bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4877: A modular software solution (under development) to expedite sequencing workflow and mitigate legacy workflow issues in regulatory environments
Authors: Kelly Lisa , Gordon Jessica 
Published: August 2015

Abstract
One of the challenges of working in regulatory environments is the need to revalidate legacy workflows when incorporating new information or tools. Even in unregulated environments, updating and integrating workflows can require a considerable expenditure of time and labor. To mitigate these issues, Illumina is developing an analysis framework software as part of the Universal Oncology Test System for the MiSeqDx™ System, the first next generation sequencer to achieve FDA clearance. By incorporating plug-in workflow modules that seamlessly integrate with the framework - yet remain self-contained and separately versioned from other workflow modules - the software will expedite and ensure scalable operations. Installing new modules to the framework will incur no need for code changes to the legacy workflows, a key consideration for development and validation in regulated environments. The updated MiSeqDx analysis framework includes user authentication and sample sheet setup, reducing the number of disparate application interactions and bringing them together in a clean, clinical user interface accessible via any computer web browser.
The Universal Oncology Test System software workflow module will allow an investigator to identify variants of interest via three methods: an eligibility list of specific coordinate nucleotide changes, configurable rules based on variant type and region, and an amplification gene list with specified amplification type. This flexible software solution can be used to produce, for example, clinical trial reports that require masking of non-investigational variants while not precluding the opportunity to informatically unfilter new information. A report definition can be applied per sample, and updated post-sequencing for a reanalyzed report. The in vitro diagnostic report, also in development, aims to support the pathologist end user by separate categorization of pathogenic variants based on companion diagnostics.
The MiSeqDx analysis software platform combined with the Universal Oncology Test System workflow module can help expedite immediate clinical trial uptake and detection of variants for interpretation and future patient care.
Citation Format: Lisa Kelly, Jessica Gordon. A modular software solution (under development) to expedite sequencing workflow and mitigate legacy workflow issues in regulatory environments. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4877. doi:10.1158/1538-7445.AM2015-4877
Abstract 4880: Characterization of genetic concordance between primary tumor cells, circulating tumor cells, and metastatic tumor cells from patients with prostate cancer
Authors: Yang Lixin , Chen Linling , Wang Yafan , Jones Jeremy , Yen Yun , Loera Sofia , Pillai Raju , Chu Peiguo , Weisenburger Dennis 
Published: August 2015

Abstract
Circulating tumor cells (CTCs) which disseminate from the primary tumor site have been found to be a major source of metastatic tumor. However, CTCs are heterogeneous and most CTC DNA is fragmented due to apoptosis. To better understand the molecular pathogenesis of metastasis, it is imperative to obtain single, non-apoptotic CTCs and investigate the genetic concordance between primary tumor cells, CTCs and metastatic tumor cells. Due to the abundance of normal cells present in the blood and in tumor tissue, isolation of single tumor cells or pure cell populations of these cells is extremely difficult. The DEPArray platform is designated to collect single CTCs after Cell-Search enrichment, and to sort pure intact tumor cells from formalin-fixed, paraffin-embedded (FFPE) tissues. Taking advantage of this technology, we have isolated single CTCs from prostate cancer patients. Whole genome amplification was performed and genomes with high integrity were used to evaluate the hotspot mutations in PIK3CA. For comparison, we also made single cell suspensions from FFPE tissue blocks of primary tumors and metastatic tumor in lymph nodes from the same patients. Immunofluorescence staining for cytokeratin (CK) and vimentin (Vim) was performed, followed by isolation of pure tumor cells (CK+), stromal cells (Vim+) and double-positive cells (CK+/Vim+) from both primary tumor and lymph node samples. We plan to do genetic analysis on these cells and compare the results to determine the genetic concordance between primary tumor cells, CTCs and metastatic tumor cells. By using the DEPArray, we have successfully isolated single CTCs, and populations of tumor cells, stromal cells and double-positive cells from primary and metastatic tumors. We will present new data on the genetic concordance between these cells, which will provide new insight into our understanding of metastasis in prostate cancer.
Citation Format: Lixin Yang, Linling Chen, Yafan Wang, Jeremy Jones, Yun Yen, Sofia Loera, Raju Pillai, Peiguo Chu, Dennis Weisenburger. Characterization of genetic concordance between primary tumor cells, circulating tumor cells, and metastatic tumor cells from patients with prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4880. doi:10.1158/1538-7445.AM2015-4880
Abstract 4884: Highly sensitive fusion transcript detection and quantification in cancer
Authors: Watson Lisa C. , Gross Stephen M. , Khrevtukova Irina , Pathak Smita , Attwooll Claire , Goode Jason , Mai Anthony , Schroth Gary P. 
Published: August 2015

