bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2707: Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential
Authors: Nadarajah Niroshan , Meggendorfer Manja , Haferlach Torsten , Kern Wolfgang , Haferlach Claudia 
Published: July 2017

Abstract
Introduction: The genomic landscape of hematological malignancies has been resolved mainly based on whole exome and whole genome sequencing, primarily targeting gene mutations. In addition to mutations, gene fusions have also been identified as therapeutic targets, impressively shown e.g. for BCR-ABL1 and ETV6-PDGFRB. Even though fluorescence in situ hybridization (FISH) is the current gold standard in fusion detection, it is by concept limited to the selected genes it is applied to. In contrast, targeted RNA sequencing is a valuable hypothesis-free approach to discover all possible fusion junctions in a single reaction.
Aim: Explore the value of targeted RNA sequencing in a routine diagnostic work up.
Patients and Methods: We sequenced 134 cases in parallel to our routine diagnostics workflow using chromosome banding analysis (CBA), FISH and real-time quantitative (RQ-PCR). Targeted RNA sequencing was performed on the NextSeq 500 using the TruSight RNA Fusion panel (Illumina, San Diego, CA) consisting of 7690 probes covering 507 genes known to be involved in gene fusions. Analysis was performed with the RNA-Seq Alignment App v1.2.0 (BaseSpace Sequence Hub) using Star for Alignment and Manta for gene fusion calling with default parameters (Illumina, San Diego, CA).
Results: In 127 of 134 (95%) cases the results of FISH, subsequently confirmed with RT-PCR were also picked up by RNA Seq. This included diagnostically highly relevant fusions like BCR-ABL1 (n=8), KMT2A rearrangements (n=7), PML-RARA (n=4), and ETV6 and NPM1 rearrangements. In addition to the confirmation of orthogonal results, we were able to identify novel rare gene fusions, which we subsequently confirmed by RQ-PCR. This included immediately targetable fusions like TNIP1-PDGFRB and ETV6-EFL1, ETV6-FOXO1, IRF2PB1-RARA, RARA-SAE1).
Conclusion: 1) In the vast majority of instances targeted RNA sequencing confirmed results obtained by FISH/RT-PCR and in addition discovered new rare gene fusions 2) Targetable genetic aberrations were identified, which were not identifiable by chromosome banding analysis but would now lead to more individualized treatment. 3) Thus, targeted RNA sequencing may be a valuable tool in routine diagnostics and for patients with rearrangements unresolved by standard techniques, also paving the way to precision medicine in a considerable number of patients.
Citation Format: Niroshan Nadarajah, Manja Meggendorfer, Torsten Haferlach, Wolfgang Kern, Claudia Haferlach. Targeted RNA sequencing reveals thus far unknown diagnostically relevant fusion partners confirming its diagnostic potential [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 2707. doi:10.1158/1538-7445.AM2017-2707
Abstract 2708: A custom gene expression panel for consensus molecular subtype classification of archival primary and metastatic colorectal cancers
Authors: Huw Ling-Yuh , Piskol Robert , Melo Felipe de Sosa e , Kim Doris , Qu Xueping , Koeppen Hartmut , Lackner Mark , Hampton Garret , Kabbarah Omar , Tam Rachel 
Published: July 2017

Abstract
Stratification of Colorectal Cancer (CRC) into actionable molecular subtypes has tremendous clinical value. Recently, a consolidated classifier identified four molecularly distinct CRC subtypes (CMS1-4) that were associated with unique biology and clinical outcomes based on global transcriptional analysis of frozen tissues. Here, we developed and applied a novel CRC panel that is ideally suited for transcriptional classification of archival clinical samples. Findings from in silico analysis demonstrated that the 800 genes on our panel could accurately classify CRC samples from external public datasets into the correct CMS subtypes. We applied our panel in the analysis of a novel cohort of 312 formalin-fixed paraffin-embedded (FFPE) tissues from 205 patients, and were able to detect all 4 CMS subtypes in primary CRCs and in metastases. When we examined the CMS subtypes of primary tumors and matched metastases from 50 patients we found 70% of cases to be concordant, as were key biologies, such as WNT/MYC pathway activation in CMS2 and EMT features in tumors of the CMS4 subtypes. This was confirmed by in situ hybridization (ISH) using the markers ASCL2 for CMS2 and SPARC for CMS4, respectively. Discordance in the CMS subtypes between primary tumors and matched metastases were observed in 30% of cases and may reflect tumor heterogeneity. Our findings suggest that our CRC-focused panel many have clinical utility for CMS classification of FFPE samples, and point to potential risks of using CMS subtypes of primary tumors to inform clinical decision-making at the metastatic stage in a subset of patients.
