bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of prognostic molecular signatures in Asian and Caucasian AML populations.
Authors: Kim Miyoung , Weeraratne S Dilhan , Snowdon Jane , Felix Winnie , Lim Lionel , Lee Young Kyung , Lee Eunyup , Jeon Kibum , Lee Jiwon , Zang Dae Young , Han Boram 
Published: May 2019

e13025 Background: Next generation sequencing (NGS) studies on various cancer types have revealed clinical insights on the molecular etiology of tumors and defined new treatment paradigms. However, the genomic landscape of a tumor type may be predicated on race. Application of broad-brush findings from one population to another may lead to erroneous treatment decisions. While the majority of published NGS cancer studies focus on Caucasian populations, few studies evaluate the molecular profiles of a tumor type between different demographies. In this study, acute myeloid leukemia (AML) patients of East Asian descent were sequenced at a South Korean hospital, interpreted, and compared with the Caucasian population from The Cancer Genome Atlas (TCGA). Methods: 23 South Korean AML patients were sequenced in 2018 using the 54 gene Illumina TruSight Myeloid Panel at Hallym University, College of Medicine. Orthogonal testing for FLT3-internal tandem duplication (ITD) was done by Sanger sequencing. Watsonä for Genomics (WfG), an artificial intelligence decision-support system, was used for variant interpretation and annotation. Additionally, 181 AML patients of Caucasian descent from the TCGA dataset were analyzed for comparison. Results: WfG identified at least 1 clinically actionable therapeutic alteration in 70% (16/23) of all Asian cohort cases. FLT3-ITD or tyrosine kinase domain (TKD) mutations were reported in 27% (49/181) of cases in the TCGA cohort but only 9% (2/23) of the Asian cohort. DNMT3A mutations were detected in 25% (45/181) and 74% (17/23) of the TCGA and Asian cohorts, respectively. Other oncogenic mutations in AML including NRAS, IDH1, IDH2, CEBPA, TET2, and NPM1 were represented at comparable frequencies between the two populations. Conclusions: Tumor biomarkers that affect prognosis can be informative in the clinical setting. In our study, FLT3 and DNMT3A, predictors of poor prognosis in AML, demonstrated decreased and increased respective frequencies in South Koreans compared to Caucasians, suggesting that some mutational signatures that predict cancer outcome may vary by race.
RAS activation and CDKN2A deletion to predict prognosis in cancer of unknown primary.
Authors: Bochtler Tilmann , Reiling Anna , Endris Volker , Hielscher Thomas , Volckmar Anna-Lena , Neumann Olaf , Kirchner Martina , Budczies Jan , Heukamp Lukas , Leichsenring Jonas , Allgäuer Michael , Schirmacher Peter , Stenzinger Albrecht , Kraemer Alwin 
Published: May 2019

e13026 Background: Cancer of unknown primary (CUP) denotes a malignancy with histologically confirmed metastatic spread while the primary tumor remains elusive. Given the typically dismal response to empiric chemotherapy, the deciphering of molecular profiles holds a particular promise for targeted therapy. Here, we address the prognostic implications of mutations and copy number variations (CNVs) detected in tumor tissue in the context of a comprehensive clinical risk assessment. Methods: We performed targeted panel sequencing in a series of 252 CUP patients. Median age was 60.3 years and 59.1% were female. 71.2% of patients had unfavorable CUP. Lymph nodes, bone marrow, lung, peritoneum and pleura were the most frequent metastatic sites. Among histologic subtypes, adeno- (74.7%) and squamous cell carcinomas (13.7%) prevailed. DNA was extracted from micro-dissected formalin-fixed, paraffin-embedded tissue samples. For library preparation mostly multiplex PCR-based Ion Torrent AmpliSeq technology (Life Technologies) with Oncomine comprehensive assays v1 and v3 was used. Results: The prevailing genetic alterations were deletions in tumor suppressor genes TP53 (49.6%), CDKN2A (19.0%) and NOTCH1 (14.1%) as well as oncogenic activation of KRAS (23.4%), FGFR4 (14.9%) and PIK3CA (10.7%). KRAS activation was predominantly found in adenocarcinomas (p = 0.01) and PIK3CA activation in squamous cell carcinomas (p = 0.03). Regarding prognosis, male sex, high ECOG score, unfavorable CUP subtype, a higher number of involved organs as well as RAS activation predicted decreased event-free and overall survival in multivariate analysis. Deletions in CDKN2A were a poor prognostic factor regarding overall survival. Markedly, TP53 mutations did not significantly influence prognosis. Since July 2015, 17/198 (8.6%) patients received a recommendation for molecularly guided therapy. However, due to lack of coverage by insurers or rapid clinical deterioration only 7 of these patients (3.5%) actually received targeted treatment. Conclusions: Besides offering targets for therapy, targeted panel sequencing in CUP is prognostically relevant, with RAS activation and CDKNA2 deletion emerging as independent risk factors in a comprehensive assessment with clinical risk factors.
Analysis of mutation detection in cell-free DNA in ascites using comprehensive NGS panel.
Authors: Shi Chunmei , Zhang Yan , Zhu Lingjun , Dai Pingping , Tang Yong , Zhang Junping , Gao Jie , Zhang Chi , Guan Yan-Fang , Xia Xuefeng , Yang Ling , Yi Xin 
Published: May 2019

