and high throughput manner resulting in sensitive and accurate gene expression measurements. The new S5™XL System combined with automated library and template preparation on the Ion Chef™ system enable a simple RNA to gene expression data workflow requiring only 45 minutes of hands on time from 10ng of FFPE RNA.

Citation Format: Varun Bagai, Jeoffrey Schageman, Kelli Bramlett, David J. McConkey, Woonyoung Choi. Global gene expression profiles from bladder tumor FFPE 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 1836.

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.

Analysis of the RNA content of the exosomes derived from blood serum and urine and its potential as biomarkers

Exosomes are tiny vesicles (30-150 nm) constantly secreted by all healthy and abnormal cells, and found in abundance in all body fluids. These vesicles, loaded with unique RNA and protein cargo, have a wide range of biological functions, including cell-to-cell communication and signalling. As such, exosomes hold tremendous potential as biomarkers and could lead to the development of minimally invasive diagnostics and next generation therapies within the next few years. Here, we describe the strategies for isolation of exosomes from human blood serum and urine, characterization of their RNA cargo by sequencing, and present the initial data on exosome labelling and uptake tracing in a cell culture model. The value of exosomes for clinical applications is discussed with an emphasis on their potential for diagnosing and treating neurodegenerative diseases and brain cancer.

Abstract 1870: Development of a standard operating procedure for exosome isolation and analysis using clinical samples: Application to cancer biomarker discovery

Exosomes are small vesicles (30-150 nm) found in abundance in human body fluids which function as carriers of different species of RNA and protein between diverse locations in the body. The spectrum of current scientific interest in exosomes is wide and ranges from studying their functions and pathways to utilizing them in diagnostics and therapeutics development. As such, there is a growing need for quick and easy methods for both isolation of exosomes and analysis of their cargo.

We present herein a workflow for exosome isolation and analysis which entails: (i) fast and efficient isolation of exosomes from serum, plasma, and urine of both healthy donors and patients with prostate cancer, using Total Exosome Isolation reagents; (ii) characterization of their size distribution and count with Nanosight LM10 instrument; (iii) extraction of exosome “cargo” with Total Exosome RNA and Protein Isolation kit; (iv) characterization of exosomal RNA content using the Ion Torrent PGM sequencing and qRT-PCR.

The protocol described herein lays the groundwork for the development of a standardized operating procedure (SOP) for isolation of exosomes and downstream analysis of their constituents, using clinical samples.

We demonstrate that cancer-specific RNA signatures residing within the exosomes can be delineated from different patient cohorts. This is the first step towards developing a method whereby performance characteristics can be measured and used to optimize a validated assay useful for routine testing of clinical samples.

Citation Format: Robert A. Setterquist, Alex J. Rai, Emily Zeringer, Mu Li, Tim Barta, Jeoffrey Schageman, Susan Magdaleno, Alexander V. Vlassov. Development of a standard operating procedure for exosome isolation and analysis using clinical samples: Application to cancer biomarker discovery. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1870. doi:10.1158/1538-7445.AM2014-1870

Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease

BACKGROUND

Bronchial airway expression profiling has identified inflammatory subphenotypes of asthma, but the invasiveness of this technique has limited its application to childhood asthma.

OBJECTIVES

We sought to determine whether the nasal transcriptome can proxy expression changes in the lung airway transcriptome in asthmatic patients. We also sought to determine whether the nasal transcriptome can distinguish subphenotypes of asthma.

METHODS

Whole-transcriptome RNA sequencing was performed on nasal airway brushings from 10 control subjects and 10 asthmatic subjects, which were compared with established bronchial and small-airway transcriptomes. Targeted RNA sequencing nasal expression analysis was used to profile 105 genes in 50 asthmatic subjects and 50 control subjects for differential expression and clustering analyses.

RESULTS

We found 90.2% overlap in expressed genes and strong correlation in gene expression (ρ = .87) between the nasal and bronchial transcriptomes. Previously observed asthmatic bronchial differential expression was strongly correlated with asthmatic nasal differential expression (ρ = 0.77, P = 5.6 × 10(-9)). Clustering analysis identified TH2-high and TH2-low subjects differentiated by expression of 70 genes, including IL13, IL5, periostin (POSTN), calcium-activated chloride channel regulator 1 (CLCA1), and serpin peptidase inhibitor, clade B (SERPINB2). TH2-high subjects were more likely to have atopy (odds ratio, 10.3; P = 3.5 × 10(-6)), atopic asthma (odds ratio, 32.6; P = 6.9 × 10(-7)), high blood eosinophil counts (odds ratio, 9.1; P = 2.6 × 10(-6)), and rhinitis (odds ratio, 8.3; P = 4.1 × 10(-6)) compared with TH2-low subjects. Nasal IL13 expression levels were 3.9-fold higher in asthmatic participants who experienced an asthma exacerbation in the past year (P = .01). Several differentially expressed nasal genes were specific to asthma and independent of atopic status.

CONCLUSION

Nasal airway gene expression profiles largely recapitulate expression profiles in the lung airways. Nasal expression profiling can be used to identify subjects with IL13-driven asthma and a TH2-skewed systemic immune response.

All human genes of the uteroglobin family are localized on chromosome 11q12.2 and form a dense cluster

Rabbit uteroglobin is the founder member of a family of mammalian proteins that has expanded to more than 20 members within the last few years. All members are small, secretory, rarely glycosylated dimeric proteins with unclear physiological functions and are mainly expressed in mucosal tissues. A phylogenetic analysis shows that the family can be grouped into five subfamilies, A to E. Subfamily A contains rabbit uteroglobin and its orthologues from various species; most of these have been described to form antiparallel homodimers via two intermolecular disulfide bonds. All other subfamily members contain a third conserved cysteine and, from existing biochemical data, it can be predicted that a member of subfamily B or C will likely form heterodimers with a partner from subfamily E or D, respectively. Besides the mentioned cysteines, only one central lysine is conserved in all family members. In the known uteroglobin structures, this lysine forms an exposed salt bridge with an aspartate side chain, which is conserved in almost all sequences. Using radiation hybrid mapping and P1 clone analysis and utilizing data from the human genome project, we show that all known five human family members (Clara cell 10-kDa protein, lipophilins A and B, lacryglobin, mammaglobin) and a new member, we call lymphoglobin, are localized on chromosome 11q12.2 in a dense cluster spanning not more than approximately 400 kbp.

The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1

The gene encoding the insulin-like growth-factor type-2 receptor (Igf2r) is maternally expressed and imprinted. A CpG island in Igf2r intron 2 that carries a maternal-specific methylation imprint was shown in a transgenic model to be essential for Igf2r imprinting and for the production of an antisense RNA from the paternal allele. We report here that the endogenous region2 is the promoter for this antisense RNA (named Air, for antisense Igf2r RNA) and that the 3' end lies 107,796 bp distant in an intron of the flanking, but non-imprinted, gene Mas1.