Citation Format: Ling-Yuh Huw, Robert Piskol, Felipe de Sosa e Melo, Doris Kim, Xueping Qu, Hartmut Koeppen, Mark Lackner, Garret Hampton, Omar Kabbarah, Rachel Tam. A custom gene expression panel for consensus molecular subtype classification of archival primary and metastatic colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2708. doi:10.1158/1538-7445.AM2017-2708
Abstract 272: Circadian disruption and cancer risk in the United States
Authors: Caporaso Neil E. , Gu Fangyi , Xu Shangda , Devesa Susan S. , Zhang Fanni , Klerman Elizabeth B. , Graubard Barry 
Published: July 2017

Abstract
Circadian disruption is a probable human carcinogen. Dawn and dusk times occur latter in western compared to eastern regions of each time zone, producing discrepancies between individuals’ biological clock and social time which may lead to circadian disruption and increased risk of cancer. We examined associations between longitude distance from the time zone meridian and age-standardized county-specific cancer incidence rates for total and 23 specific cancers by gender. Four million whites were diagnosed with cancer during 2000-2012 in the Surveillance, Epidemiology and End Results Program in residents of 607 counties in 11 continental US states. The models were adjusted for latitude, poverty, smoking, and state as well as rural/urban location, obesity, and Hispanic composition.
The total cancer incidence rates for counties located in the western regions of time zones were significantly elevated for both men and women after Bonferroni correction. The rate ratio (RR) per five degrees of longitude toward the west (corresponding to 20 minutes delay of sunrise) was 1.03 (95% confidence intervals, CI, 1.02-1.04, p=2.7×10-6) for men and 1.04 (95% CI, 1.03-1.05, p=3.8 ×10-10) for women. Chronic lymphocytic leukemia rates for counties in the western portions of time zones were significantly elevated for both men (RR=1.13, 95% CI=1.08-1.20, p=3.1 x10-6) and women (RR=1.12, 95%CI=1.05-1.19, p=3.7 x10-4). Among men, western location within a time zone was associated with elevated risk of prostate cancer (RR=1.04, 95% CI=1.02-1.07, p=4.8 x 10-4). Among women, western location within a time zone was associated with an increase in breast cancer (RR=1.04, 95% CI=1.02-1.06, p=6.5 x 10-5) and corpus uteri cancer (RR=1.10, 95% CI=1.07-1.14, p=2.4 x 10-9 among others.
The increased cancer risk with western residency within a time zone is in accord with the circadian disruption hypothesis. Our findings suggest that circadian disruption is not a rare phenomenon affecting only shift workers or international travelers but may be widespread in the general population which has broader implications for public health than generally appreciated.