e13029 Background: Ascites is one of complications for patients with malignancies in advanced stage. Detection and characterization of cell-free DNA (cfDNA) from ascites effusions have not yet been studied. Herein, we analysis genomic alterations present in advanced cancer with ascites. Methods: We implemented targeted capture NGS with a panel of 1021 cancer-relevant genes on 85 ascites ctDNA, also on 46 matched plasma and 9 tissue from 85 patients. Results: Among 85 patients with advanced cancer, 42 digest system cancer (DC), 16 gynecologic cancer (GC), 14 non-small cell lung cancer(NSCLC) and 13 other solid tumors included. Overall, 90%(77/85) patients detected somatic mutations, which were identified predominantly in TP53 and KRAS for DC and TP53 for GC. Among NSCLC patients with ascites, nine were treated with EGFR TKI-targeted therapy previously. Mutations lead to the resistance of EGFR-TKI were identified in 55.6% (5/9) cases, including acquired EGFR T790M/C797S and primary BRAF V600E. These indicate ctDNA in ascites can used to guide tumor treatment and monitor of resistance. For the 46 pairs of ascites and plasma samples, actionable variations with on label, off-label, or experimental drugs available, were identified in 61% (n = 28) of ascites effusion samples, whereas plasma was 46% (n = 21). Median number of ascites somatic mutations was 4, while the median number was 3 in plasma samples. Of that, 85% and 61% of plasma ctDNA and ascites cfDNA samples were observed with the highest MAF above 1%. In addition, 63% and 35% of plasma ctDNA and pleural cfDNA samples were observed with the highest MAF above 10%. For the 9 groups of plasma, ascites and tumor tissue samples, at least 1 mutations within tissue was detected in 8 ascites samples and 6 in plasma samples. Conclusions: Our results suggest that cfDNA from ascites is more sensitive than plasma and had higher similarity with the tumor tissues for advanced cancer patients. With higher MAF and detection rate of actionable variations, cfDNA from ascites might provide additional information not detected with plasma cell-free DNA guide more precise cancer treatment.
RNA sequencing analysis for profiling activation of cancer-associated molecular pathways.
Authors: Buzdin Anton , Garazha Andrew , Sorokin Maxim , Glusker Alex , Aleshin Alexey , Allina Daria , Suntsova Maria , Tkachev Victor , Borger Pieter , Borisov Nikolay , Gaifullin Nurshat 
Published: May 2019

