bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concurrent targeted resequencing for translocations and mutations in tumor samples.
Authors: Chen Li 
Published: May 2019

e14597 Background: Genetic variations are diverse, and proper nucleic acid templates should be analyzed for optimal outcomes. Previous NGS assays separately treat DNA and/or RNA, and are costly and produce limited information. Here we present a concurrent assay simultaneously converting both RNA and DNA templates in a single-tube format to streamline variant detection process. Methods: We developed a high-throughput targeted resequencing assay utilizing both DNA and RNA templates for mutation and fusion detection, and applied to a cohort of over 1000 lung tumor samples. Total nucleic acids from tissue samples were processed in a single-tube format throughout, and post-assay data analysis split RNA and DNA signals for corresponding variant calling. Sensitivity and specificity were sufficient for tissue samples. Results: In addition to common EGFR, KRAS, BRAF, PIK3CA mutations and ALK, ROS1, RET fusions and MET Exon 14 skipping, we also identified rare HLA-DRB1---MET and MSN---NTRK2 fusions. We found that MET exon 14 skipping was abundant, and that EGFR T790M is more associated with Exon 19 deletion than with L858R. We also found baseline mutation frequency for FFPE samples at 4-5%. Conclusions: Overall, this method is robust and convenient for clinical molecular diagnosis for tissue samples where variant types are diverse and time and budgets are constrained. Extreme caution is suggested for making positive calls below 5% MAF.
Real-world experience in advanced NSCLC using FDA approved NGS CDx.
Authors: Elkhouly Ehab , Zhou Li , Kurtis Boaz , Wang Lan , Israyelyan Anna 
Published: May 2019

e14602 Background: The number one challenge in clinical biomarker testing for non-small cell lung cancer (NSCLC) has been the sample adequacy, given that the majority of patients are diagnosed based on minimally invasive sampling of tumor tissue. The increasingly evolving integration of high-throughput next-generation sequencing (NGS) has redefined molecular diagnostic lab practice allowing for time- and cost-efficient parallel testing of multiple biomarkers with limited specimen. Two NGS companion diagnostic (CDx) tests have been approved by FDA, FoundationOne CDx (F1CDx) and Oncomine Dx Target Test (Oncomine Dx), but with different sample acceptance criteria. The minimum tumor content requirement for F1CDx is 20% while it is 10% for Oncomine Dx. The surface area requirement for F1CDx is 25mm2 while there is no required minimum surface area for Oncomine Dx. The difference in sample acceptance criteria may have a major impact on the number of advanced NSCLC patient samples that can be accepted and tested successfully, affecting biomarker-directed therapy. Methods: The analysis of 153 NSCLC patient samples tested by Oncomine Dx at Cancer Genetics, Inc. CLIA-certified and CAP-accredited lab from October 2017 to September 2018 evaluated the sample acceptance rate, biomarker results, and testing turn-around time (TAT). Results: Based on the data, a significant portion of the samples submitted for routine clinical testing consists of extremely small specimen, including FNA cytology, with 42% less than 1mm2. 83% of samples are acceptable by Oncomine Dx criteria, compared to 14% by F1CDx. Of the 82 samples that would not be acceptable by F1CDx but generated results by Oncomine Dx, 5 were positive for EGFR exon 19 deletions and L858R, 1 for BRAF V600E, 1 for a ROS1 fusion, and the remaining 35 were positive for other actionable alterations. Average TAT was 9.2 days, consistent with recommendation by IASLC/AMP/CAP guideline of within 10 days. Conclusions: The real-world routine clinical testing of NSCLC patient samples demonstrated that a higher number of specimens with limited tumor tissue could be tested with the FDA-approved NGS CDx Oncomine Dx providing rapid TATs, actionable insights, and impacting the patient treatment outcomes.
Tumor volumetric correlation with plasma cell free DNA (cfDNA) mutation detection in metastatic lung cancers.
Authors: Haseltine Justin , Offin Michael , Myers Mackenzie L. , Makhnin Alex , Adamski Ariana , Li Henry , Li Mark , Shaffer Tristan , Henderson Samantha , Shen Ronglai , Ladanyi Marc , Arcila Maria E. , Jones David Randolph , Rusch Valerie W. , Rudin Charles M. , Isbell James M. , Li Bob T. , Rimner Andreas 
Published: May 2019