Citation Format: Neil E. Caporaso, Fangyi Gu, Shangda Xu, Susan S. Devesa, Fanni Zhang, Elizabeth B. Klerman, Barry Graubard. Circadian disruption and cancer risk in the United States [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 272. doi:10.1158/1538-7445.AM2017-272
Abstract 2724: Brush biopsy miRNA based OSCC detection and diagnosis
Authors: Adami Guy R. , Schwartz Joel L. , Zhou Yalu , Tang Jessica L. , Markiewicz Michael , Jefferson Gina D. , Epstein Joel , Kolokythas Antonia 
Published: July 2017

Abstract
RNA based diagnosis and prognosis of squamous cell carcinoma has been slow to come to the clinic. Improvements in RNA measurement, statistical evaluation, and sample preservation still have not made these methods accurate enough to allow truly independent external validation. We propose that in the case of squamous cell carcinoma of the oral cavity that a chief source of variability is sample dissection which leads to variable amounts of stroma mixed in with tumor epithelium. We have used brush biopsy of suspicious lesions to characterize miRNA expression in OSCC epithelium. We used it to show an 11 miRNA signature for OSCC that can differentiate OSCC in both smokers and never smokers from normal tissue. We will report on efforts to optimize this classifier to distinguish OSCC from benign oral lesions such as lichen planus and leukoplakia that can be mistaken for OSCC. We also provide evidence that body fluid samples show similar changes in RNAs with OSCC that are seen in brush biopsy samples -suggesting much of the RNA is coming from the same source tumor epithelium. Finally, using a variation of mirPath designed to eliminate false positive, we have identified the neurotrophin signaling pathway as disregulated in most OSCC epithelium, and for the first time highlight the miRNAs that may control this pathway in OSCC, miR-486-5p, miR-7-5p, miR-146-5p, miR-101-3p, miR-18b-5p, miR-10b-5p, miR-21-5p, miR-20b-5p, miR-126-3p and miR-31-5p.
Citation Format: Guy R. Adami, Joel L. Schwartz, Yalu Zhou, Jessica L. Tang, Michael Markiewicz, Gina D. Jefferson, Joel Epstein, Antonia Kolokythas. Brush biopsy miRNA based OSCC detection and diagnosis [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 2724. doi:10.1158/1538-7445.AM2017-2724
Abstract 2727: Clinical significance of PTEN in UTUC
Authors: Li Liang-Chen , Chuang Cheng-Keng , Chiang Hung-Ying , Chen Ying-Tzu , Lin Po-Hung , Yu Kai-Jie , Pang See-Tong , Weng* Wen Hui 
Published: July 2017

Abstract
Upper tract urothelial carcinoma (UTUC) is a rare malignancy accounts for about 5% of all urothelial tumours. The cancer cells start in the layer of tissue urothelium, and found in the renal pelvis, renal calyces or ureters. When compare the UTUC to the bladder urothelial carcinoma, the pathological and clinical findings are often look and act alike. Previous studies indicated that deletion of phosphatase and tensin homologue (PTEN) gene is common to be found in bladder cancer. As known tumor suppressor gene PTEN is located on chromosome ten and considered as an important negative regulator for the PIP3/Akt signaling pathway to promote cell proliferation and inhibit apoptosis. Thus, this study we aimed to determine clinical significance of PTEN in UTUC. We collected sixty-eight formalin-fixed paraffin-embedded (FFPE) UTUC samples, the tumor stage was according to American Joint Committee on Cancer (AJCC) with Ta (n=15), T1 (n=11), T2 (n=10), T3 (n=18), T4 (n=7) and seven patients with unknown; in which male no.32, female no.36; the median age is 68 y/o (range 40-85 y/o). Fluorescence in situ hybridization (FISH) was performed to exam the PTEN gene copy number or gene structure alterations of UTUC; besides, immunohistochemistry (IHC) analysis were used to observe the PTEN protein expression in the tumor. Our results showed PTEN mutations were observed in twenty-two tumors with heterozygous PTEN deletion; one tumor with homozygous PTEN deletion, and three tumors with PTEN monosomy. Further, heterozygous PTEN deletion was shown significantly associated with stage of pTa, pT1 and pT2 (P=0.048) and history of smoking (P=0.030). The IHC results showed lower expression level was common to be observed in the tumor area. Our findings suggest loss of PTEN is associated with the low-risk group of UTUC but not the high-risk group, the unknown mechanisms between these two subtypes might be existed. Besides, smoking could also as a factor highly emerge from genetic alterations in UTUC. In conclusion, PTEN genomic loss might act a predictive indicator of classification of UTUC, however, the clinical treatment could be different due to the underlying diversity of the molecular activities.