Abstract
Gene fusion detection in cancer samples can provide tumor-specific information for cancer research, clinical diagnosis and targeted treatment. Common fusion detection methods such as qPCR and FISH are restricted to known fusion junctions and limited in the number of genes that can be detected in parallel. In contrast, RNA sequencing is a powerful approach for simultaneous discovery of all possible fusion junctions in a single reaction. But, the sequencing depth required for sensitive detection of fusions from whole-transcriptome libraries can be cost-prohibitive. Here we describe a cancer-specific capture-based approach for fusion detection by RNA sequencing that requires only a fraction of the sequencing depth of whole-transcriptome methods. We designed oligo probes that densely target coding regions of over 200 clinically relevant gene fusions and cancer-associated genes. This oligo panel was used to capture cancer-specific fusions from total RNA-Seq libraries. We used commonly studied cancer cell lines including MCF-7, K562, PC-3, LnCAP, A431 and Universal Human Reference RNA (UHRR) to compare the sensitivity of fusion detection across three RNA-Seq library prep methods: (1) cancer panel library capture (2) whole-transcriptome library capture and (3) PolyA selection. We show that probes targeting individual exons can robustly capture well-characterized cancer gene fusions such as BCR-ABL and BCAS4-BCAS3, as well as translocations where fusion junctions are unknown. Furthermore, these comparisons demonstrate the enhanced sequencing efficiency of the targeted cancer panel, while maintaining highly accurate quantitation of gene expression. We show that selective enrichment of RNA-Seq libraries with cancer-specific capture probes enables high-resolution mapping of genomic rearrangements in patient cancer samples, even those derived from FFPE, facilitating sequencing studies that were not previously possible.
Citation Format: Lisa C. Watson, Stephen M. Gross, Irina Khrevtukova, Smita Pathak, Claire Attwooll, Jason Goode, Anthony Mai, Gary P. Schroth. Highly sensitive fusion transcript detection and quantification in cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4884. doi:10.1158/1538-7445.AM2015-4884
Abstract 4890: Duplex sequencing of AML reveals extensive sub clonal heterogeneity
Authors: Loeb Lawrence A. , Schmitt Michael W. , Prindle Mark J. , Becker Pamela S. 
Published: August 2015

Abstract
Subclonal mutations, that are present in a small subset of tumor cells prior to chemotherapy, could serve as a reservoir for the emergence of drug resistance. These could selectively expand during chemotherapy and result in relapse and death. We have used Duplex DNA Sequencing (DS) to detect low frequency subclonal mutations in AML, both prior to treatment and after relapse. DS focuses on a limited number of target genes at the level of single DNA molecules. Mutations are scored only if they are present at the same position in both strands of the same DNA molecule and are complementary, resulting in sequencing accuracy that is more than 10,000-fold greater than that of conventional next-generation DNA sequencing (NGS).
To follow the course of mutation accumulation in AML, we used capture hybridization to enrich for 15 genes previously reported to be mutated in AML. We identified multiple subclonal mutations prior to therapy that would not be detected by routine NGS. For example, in one relapse sample, we identified a mutation in NRAS that was present in 32% of the cells. The identical mutation was detected by DS prior to treatment in 1% of cells. To further assess the frequency of subclonal mutations in AML, we targeted a 30 kb panel of genes at 500,000 fold depth, which facilitates detection of mutations present in fewer than 0.01% of cells. 5 subclonal mutations were identified within the 30 kb target, corresponding to a frequency of 170 mutations per megabase, Extrapolation of these results to the whole genome indicates that there are approximately 500,000 subclonal mutations per AML genome, which is 1,000 fold higher than the frequency of clonal mutations. These subclonal mutations would be unevenly distributed throughout the genome and be an important source for the selection of drug resistance during therapy.
Citation Format: Lawrence A. Loeb, Michael W. Schmitt, Mark J. Prindle, Pamela S. Becker. Duplex sequencing of AML reveals extensive sub clonal heterogeneity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4890. doi:10.1158/1538-7445.AM2015-4890
Abstract 4894: Targeted sequencing of myeloid cancers using single-molecule enrichment in picodroplets
Authors: Samuels Michael L. , Kotsopoulos Steve K. , Long Frances , Gettler Holly , Clement Omo , Olson Jeff 
Published: August 2015