e14610 Background: In patients with metastatic lung cancers, analysis of cfDNA is increasingly used to detect oncogenes, frequently allowing matched targeted therapy. Mutation detection in cfDNA may be influenced by several factors, such as disease burden. We hypothesized that volumetrics, as routinely analyzed during radiation simulation, correlates with mutation detection in cfDNA. Methods: Patients underwent cfDNA analysis between 10/2016 and 1/2018. Those with metastatic NSCLC, adequate imaging for volumetric analysis (PET/CT and MRI brain), and who were treatment naïve at plasma draw were included. Plasma underwent a 21-gene next generation sequencing assay (Resolution Bioscience). A single observer segmented tumor volumes. Volume of disease was correlated with mutation detection in cfDNA for all 21 genes including the 8 NCCN oncogenes (EGFR, ALK, ROS1, BRAF, KRAS, HER2, RET, MET) with univariate Mann-Whitney. Results: Of the 210 pts with plasma, 52 met inclusion criteria. There were 22 males (42%), median age 67yo (IQR 59-74), 24 former smokers (median pack-years: 25), 44 adenocarcinomas (85%), 21 matched to targeted therapy based on cfDNA results (40%), and median cfDNA extracted concentration was 1.56 ng/mL (IQR 1.1 – 2.6 ng/mL). Involved sites included lymph nodes (n = 43), bone (n = 25), brain (n = 15), liver (n = 13), and adrenals (n = 12). Median total tumor volume was 67.0 mL (IQR 36.6-184.6 mL). When evaluating all 21 genes, cfDNA was mutation positive in 40 pts and negative in 12 pts. Median tumor volume was 77.6 mL and 40.4 mL for positive and negative, respectively (p = 0.12). For the 8 NCCN oncogenes, cfDNA was positive in 18 pts and negative in 34 pts. Median tumor volume was 105.3 mL and 67.0 mL for positive and negative, respectively (p = 0.40). Conclusions: Volumetric analysis showed there was a non-significant trend toward larger tumor volume among pts with positive cfDNA mutation detection. As the use of cfDNA continues to expand into earlier disease stage settings, volumetrics at diagnosis may become an increasingly important tool to help predict cfDNA mutation detection to guide targeted therapy. Further studies of volumetrics and cfDNA analysis are warranted.
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.
Authors: Williamson John B. , Solano Luis , Yuki Akemi , Burkhart Vanessa D. , Chitwood James , Cao Ru , Schageman Jeoffrey , Saunders Hannah , Cheng Angie , Ha Thomas , Ojcius Cecilia , White Roxana , McCall Kimberly , Salazar Suzanne , Bramlett Kelli , Tian Huan , Ramsamooj Rajendra 
Published: May 2019

e14614 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.
Mapping the activation landscape of the MAPK\ERK pathway for variants of unknown significance (VUS) using convolutional neural networks (CNN).
Authors: Tarcic Gabi , Zimmerman Lior , Aizenman Arie , Barbash Zohar , Zelichov Ori , Vidne Michael 
Published: May 2019