Citation Format: Liang-Chen Li, Cheng-Keng Chuang, Hung-Ying Chiang, Ying-Tzu Chen, Po-Hung Lin, Kai-Jie Yu, See-Tong Pang, Wen Hui Weng*. Clinical significance of PTEN in UTUC [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 2727. doi:10.1158/1538-7445.AM2017-2727
Abstract 2728: Frequency and prognostic value of PI3KCA mutations in early stage of colorectal cancer in Mexican patients
Authors: Ruiz-Garcia Erika , Ortega Alette , Bahena Antonio , Fernandez Edith , Calderillo German , Camarillo Cesar Lopez , Marchat Laurence , Guadarrama Jorge , Meneses-Garcia Abelardo , Vega Horacio Astudillo-de la 
Published: July 2017

Abstract
Background: There are molecular associations between mutated profiles and microsatelital instability, both related with tumor growth and oncogenic development by activating tyrosine receptors families in colorectal cancer (CRC). It is known that exon 9 and exon 20 (H1047R) mutations in PIK3CA increased PI3K activity. Moreover, PIK3CA mutations are significantly associated with tumor recurrence and poor overall survival. The frequency of PIK3CA mutations in CCR occurs in 15-20%, being the catalytic subunit more frequently affected. The aim of our study was to investigate the frequencies and clinical implications of these genetic alterations in advanced CRC.
Methods: Retrospectively, we analyzed the initial paraffin embedded tissue block of 71 Mexican patients with CCR stage II. We evaluated mutations frequency of PIK3CA exon 9 (E542K, E545K) and exon 20 (H1047R) using qBiomarker Somatic Mutation PCR for real-time PCR-based. These methodology increases specificity, multiplex PCR and allelic discrimination. The data analysis was done using Ct values and Analysis Webportal.
Results: We found in our population a frequency of PIK3CA mutations of 26%. Of those, double mutants were present in 7% with a higher frequency for E545K/H1047R. Clinical implication that we found is that any active mutation of PIK3CA is associated to an increase of recurrence risk (HR 1.86;CI 95% =0.46-7.5), but most important is for E545K mutation (HR 4.17; CI 95% 0.85-20.39), meanwhile comparing no mutated with H1074R mutated samples there were no differences in HR (0.53 vs. 0.60, respectively).
Conclusions: We found a higher number of PI3KCA mutations that literature reports and that E545K mutation have a worst prognostic implication but we need to increase our sample looking for statistical significance results. Data from H1047R mutation raise de hypothesis that it could exist a compensatory mechanism related to structural interactions between both helicoidal and catalitic domains.
Citation Format: Erika Ruiz-Garcia, Alette Ortega, Antonio Bahena, Edith Fernandez, German Calderillo, Cesar Lopez Camarillo, Laurence Marchat, Jorge Guadarrama, Abelardo Meneses-Garcia, Horacio Astudillo-de la Vega. Frequency and prognostic value of PI3KCA mutations in early stage of colorectal cancer in Mexican patients [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 2728. doi:10.1158/1538-7445.AM2017-2728
Abstract 2739: Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA
Authors: Chen Xiaoji , Spoerke Jill M. , Yoh Kathryn , Darbonne Walter C. , Huw Ling-Yuh , Gendreau Steven , Huang Shih-Min A. , Lackner Mark R. 
Published: July 2017

Abstract
Circulating tumor DNA (ctDNA) is released from necrotic/apoptotic tumor cells into the bloodstream. Recent studies have demonstrated the value of using ctDNA as biomarkers in cancer diagnosis, prognosis, and drug resistance. Unlike local tissue biopsy, ctDNA collection and analysis is non-invasive, allows continuous monitoring of clonal evolution, and provides an overview of tumor heterogeneity. Copy number variations (CNVs) play an important role in cancer biology. However, traditional CNV analyses of ctDNA using droplet digital PCR (ddPCR) and SNP arrays can only assess a small number of genes due to the low abundance of ctDNA in the majority of patient samples. Next generation sequencing (NGS) offers a more efficient and high-throughput way to study CNVs in ctDNA.