e13032 Background: Intracellular molecular pathways (IMPs) control all major events in the living cell. They are considered hotspots in contemporary oncology because knowledge of IMPs activation is essential for understanding mechanisms of molecular pathogenesis in oncology. Profiling IMPs requires RNA-seq data for tumors and for a collection of reference normal tissues. However, there is a shortage now in such profiles for normal tissues from healthy human donors, uniformly profiled in a single series of experiments. Access to the largest dataset of normal profiles GTEx is only partly available through the dbGaP. In TCGA database, norms are adjacent to surgically removed tumors and may be affected by tumor-linked growth factors, inflammation and altered vascularization. ENCODE datasets were for the autopsies of normal tissues, but they can’t form statistically significant reference groups. Methods: Tissue samples representing 20 organs were taken from post-mortal human healthy donors killed in road accidents no later than 36 hours after death, blood samples were taken from healthy volunteers. Gene expression was profiled in RNA-seq experiments using the same reagents, equipment and protocols. Bioinformatic algorithms for IMP analysis were developed and validated using experimental and public gene expression datasets. Results: From original sequencing data we constructed the biggest fully open reference expression database of normal human tissues including 465 profiles termed Oncobox Atlas of Normal Tissue Expression (ANTE, original data: GSE120795). We next developed a method termed Oncobox for interrogating activation of IMPs in human cancers. It includes modules of expression data harmonization and comparison and an algorithm for automatic annotation of molecular pathways. The Oncobox system enables accurate scoring of thousands molecular pathways using RNA-seq data. Oncobox pathway analysis is also applicable for quantitative proteomics and microRNA data in oncology. Conclusions: The Oncobox system can be used for a plethora of applications in cancer research including finding differentially regulated genes and IMPs, and for discovery of new pathway-related diagnostic and prognostic biomarkers.
Clinical impact of comprehensive versus targeted genomic analysis for precision oncology.
Authors: Lamping Mario , Rieke Damian Tobias , Klauschen Frederick , Jöhrens Korinna , Anagnostopoulos Ioannis , Lenze Dido , Tinhofer Inge , Benary Manuela , Ochsenreither Sebastian , Klinghammer Konrad Friedrich , Burock Susen , Jann Henning , Stüven Anna Kathrin , Ditzen Doreen , Beule Dieter , Messerschmidt Clemens , Blanc Eric , Schäfer Reinhold , Keilholz Ulrich 
Published: May 2019

e13033 Background: Panel sequencing (PS) has become a standard-of-care in cancer diagnostics. More comprehensive analyses such as whole-exome (WES) or RNA sequencing (RNAseq) allow for the detection of rare and unknown genetic aberrations that are not covered by predefined assays. The clinical impact of targeted versus comprehensive genomic assays were analyzed in patients presented at the Charité Molecular Tumor Board (MTB). Methods: Patients (pts) with advanced and/or metastatic cancer for whom no standard therapy was available were discussed in the MTB to allocate diagnostic profiling and guide biomarker-based treatment (BBT). Pts had to be < 50 years of age or diagnosed with a rare tumor entity to undergo WES/RNAseq, performed on fresh tissue. If ineligible, standard PS was performed on archival tissue. BBT recommendations, ranked by pre-specified evidence levels, were made by the MTB and pts were followed up. Results: 228 patients (median age 49 years, 108 female and 120 male) were discussed in the MTB between January 2016 and February 2019. We assigned 73 and 155 pts to PS and WES/RNAseq and results were obtained for 78.1% (n = 57/73) and 54.8% (n = 85/155) pts, respectively. Sequencing failed for 11 (PS; 15.1%) and 62 (WES/RNAseq; 40%) pts, most commonly due to insufficient tissue (n = 29). Sequencing was ongoing in 5 (PS) and 8 (WES/RNAseq) pts at the time of analysis. A median of 2 BBTs were recommended for 75.4% (43/57) of PS (range r: 1-3) and 90.6% (77/85) of WES/RNAseq pts (r: 1-6) each. 22% (n = 17/77) of WES/RNAseq pts had ≥4 BBTs made by the MTB. Treatment was initiated in 30.2% (n = 13/43) of PS and 40.2% (n = 31/77) of WES/RNAseq pts. Clinical benefit rates (CBRs) were 23.1% (2 PR, 1 SD) for PS and 45.2% (2 CR, 3 PR, 9 SD) for WES/RNAseq pts. Overall survival data was immature at the time of analysis. Conclusions: Utilizing WES/RNAseq is a feasible approach to perform tumor profiling in a heterogeneous cohort. We here show a higher rate of pts receiving confident evidence-based treatment recommendations in the WES/RNAseq group and a higher rate of treatment initiation. The CBR nearly doubled in the WES/RNAseq cohort when compared to standard PS pts, thus emphasizing the need for larger comparative analyses to guide diagnostic decision-making.
Diagnostic accuracy of the Videssa protein-based liquid biopsy for breast cancer in suspicious mammography.
Authors: Chen Cynthia , Poole Lisa , Sizer Lina , Carter W. Bradford , Frazier Thomas G. 
Published: May 2019