e14615 Background: The MAPK\ERK signaling pathway is a major determinant in the control of diverse cellular processes. This pathway is often up-regulated in human tumors and as such has been an attractive target for the development of anticancer drugs. Mapping the activation landscape of MAPK\ERK is a necessary step in understanding tumor progression and determining the significance of a mutation as well as the relevance of available treatments. Here we present a CNN model, combined with an in-vitro system to investigate the activation landscape of various members of the MAPK\ERK pathway Methods: A novel multi-resolution multi-channel deep neural network was trained to classify images of cells that were transfected with known activating mutated forms of MAPK activating proteins versus WT forms of the proteins. The cells were also transfected with a fluorescently tagged ERK2 expression construct that was one of the three channels imaged by a fluorescent microscopy system. The trained network was subsequently tested on its ability to score images of cells that were transfected with VUS forms of the proteins, or images of cells that were transfected with VUS forms of MAPK proteins and were incubated with the relevant targeted therapies Results: We analyzed 6 proteins activating MAPK\ERK carrying over 100 unique VUS as well as many known oncogenic mutations and determined the pathogenicity score outputted by the network. Analysis of the performance of our model showed that our predictions exceed 95% accuracy and AUC > 0.95. Interestingly, analysis of deeper layers of the network revealed that each gene and mutation exhibit a unique ERK2 activation signal which is considerably different between active and non-active mutations as well as the ability to recognize what mutated gene was transfected, which means that each mutated gene induces different phenological attributes to the cells Conclusions: The use of deep-learning algorithms is providing increasing clinical relevance in several medical fields, most notably pathology. We show that using a cell-based assay combined with high throughput microscopy and CNN based analysis can be used to determine the activity of a wide set of mutations and potentially assist the prediction of targeted therapy outcome. Our results highlight the role of functional interpretation of molecular profiles, enabling more accurate prediction of oncogenic mutations.
Notch family gene mutations associate with high tumor mutational burden in diverse cancers.
Authors: Jiang Da , Niu Zhaojian , Zhang Jianli , Wang Yanlei , Shang Liang , Li Bixun , Guo Jun , Wang Baogui , Zhao LingQin , Wang Wenjing , Cui Qiang , Pan Xiaodong , Hu Jinwei , Zhang Shiyue , Wang Kai 
Published: May 2019

e14616 Background: The Notch pathway has an important role in tumorigenesis in many types of cancer. Clinical trials with Notch inhibitors are ongoing. Recently, Notch pathway has been reported to be part of tumor immunity and patients with NOTCH1 mutations (mut) showed better outcome to PD-1 inhibitors, however, the underlying mechanism is unknown. Methods: Next generation sequencing (NGS) panel of 450 cancer genes was performed on FFPE tissue and matched blood samples from 1341 solid tumors, including hepatocellular carcinoma (HCC, n = 644), esophageal carcinoma (EC, n = 255), breast cancer (BC, n = 175), small cell lung cancer (SCLC, n = 141), head and neck cancer (HNC, n = 77). Notch family gene (NOTCH1/2/3/4) muts were analyzed. Genomic alterations including single base substitution, short and long insertions/deletion, copy number variation, gene fusion and rearrangement were assessed. Tumor mutational burden (TMB) was calculated in all patients by NGS algorithms. TMB high (TMB-H) was defined as TMB values ≥75% tumors in each tumor type. Results: For all patients, Notch family gene mut (substitution/indel/truncation) were found in 27% EC, 19% SCLC, 12% HNC, 6% BC and 5% HCC. The median TMB was 6.1 muts/Mb. In general, tumors with Notch family gene mut had significantly higher median TMB in pan-cancer cohort when compared with tumors without Notch family gene mut (9.2 vs. 6.1 muts/Mb, p < 0.001). Specifically, tumors with NOTCH1 mut had higher TMB in HCC (8.5 vs 5.5, p = 0.034), in BC (23.2 vs. 4.6, p = 0.006) and in SCLC (14.0 vs. 9.4, p = 0.002), while NOTCH2 mutant tumors presented higher TMB in HCC (18.5 vs. 5.5, p = 0.026), in EC (14.7 vs. 6.9, p = 0.001) and in SCLC (13.2 vs. 4.6, p = 0.026). We found 65% of NOTCH1 mut were located in epidermal growth factor (EGF)-like repeats domain. Classes of the NOTCH1 mutation type were substitution/indel (non-frameshift) (58%) and truncation (42%), while NOTCH2 mut were 88% and 12%. In TMB-H tumors, substitution/indel is the predominant mutation type of Notch family gene (NOTCH1 61%, NOTCH2 100%). Conclusions: Tumors with Notch family gene mut presented higher TMB in multiple cancer types, indicating a potential strategy for targeted and immunotherapy in NOTCH mutant cancers.
Characterization of OASEP1 as a biomarker and therapeutic target for oral cancer.
Authors: Takano Atsushi , Yoshitake Yoshihiro , Shinohara Masanori , Daigo Yataro 
Published: May 2019