Here, we evaluated the use of low-pass whole genome sequencing (WGS) in determining CNVs in ctDNA. In this work, cell-free DNA was isolated from 1-5 ml of plasma from phase II clinical trial patients with metastatic breast cancer and non-small cell lung cancer (NSCLC) using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). DNA yield was determined by ddPCR, with a range from 2-4000 ng. Sequencing libraries were prepared using 2-10 ng DNA by the ThruPLEX Plasma-Seq Kit (Rubicon Genomics). WGS at 0.1x, 0.25x, 0.5x, and 1x coverage was performed on Illumina NextSeq, and data was analyzed using Nexus Copy Number software (BioDiscovery). As a reference, we sequenced DNA from peripheral blood mononuclear cells (PBMCs) of 20 healthy donors at the same coverage. Low-pass WGS was also performed on a subset of matched tumor tissue samples as comparisons.
Our results showed that WGS of ctDNA at 0.5x coverage was efficient to identify CNVs. CNVs were detected in ctDNA from about half of the patients analyzed, and in general CNVs identified in ctDNA matched the ones found in tumor tissue from the same patient. We also found that CNV patterns from different time points of the same patients clustered together. With this promising system, we will present CNV analysis in ctDNA from breast cancer and NSCLC patients enrolled in phase II clinical trials of the PI3K inhibitor pictilisib. We will evaluate the ability of the method to classify patients into different subgroups, monitor tumor progression, and identify drug resistance mechanisms.
Citation Format: Xiaoji Chen, Jill M. Spoerke, Kathryn Yoh, Walter C. Darbonne, Ling-Yuh Huw, Steven Gendreau, Shih-Min A. Huang, Mark R. Lackner. Low-pass whole genome sequencing detects copy number variations in circulating tumor DNA [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 2739. doi:10.1158/1538-7445.AM2017-2739
Abstract 2744: Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA
Authors: Yaung Stephanie , Lovejoy Alex , Klass Dan , Casey Fergal , Arcot Aruna , Loyzer Melissa , Chiu William , Azhar Nabil , Beckert Sophie , Lange Maria , Siemann Sandra , Froehler Sebastian , Gunn Shelly , Palma John F. 
Published: July 2017

Abstract
The combination of liquid biopsies and ultra-sensitive next-generation sequencing (NGS) holds tremendous promise in oncology for the detection and surveillance of somatic mutations that correlate with diagnosis, prognosis, response prediction, resistance monitoring and tumor burden. We have developed a capture-based NGS workflow that provides ultra-sensitive detection of 4 mutation classes - single nucleotide variants (SNVs), insertions/deletions, copy number amplifications (CNAs) and fusions - from low input cell-free DNA isolated from plasma. Sensitivity and specificity of 2 different AVENIO ctDNA Analysis Kits (for Research Use Only) across 3 sites for 48 samples that included contrived DNA blends with known mutations validated by digital PCR and normal reference plasma samples were assessed. The AVENIO ctDNA Targeted Kit (Targeted) was designed to detect mutations in 17 genes, across 80kb, included in NCCN Guidelines for solid tumors plus additional variants relevant for therapy selection. The AVENIO ctDNA Expanded Kit (Expanded) was designed to detect mutations in 77 genes, across 200kb, associated with solid tumor including variants relevant for clinical trial research. Testing sites achieved 100% sensitivity for SNVs and fusions at 0.5% and 1% allelic frequency, respectively, from 30 ng of input DNA for both kits. Median coverage of 4,200-6,400X was greater with the Targeted kit relative to that of 2,700-3,800X with the Expanded kit. Specificity was 100% for the Targeted kit either by sample or variant. The Expanded kit had a specificity of 91.7-100% by sample and 99.7-100% by variant. At an expected 5X or 8X copy number amplification for multiple genes, both the Targeted and Expanded kits were 100% sensitive and 93.1-98.4% specific per gene. The specificity for fusion detection was 100% for both kits down to 1% mutant allele frequency. The AVENIO ctDNA Analysis Kits for plasma and NGS applications provide exquisite sensitivity and specificity for the simultaneous detection of 4 different mutation classes.
Citation Format: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma. Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA [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 2744. doi:10.1158/1538-7445.AM2017-2744