Interleukin-2 (IL-2) therapy has been demonstrated to induce responses in 10-20% of advanced melanoma and renal cell carcinoma patients, which translates into durable remissions in up to half of the responsers. Unfortunately the use of IL-2 has been associated with severe toxicity and death. It has been previously observed and reported that IL-2 therapy causes a major drop in circulating levels of ascorbic acid (AA). The IL-2 induced toxicity shares many features with sepsis such as capillary leakage, systemic complement activation, and a relatively non-specific rise in inflammatory mediators such as TNF-alpha, C-reactive protein, and in advanced cases organ failure. Animal models and clinical studies have shown rapid depletion of AA in conditions of sepsis and amelioration associated with administration of AA (JTM 9:1-7, 2011). In contrast to other approaches to dealing with IL-2 toxicity, which may also interfere with therapeutic effects, AA possesses the added advantage of having direct antitumor activity through cytotoxic mechanisms and suppression of angiogenesis. Here we present a scientific rationale to support the assessment of intravenous AA as an adjuvant to decrease IL-2 mediated toxicity and possibly increase treatment efficacy.
Solid tumor profiling assays need to deliver accurate and consistent results in the face of decreased quality and quantity of nucleic acids extracted from FFPE samples. Understanding the performance of a particular solid tumor profiling assay with FFPE tissue is critical, but with limited and non-renewable samples available to most assay-developers, the sample number used to understand this performance can be small. TruSight® Tumor 1701 is an Illumina-developed comprehensive solid tumor profiling panel targeting 170 genes using DNA and RNA from FFPE samples. In order to confirm the robustness of the assay with FFPE tissue, 2310 FFPE samples were brought in-house and evaluated. Quantity of both DNA and RNA extraction were determined by various methods, including AccuClear™, Qubit™ and Quantifluor® fluourometric assays. Overall, >95% of the samples achieved the minimum concentrations required for the TruSight® Tumor 170 assay. As a surrogate for DNA quality, we measured the amplification potential of the nucleic acid by assessing a ΔCq value using quantitative PCR after normalization to a fixed input mass. To assess RNA quality, we used the DV200 metric, which measures the percentage of RNA fragments >200 nucleotides in length. We examined ΔCq and DV200 values across different tissues and didn’t find a significant difference between tissues. Finally, we assessed the ability of samples to pass the sample quality control (QC) metrics in the TruSight® Tumor 170 assay. These QC metrics ensure accurate variant calling, with a sensitivity and specificity of ≥95%. We found that samples that had a ΔCq value of ≤5 and a DV200 value of ≥20 achieved a QC success rate above 95%. This data highlights the need for further investigation into the methods for extraction, quantification and quality assessment of nucleic acids for solid tumor profiling and underscores the robustness of TruSight® Tumor 170 with FFPE samples. 1 For Research Use Only. Not for use in diagnostic procedures. Citation Format: Jennifer S. LoCoco, Li Teng, Danny Chou, Xiao Chen, Byron Luo, Jennifer Sayne, Ashley Adams, Naseem Ajili, Cody Chivers, Beena Murthy, Laurel Ball, Allan Castaneda, Katie Clark, Brian Crain, Anthony Daulo, Manh Do, Tingting Du, Sarah Dumm, Yonmee Han, Michael Havern, Chia-Ling Hsieh, Tingting Jiang, Suzanne Johansen, Scott Lang, Rachel Liang, Jaime McLean, Yousef Nassiri, Austin Purdy, Jason Rostron, Jennifer Silhavy, June Snedecor, Natasha Talago, Li Teng, Kevin Wu, Chen Zhao, Clare Zlatkov, Ali Kuraishy, Karen Gutekunst, Sohela De Rozieres, Matthew Friedenberg, Han-Yu Chuang, Anne C. Jager. Evaluation of quantity, quality and performance with the TruSight® Tumor 170 solid tumor profiling assay of nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) tissue sections [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 5354. doi:10.1158/1538-7445.AM2017-5354
Background: As our knowledge of how DNA alterations can drive cancer progression increases, assays that can simultaneously detect multiple types of variants in a simple and cost-effective manner are becoming increasingly crucial. This holds true of copy number variations (CNVs), where evaluation of this type of variant is an important and necessary feature of any solid tumor profiling assay. Conventional methods for detecting CNVs such as immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), and quantitative PCR (qPCR) are limited to detecting only one gene amplification at a time. This can be a significant drawback with FFPE samples, where the DNA is of low abundance and often heavily degraded, while the number of gene amplifications known to be important in cancer continues to grow. Additionally, different tumor types may express amplifications at different rates and expression may be heterogeneous within the tumor, potentially with irregular staining patterns - all of which illustrate the need for new approaches to CNV detection. Methods: Next-generation sequencing (NGS) offers the ability to assess variants in multiple genes using one sample. To that end, Illumina is developing a comprehensive, hybrid capture-based NGS assay targeting 170 key cancer genes for sequencing on the NextSeq1 platform. The assay consists of a DNA workflow for the identification of single-nucleotide variants (SNVs), small insertions and deletions (indels), as well as an RNA workflow for the identification of splice variants and gene fusions. In addition, using the DNA workflow, a novel analysis pipeline, and CNV caller, CNVs from 57 different genes can be simultaneously assessed all by sequencing of a single sample. Results: Here we present data on both cell lines and FFPE samples of SNVs and indels down to 5% allele fraction and CNVs down to ∼2-fold amplification, all from 40 ng of DNA. To demonstrate the accuracy and precision of our CNV detection method, we tested 7 samples for CNVs using orthogonal CNV detection methods. The Illumina NGS assay detected ERBB2 amplifications in 4 out of 7 samples. Of the 4 Illumina NGS positive samples, 3 samples were positive by FISH and all 4 were positive by droplet digital PCR (ddPCR) and the Illumina TruSight Tumor 15 panel. The 3 samples that were negative for ERBB2 amplifications by the Illumina NGS assay were also negative by both FISH and ddPCR. Within these samples we also found a previously unknown FGFR1 amplification. Conclusions: The novel Illumina NGS library preparation method is an innovative and useful tool to find multiple CNVs, along with other variant types, within a single sample. The assay can detect multiple CNVs within a single FFPE sample and identify previously uncharacterized CNVs that could be important in finding the correct treatment for a cancer patient. Citation Format: Chia-Ling Hsieh, Clare Zlatkov, Byron Luo, Chen Zhao, Kathryn Stephens, Han-Yu Chuang, Lisa Kelly, Katherine Chang, Rachel Liang, Jianli Cao, Scott Lang, Ashley Adams, Naseem Ajili, Laurel Ball, Glorianna Caves, Danny Chou, Katie Clark, Brian Crain, Anthony Daulo, Sarah Dumm, Ridwana Ekram, Yonmee Han, Anne Jager, Suzanne Johansen, Li Teng, Jenn Lococo, Jaime McLean, Juli Parks, Jason Rostron, Jennifer Sayne, Jennifer Silhavy, June Snedecor, Mckenzi Toh, Stephanie Tong, Elizabeth Upsall, Paulina Walichiewicz, Xiao Chen, Amanda Young, Ali Kuraishy, Karen Gutekunst, Matt Friedenberg, Charles Lin. Development of a comprehensive and highly sensitive next-generation sequencing assay for detection of copy number variations. [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 3624.
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