e14627 Background: The improved understanding of cancer-specific oncoproteins could lead to the development of new biomarkers or therapeutic strategies for oral cancers. Methods: We conducted this study as follows: i) Identification of up-regulated genes in oral cancers by means of cDNA microarray, ii) Validation of clinicopathological significance of their protein expression by tissue microarray, iii) Examination of the growth on cancer cells by siRNA, iv) Elucidation of their biological effects on tumor growth. Results: We selected a secreted protein, OASEP1 (oral cancer-associated serum protein 1) as a candidate. Immunohistochemical staining showed that OASEP1 protein expression in cytoplasm was observed in 73 (74.4%) of 98 oral cancers that had undergone curative surgery. In addition, high level of OASEP1 expression was associated with poor prognosis for oral cancer patients ( P = 0.0158, by log-rank test). Suppression of OASEP1 expression by siRNA for OASEP1 significantly suppressed the growth of oral cancer cell lines partly through apoptosis as detected by flow cytometric analysis, apoptosis assays, and time lapse imaging. In addition, siRNAs for a candidate receptor of OASEP1 also significantly inhibited its expression and the growth of oral cancer cells, indicating that the functional interaction between OASEP1 and its receptor could regulate the growth of oral cancer cells. Conclusions: Our data suggest that OASEP1 is a possible prognostic biomarker and therapeutic target for oral cancer.
A novel function for cyclin D1 as a transcriptional role in oncogenesis and tumor development by ChIP-Seq and RNA-Seq.
Authors: Xiong Yudi , Zhou Yunfeng 
Published: May 2019

e14628 Background: Cancer is a major public health problem and remains one of the most leading causes of death worldwide. Aberrations in cell cycle control is defined as one of the hallmarks of cancer.While cyclin D1 is an essential protein to cell cycle which promote G1 phase into S phase, and frequently overexpressed in many human cancers.Although the participation in cell cycle and tumorigenesis has not been well characterized,new functions have been identified in transgenic mice models, including the transcription of genome,the development of chromosome instability and DNA repair.However,it remains unclear that the function of cyclin D1 indenpend of involving cell cycle.In this research,our aim is to find the function of cyclin D1 in transcription in human cancers. Methods: We chose the human cervical cancer cell line,C33A as our main research object.Using chromatin immunoprecipitation sequencing (ChIP-seq) coupled with RNA sequencing (RNA-seq),to find out the genes differentially expressed in C33A,cyclin D1 knock-in C33A and cyclin D1 knock-down C33A. Results: We detected 5590 genes involved in binding with cyclin D1 by ChIP-seq,screened 2811 genes up-regulation,2727 genes down-regulation in cyclin D1 knock-in cells,2244 genes up-regulation,1738 genes down-regulation in cyclin D1 knock-down cells by RNA-seq.Through analysis of the results of ChIP-seq and RNA-seq,we finally identified 422 genes differentially expressed at the RNA level.These genes are highly enriched in Gene Ontology categories and involve in diverse cellular functions via KEGG classification , including translation,replication and repair,signal transduction,cell growth and death. Conclusions: These findings suggested that cyclin D1 can serve both to activate and downregulate gene expression as a transcriptional role directly binding with genome DNA,which means that cyclin D1 may be a key protein during oncogenesis and tumor development.
DDP4 inhibitors as novel agents in improving survival in diabetic patients with CRC and lung cancer: A SEER-Medicare study.
Authors: Bishnoi Rohit , Hong Young-Rock , Shah Chintan , ali azka , Skelton William Paul , Huo Jinhai , Dang Nam H. , Dang Long H. 
Published: May 2019