Abstract
A new method for enrichment of targeted genomic regions for next generation sequencing (NGS) is the use of single-molecule formatted PCR amplification, with the sample's target DNA partitioned into uniform picoliter volume droplets such that there are either zero or one target molecule in each droplet. All the droplets contain all of the primers and PCR reagents, ensuring that every target molecule from the sample is amplified, minimizing the amount of input required. Endpoint PCR using this single molecule format results in highly uniform yields that facilitate efficient use of the sequencing platform. In addition, the primers contain ‘Illumina tails’ that enable easy sample indexing and a workflow for loading directly onto a MiSeq without additional library preparation.
Here we detail the use of this method with the ThunderBolts Myeloid Cancer Panel, which targets ∼550 commonly mutated regions in 49 genes implicated in the causation, prognosis, and recurrence of myeloid disorders. The panel targets include an expert-curated set of 16 full genes and 33 mutational hotspot regions, including challenging targets such as CEBPA and NOTCH1. We present results showing sample inputs as low as 10 nanograms (no pre-amplification used) provide sequencing metrics with 100% coverage at &gt;100x depth (&gt;95% at &gt;500x depth) with a normalized mean read depth of 2500x and high uniformity (&gt;90% of amplicons within 0.2x of the mean), enabling detection of low minor allele frequencies (&lt;5%). The workflow is easy and rapid, with &lt;2 hours hands-on time and sample-to-results in &lt;48 hours. In addition, we demonstrate similar performance metrics when adding additional primer pairs (ThunderBolts PLUS), ensuring continued flexibility for researchers to use the core panel plus additional key targets as they are identified and validated.
In summary, the ThunderBolts Myeloid Cancer Panel shows excellent sequencing coverage, high read depth and uniformity, and detection of low frequency mutations implicated in myeloid cancers. Starting from low input DNA samples, the workflow is easy and fast, enabling low cost targeted Illumina NGS sequencing with an expert curated panel that provides flexibility for expansion.
Citation Format: Michael L. Samuels, Steve K. Kotsopoulos, Frances Long, Holly Gettler, Omo Clement, Jeff Olson. Targeted sequencing of myeloid cancers using single-molecule enrichment in picodroplets. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4894. doi:10.1158/1538-7445.AM2015-4894
Abstract 4895: A one-tube assay for simultaneous detection of gene mutation, fusion, copy number alteration and expression
Authors: Zheng Zongli , Shetty Ranjit , Liebers Matthew , Cambry Jessica L. , Bernardo Lindsay A. , Borger Darrell , Le Long P. , Iafrate John A. 
Published: August 2015