e13034 Background: The Videssa protein-based blood test (Provista Diagnostics) is a combined proteomic biomarker assay that aims to detect established breast cancer – rendering it useful in patients with abnormal or difficult-to-interpret mammograms. Since the incidence of malignancy for BI-RADS 4 biopsies is approximately 20%, a significant percentage of patients undergo needle biopsy unnecessarily. The Videssa assay provides an alternative diagnostic method by way of a non-invasive liquid biopsy. Methods: Our goal was to assess whether this liquid biopsy combined with 3D tomographraphic mammography could accurately predict disease status to reduce the amount of unnecessary tissue biopsies. An IRB-approved, prospective, single-arm study had patients with BI-RADS4 lesions with calcifications requiring tissue biopsy undergo the blood test prior to stereotactic core biopsy. Subsequent results and biopsy pathology were correlated. Results: 46 patients were initially entered with BI-RADS4 calcifications. 9 patients had DCIS (19.6%) and 37 patients had benign calcifications (80.4%). No patient had invasive cancer. Liquid biopsy results were elevated in 2 patients with DCIS (22% sensitivity) and in 5 patients with benign biopsies (10.8%). At interim analysis, the liquid biopsy demonstrated a 28.5% positive predictive value (PPV) and 82% negative predictive value (NPV). Tumor grade did not affect results. We subsequently discontinued using the blood test for BI-RADS4 calcifications and enrolled 13 patients with non-palpable solid lesions to determine the correlation. The liquid biopsy was elevated in 1 of 4 patients with invasive cancer (25% sensitivity) and was not elevated in all 9 patients with benign biopsies (100% NPV). At one-year follow-up, 3 of the 5 patients with an elevated blood assay and negative biopsy have had no incidence of cancer on subsequent imaging. The remaining 2 patients are scheduled for follow-up. Conclusions: In our study, the NPV of the Videssa liquid biopsy is not robust enough to defer tissue biopsy in any patient with indeterminate calcifications on imaging, nor is it specific enough to help predict results in high risk solid lesions. We do not see this liquid biopsy changing our current practice.
Low likelihood that potential germline findings identified during somatic tumor testing are evaluated: Room for improvement.
Authors: Wright Heather , Melissa Cuke , Folefac Edmund , Verschraegen Claire F. , Wood Marie 
Published: May 2019

e13037 Background: Genomic testing, useful for treatment planning, may indicate the presence of a germline mutation. We evaluate the incidence of potentially actionable germline mutations detected via genomic testing and determined rates of follow-up referrals for genetic counseling and germline testing among patients with potential germline mutations. Methods: This was a retrospective chart review of patients who underwent genomic testing at The University of Vermont Cancer Center (UVMCC). Test reports were reviewed for mutations in 24 genes associated with hereditary cancer and recognized as clinically actionable by the American College of Medical Genetics. Medical record review was performed to identify patients referred for genetic counseling and results of germline testing. Results: Between 8/2009 and 9/2016 157 patients underwent genomic testing at UVMCC. Eighty-one percent (127/157) had a mutation in ≥ 1 gene associated with hereditary cancer (range 0-4 mutations per patient), and 46% (73/157) had mutations in more than one gene. Potential germline mutations were most commonly identified in TP53, CDKN2A, RB1, PTEN, STK11 and APC (each with mutations in > 10% of patients). To date only 12% (15/127) of patients with potential germline mutations have been referred for genetic counseling. Two were referred for evaluation of findings seen on genomic testing others being referred for personal or family history of cancer. The majority (11/15) of referred patients have undergone genetic testing with 27% (3/11) having germline mutations identified; 2/3 of which were also identified on genomic testing. Conclusions: Genomic testing can be an important tool for identifying hereditary cancer syndromes. While the majority (81%) of patient’s undergoing genomic testing had mutations genes associated with hereditary cancer, the low rate of referral (12%) for genetic counseling to determine if these are truly germline represents a significant missed opportunity. Identification of germline mutations has implications for both the patient (for treatment and risk of second cancers) and their family. Patients and their providers should be aware of the potential for germline findings when genomic testing is performed.
Implementation of HPV vaccination pilot project in Kazakhstan: Successes and challenges.
Authors: Kaidarova Dilyara , Chingissova Zhanna , Dushimova Zaure , Kukubassov Yerlan , Zhylkaidarova Alma , Sadykova Tolkyn , Bolatbekova Raikhan 
Published: May 2019