e14633 Background: DPP4 is a cell surface protein that is widely expressed on different tissues and can play important role in tumor biology by acting as a tumor suppressor or activator, depending upon the level of expression and interaction with the microenvironment and chemokines. DPP4 inhibitors are a class of drug used in the clinical setting to treat diabetes mellitus type II (DM-II) while recent research has suggested that they play a role in regulating tumor growth. Methods: We conducted this large population database Surveillance Epidemiology and Endpoint Research (SEER-Medicare) study to evaluate the role of DPP4 inhibitors on the overall survival (OS) of patients with colorectal and lung cancers. Results: Our results showed that diabetic patients with colorectal cancer (CRC) or lung cancer who were treated with DPP4 inhibitors exhibited a statistically significant survival advantage (HR of 0.89; 95% CI: 0.82-0.97, p = 0.007) that remained significant after controlling for all other confounders. When DPP4 inhibitors were used in combination of metformin, which is already known to improve OS in many cancers, the survival advantage was even more pronounced (HR of 0.83; 95% CI: 0.77-0.90, p < 0.0001). When results were analyzed for CRC-only cohort, the use of DPP4 inhibitors alone had a very positive survival advantage trend (HR of 0.87; 95% CI: 0.75-1.00, p = 0.055) whereas the combined use of DPP4 inhibitors and metformin was associated with statistically significant survival advantage (HR of 0.77; 95% CI: 0.67-0.89, p = 0.003). Similarly, in the lung cancer cohort, the DPP4 inhibitor group exhibited a potential survival advantage (HR of 0.93; 95% CI: 0.83-1.03, p = 0.153), while lung cancer patients treated with the combination of DPP4 inhibitors and metformin showed statistically significant survival advantage (HR of 0.88; 95% CI: 0.80-0.97, p = 0.010). Conclusions: These results again establish that DPP4 inhibition in CRC and lung cancer is associated with the suppression of tumor growth and improved OS. The beneficial effects of DPP4 inhibitor treatment are additionally improved when DPP4 inhibitors are used in combination with metformin. While the exact mechanism involved in the observed benefit of DPP4 inhibitor treatment in cancer remains to be elucidated, one possibility may be due to the effect of DPP4 inhibition on immunoregulation of cancer.
Mechanistic study of the superior anti-cancer properties of a first-in-class small molecule targeting PCNA.
Authors: Gu Long , Lingeman Robert , Li Min , Hickey Robert , Liu Yilun , Malkas Linda 
Published: May 2019

e14636 Background: Proliferating cell nuclear antigen (PCNA), through its interaction with various proteins involved in DNA synthesis, cell cycle regulation, and DNA repair, plays a central role in maintaining genome stability. We previously reported a novel cancer associated PCNA isoform (dubbed caPCNA), which was predominantly expressed in a broad range of cancer cells and tumor tissues, but not significantly in non-malignant cells. We found that the caPCNA-specific antigenic site lies between L126 and Y133, a region within the interdomain connector loop of PCNA that is known to be a major binding site for many of PCNA’s interacting proteins. A cell permeable peptide harboring the L126-Y133 sequence inhibited PCNA function in cancer cells and selectively kills cancer cells and xenograft tumors. Methods: Based on these observations, we sought small molecules targeting this peptide region of PCNA as potential broad-spectrum anti-cancer agents. Results: Our effort led to a drug candidate, AOH1996, which selectively kills a broad range of cancer cells at high nanomolar concentrations, but is not associated with significant toxicity to non-malignant cells. It also works synergistically with DNA damaging chemotherapeutic drugs, such as cisplatin and irinotecan, to selectively kill cancer cells. This compound is orally available to animals and suppresses tumor growth in a dosage form compatible to clinical applications. Importantly, it doesn’t cause significant toxicity at 2.5 times its effective dose. Mechanistically, AOH1996 competes with T3, a known PCNA ligand, for binding to PCNA. However, the mechanism by which AOH1996 exerts its effect on cancer cells may not be identical to what have been reported for the T3 analogs. In particular, we found that AOH1996 interferes with the association of PCNA and MCM7 to euchromatin, leading to DNA replication stress, blockade of homologous recombination-mediated DNA repair, and induction of apoptosis in cancer cells. Conclusions: These findings demonstrated the potential of this compound as a novel therapeutic agent warranting clinical investigation for cancer treatment. We have started planning a phase 1 clinical study for this compound.