Abstract
There are growing demands for tumor genotyping in the clinic, with an ever-growing number of mutation/fusion targets and expression profiles needed for tumor diagnostics. We sought to develop a comprehensive yet efficient tumor genetic approach using next-generation sequencing (NGS) that would target the genomic DNA and mRNA components of a sample simultaneously, to decrease costs and labor in the lab, and take advantage of small/limited quantity tumor specimens.
We describe here a novel method termed one-tube anchored multiplex PCR (OneAMP) for combined DNA-and-RNA targeted sequencing, allowing simultaneous detection of gene expression, rearrangements, single nucleotide variations (SNVs), insertion and deletions (Indels) and copy number variation (CNV). In this approach, total nucleic acid is used as input for the assay, starting with cDNA synthesis, shearing, adenylation, and ligation with a half-functional molecule-indexed Y adaptor. The molecular index is a random oligomer and serves as a tag for tracing and counting sample templates from ligation through sequencing. Target enrichment is then achieved by two rounds of hemi-nested PCR using gene specific primers and adaptor primers. Gene specific primers for priming genomic DNA (intronic primer extension to exons for SNVs, Indels and CNV) and for priming cDNA (exonic primer extension for gene fusion and expression) have been optimized so they can be combined in one tube for PCR. A distinctive feature of OneAMP is that mRNA expression is normalized to genomic DNA copy number for the same gene, eliminating the need for normalization to housekeeping genes, which can eliminate significant bias across tissue types and individuals.
We developed a 210 gene OneAMP cancer panel that consists of important cancer genes that are mutated, fused, or with altered expression or copy number. We validated CNV calls with aCGH/FISH of the same samples and validated mRNA expression by comparing to array and qPCR. Finally SNVs, Indels, and fusions were validated with a large panel of samples with known mutation status.
We demonstrate the potential of OneAMP for the comprehensive detection of genetic abnormalities, preserving precious tumor samples, and reducing reagent usage and time.
Citation Format: Zongli Zheng, Ranjit Shetty, Matthew Liebers, Jessica L. Cambry, Lindsay A. Bernardo, Darrell Borger, Long P. Le, John A. Iafrate. A one-tube assay for simultaneous detection of gene mutation, fusion, copy number alteration and expression. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4895. doi:10.1158/1538-7445.AM2015-4895
Abstract 49: Interaction of the protein kinase C-related kinases with the TPα and TPβ isoforms of the T prostanoid receptor: role in thromboxane-induced neoplastic responses
Authors: Mulvaney Eamon P. , O'Sullivan Aine G. , Kinsella B Therese 
Published: August 2015

Abstract
Compelling epidemiological evidence concurs that long-term use of aspirin lowers the risk of many prevalent cancers. While such studies do not specify which cyclooxygenase-1/2 metabolite(s) are lowered by aspirin accounting for its prophylactic benefits, many reports show that some of its anti-cancer effects are due to its ability to inhibit thromboxane (TX)A2 generation, a substance more typically known for its role in hemostasis/thrombosis. In humans, TXA2 signals through the TPα and TPβ isoforms of the T prostanoid receptor (TP). There is increasing evidence supporting roles for the TXA2 axis in several neoplasms including prostate cancer, potentially due to the ability of TPα/TPβ to regulate key RhoA- and ERK-mediated signalling cascades that contribute to tumor growth & metastasis. Mechanistically, we recently identified protein kinase C-related kinase (PRK) 1 as a direct interacting partner of TPα/TPβ, a functional interaction essential for TXA2-induced prostate cancer (PCa) cell migration. Moreover, agonist-activation of TPα/TPβ induced phosphorylation of histone H3 at Thr11 (H3Thr11), a PRK1-catalysed marker of androgen-induced chromatin remodelling and transcriptional activation. This was the first demonstration that the TXA2/TP axis can lead to epigenetic changes previously only associated with androgens. As PRK1/PKN1 is a member of a wider subfamily that also includes PRK2/PKNγ and PRK3/PKNβ which, like PRK1, are widely implicated in cancers, we sought to investigate if PRK2 and PRK3 may interact with TPα/TPβ. Both PRK2 and PRK3 were found to interact with TPα and TPβ, interactions dynamically regulated following TP-agonist activation. Activation of the TPs also led to phosphorylation and catalytic activation of all three kinases. Furthermore, PRK1 and PRK2, but not PRK3, interacted with TPα and TPβ in PC-3 cells, while targeted disruption of PRK1 and PRK2, but not PRK3, impaired TP-mediated H3Thr11 phosphorylation, cell proliferation and migration of PC-3 cells. Considering the critical roles of TPα/TPβ and of the PRKs in cancer progression, the discovery of these distinct, yet regulated, interactions is functionally significant, not least in prostate cancer but also in other pathophysiologies where aberrant PRK1-3 &/or TPα/TPβ expression and function are implicated.
Funded by the Irish Cancer Society, Health Research Board Ireland and the Movember Foundation (# PCI12KIN, MRCG/2012/3).
Citation Format: Eamon P. Mulvaney, Aine G. O'Sullivan, B Therese Kinsella. Interaction of the protein kinase C-related kinases with the TPα and TPβ isoforms of the T prostanoid receptor: role in thromboxane-induced neoplastic responses. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 49. doi:10.1158/1538-7445.AM2015-49
Abstract 4903: Microarray gene expression analysis of human prostate cancer PC-3 cells targeted by Salmonella typhimurium A1-R
Authors: Zhao Ming , Wu Wen , Lu Chongyi , Zhang Yong , Hoffman Robert M. , Qi Hui , Yang Meng , Gu Yanqin , Lu Yiyu , Su Shibing , Zhang Hui , Zhou Qianmei , Chen Qilong 
Published: August 2015