e13056 Background: Cervical cancer (CC) is the second most frequent cancer of women after breast cancer. Prophylactic vaccines for human papillomavirus (HPV) are being introduced in many countries more than 10 years ago. The standardized incidence of СС in Kazakhstan (KZ) in 2017 was 17.1 per 100,000 women. From 2013 to 2016, there was a pilot project of school-based HPV vaccination of adolescent girls in four districts of KZ. Vaccination was carried out with two vaccines (Gardasil and Cervarix) on the choice of parents in a three-dose regimen. Due to the high rejection of vaccination, this program was completed in 2016. Aim of study was to analyze the results of HPV vaccination in KZ. Methods: The results of vaccination of adolescent girls from 9 to 15 years old were evaluated. We analyzed database registry of Kazakhstani vaccinated girls to evaluate vaccine coverage in four district of KZ. Results: A total 11,648 adolescent girls were fully vaccinated during the pilot program for 2013-2016. The average age of the vaccinated is 12.67 ± 1.04. In 2013, immunization was performed for 1,816 girls aged 11–13 years. In 2014, the age range of the target group was expanded to 15 years. The number of vaccinated girls increased to 5,699 adolescent girls. 7,136 girls were fully vaccinated in 2015. 10,004 girls have not received full doses of vaccine. Overall coverage rates of fully vaccinated were 14.8%. The majority of coverage results was stastically similar except for Almaty, where coverage was higher than the average coverage (17.9% vs. 14.8%, p < 0.05). Conclusions: Pilot project of vaccination in Kazakhstan was declared unsuccessful. This situation is associated with a lack of information campaigns on vaccination. This findings highlights the need for phased implementation of vaccination through an educational campaign of parents.
Primary prevention and smoking habit among BRCA1/2 mutation carriers.
Authors: Cordeiro Patricia , Lesta Rocio , Gómez-Randulfe Igor , Reboredo Rendo Cristina , Molina Díaz Aurea , Quindós Varela Maria , Antolín Novoa Silvia , Pérez López María Eva , Calvo Martínez Lourdes , Lopez Cortabitarte Belen , Prato Javier , Suárez Vanessa , Mosquera Martínez Joaquín , Rodríguez Sánchez Berta , Rodríguez Pedreira Montserrat , Czestokowa Carlota , Bouzón Alberto , Albaina Latorre Luis , Cereijo Garea Carmen , Graña-Suárez Begoña 
Published: May 2019

e13061 Background: Smoking is the leading cause of avoidable death in the world. Although controversial for years, current prospective studies suggest that smoking increases the risk of cancer in women with a deleterious BRCA1/2 mutation. Actually, we have very limited information about tobacco habit among BRCA1/2 carriers. Methods: We report an observational retrospective study of a consecutive sample of 198 BRCA1/2 carriers studied between April 2014 and March 2018 at the Family Cancer Clinic of the University Hospital of Coruña (NW-Spain). The main objective of the study is to know the prevalence of smoking in BRCA1/2 women, and to determine if carriers undergoing risk-reducing surgeries (RRS) abandon their tobacco habit as part of the primary prevention strategy. Results: The sample includes 136 patients affected by cancer (84% breast, 19% ovary) and 62 healthy women. During their follow-up [Median = 22, (1-43) months], 85 carriers underwent RRS (29% mammary, 54% prophylactic salpingo-oophorectomy, 16% both). At first visit, 46 were active smokers, 47 ex-smokers, 77 non-smokers and 28 did not specify their habit. The percentage of smokers and never smokers is similar between sick and healthy BRCA1/2 carriers, presenting a greater proportion of former smokers among those affected of cancer (30% vs. 23%), and of active smokers among healthy women (35% vs. 23%) [p > 0.5)]. Moreover, 23% of BRCA1/2 carriers are active smokers despite a previous diagnosis of cancer. RRS are not associated to a greater tobacco cessation, persisting in the habit 18% of the women that underwent any preventive surgery (p > 0.5). Conclusions: Smoking habit is high (55%) among BRCA1/2 carriers followed at our family cancer clinic. At least 23% of our BRCA1/2 positive women are active smokers despite a previous diagnosis of cancer.The performance of aggressive RRS is not associated with greater abandonment of tobacco in carriers, persisting in the smoking habit 18% of operated women.It is essential to improve anti-tobacco strategies in family cancer consultations if we want to be efficient in the management of high-risk cancer individuals.