Abstract
The transcriptional profile of PC-3 human prostate cancer cells infected with tumor-targeting Salmonella typhimurium A1-R (A1-R) was analyzed with by microarray. PC-3 is highly sensitive to A1-R. Numerous genes involved in diverse cellular processes, including apoptosis, necrotic cell death, neutrophil chemotaxis and innate immunity were significantly up-regulated by A1-R bacterial infection. Such up-regulated genes include TNF-a, Fos and JUN which are involved in cell death and IL-1A and CXCL which are involved in neutrophil chemotaxes. Knowledge of the up-regulated gene profile will be exploited for enhancing prostate tumor targeting by A1-R.
Keywords: Salmonella typhimurium A1-R, human prostate cancer, microarray, apoptosis, necrotic cell death, neutrophil chemotaxis, tumor-targeting.
Citation Format: Ming Zhao, Wen Wu, Chongyi Lu, Yong Zhang, Robert M. Hoffman, Hui Qi, Meng Yang, Yanqin Gu, Yiyu Lu, Shibing Su, Hui Zhang, Qianmei Zhou, Qilong Chen. Microarray gene expression analysis of human prostate cancer PC-3 cells targeted by Salmonella typhimurium A1-R. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4903. doi:10.1158/1538-7445.AM2015-4903
Abstract 4909: Increased IR-A/IR-B ratio in non-small cell lung cancers associates with lower epithelial-mesenchymal transition signature and longer survival in squamous cell lung carcinoma
Authors: Huang Jiaqi , Zhu Wei , Jiang Liyan , Streicher Katie , Morehouse Chris , Brohawn Philip , Ge XiaoXiao , Dong Zhengwei , Yin Xiaolu , Zhu Guanshan , Gu Yi , Mahadevia Parthiv , Higgs Brandon W. , Yao Yihong 
Published: August 2015

Abstract
To evaluate the insulin receptor isoform mRNA expression status in NSCLC patients RNA-seq data from 614 NSCLC [355 adenocarcinomas(LUAD) and 259 squamous cell carcinomas (LUSC)] and 92 normal lung specimens were obtained from The Cancer Genome Atlas (TCGA) to evaluate the mRNAexpression of insulin receptor isoform A (IR-A) and insulin receptor isoform B(IR-B). The differential expression status of the insulin receptor isoforms in NSCLC patients was confirmed using qRT-PCR assays with lung cancer cDNA arrays and primary tumor samples. The mRNA expression levels of IR-B were significantly lower in some NSCLC samples compared to normal lung specimens,including both LUAD and LUSC. Notably, no IR-B transcripts were detected - only the IR-A isoform was expressed in 11% of NSCLC patients. This decrease in IR-B expression contributed to an elevated IR-A/IR-B ratio, which was also associated with lower epithelial-mesenchymal transition gene signatures in NSCLC and longer patient survival under standard of care in LUSC. In addition to NSCLC, RNA-seq data from TCGA revealed a similar increase in IR-A/IR-B ratio in many other cancer types, with high prevalence in acute myeloid leukemia,glioblastoma multiforme, and brain lower grade glioma. Our results indicate a common reduction of the mRNA expression level of IR-B and an increased IR-A/IR-B mRNA ratio in NSCLC and other tumor types. The relationship of altered IR-A/IR-B ratios with cancer progression and patient survival should be prospectively explored in future studies.
Citation Format: Jiaqi Huang, Wei Zhu, Liyan Jiang, Katie Streicher, Chris Morehouse, Philip Brohawn, XiaoXiao Ge, Zhengwei Dong, Xiaolu Yin, Guanshan Zhu, Yi Gu, Parthiv Mahadevia, Brandon W. Higgs, Yihong Yao. Increased IR-A/IR-B ratio in non-small cell lung cancers associates with lower epithelial-mesenchymal transition signature and longer survival in squamous cell lung carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4909. doi:10.1158/1538-7445.AM2015-4909