bluuebunny/crossref_metadata_2025_split huggingface dataset:
BRCA1/2 germline mutations and response to PARP inhibitor treatment in lung cancer.
Authors: Fang Wenfeng , Cai Xiuyu , Zhou Huaqiang , Wang Yinguang , Zhang Yaxiong , Hong Shaodong , Shao Yang , Zhang Li 
Published: May 2019

e13007 Background: Germline mutations in BRCA1/2 (BReast CAncer genes 1 and 2), which are targets for PARP inhibitors in breast and ovarian cancer, have been previously identified in patients with non-small cell lung cancer (NSCLC). However, its prevalence and clinical outcomes to targeted therapy in NSCLC still remains unknown. Methods: We conducted a retrospective review of 9,324 Chinese NSCLC patients who underwent targeted next-generation sequencing (NGS) during 2015/11/01 and 2018/10/31. Patients with BRCA1/2 somatic and germline mutations were identified. We summarized their prevalence and explored their co-existing driver mutations. Then we initially reviewed the response to PARP-inhibitor targeted therapy in patient with BRCA2 germline mutation. Results: 459 (4.9%) patients are BRCA1/2 positive (germline/somatic mutation). Most patients are diagnosed with LUAD (372, 81.1%), with a median age of 63 years (range: 2-101). Slightly more male patients were carrying BRCA1/2 mutations (59.9%, 275 out of 459). The prevalence of BRCA1 and BRCA2 somatic mutations was similar (145, 1.56% vs. 169, 1.81%, p = 0.19). BRCA2 germline mutation was more common in lung cancer than BRCA1 germline mutation (148, 1.59% vs. 20, 0.21%, p < 0.0001). When specified to the common driver gene mutation subgroups, the prevalence of BRCA2 germline mutation is similar to the entire population (EGFR 1.79%; ALK 1.74%; KRAS 2.05%; BRAF 2.86%; ERBB2 0.93%; p > 0.05). K2729N is the most common BRCA2 germline mutation (41, 27.7%), followed by C315S (26, 17.6%), V2109I (12, 8.1%), R2108C (11, 7.4%), I2490T (10, 6.8%), T582P (5, 3.4%). About 20% patients with BRCA2 germline mutation carried at least one concomitant mutations of DNA repair genes, including MLH1, MLH3, MSH6, CHEK2, BARD1, BLM, BRCA1, MUTYH, RAD50, RECQL4 and XRCC1. One 56-year-old male LUAS patient, with germline BRCA2 rs80359490 frameshift deletion mutation (p.S1722Yfs*4), received the targeted therapy with PARP inhibitor Olaparib after multi lines therapies. This patient showed a great PR response to Olaparib, with a PFS of at least 6 months. Conclusions: BRCA1/2 germline mutations were rare in Chinese NSCLC patients. Patients with BRCA2 germline mutations might benefit from PARP-inhibitor treatment.
Comprehensive germline panel testing across cancer types: Diagnostic yield and clinical utility in 100,000 patient dataset.
Authors: Yang Shan , Michalski Scott T. , Pineda Alvarez Daniel Esteban , Lincoln Stephen E , Whitworth Pat W. , Nussbaum Robert L. , Esplin Edward D. , Esplin Edward D. 
Published: May 2019

e13013 Background: Over 608,000 patients with ovarian, breast, pancreatic, prostate and colorectal cancer are diagnosed each year. NCCN guidelines recommend offering germline genetic testing to all patients with ovarian and pancreatic cancer, and patients with prostate and breast cancer who meet specific criteria. We present data from ~113,000 patients who were tested on a comprehensive multigene panel and compare the diagnostic yield and clinical actionability with that of a limited gene panel strategy. Methods: We analyzed de-identified sequence data for 83 cancer-risk genes in patients with breast, ovarian, prostate and pancreatic cancer referred for germline genetic testing. Positive rates for a minimal gene panel for the respective indication were computed and compared to the positive rates when the comprehensive 83 gene panel was analyzed. Results: Four percent of 103,428 patients with breast, ovarian, pancreatic and prostate cancer harbored a BRCA1 or BRCA2 germline mutation including: breast 3.7%, ovarian 8.2%, prostate 5.2% and pancreatic 4.2%. When the comprehensive panel is applied, the overall diagnostic yield for all 113,107 patients increased to 16%. Excluding mono-allelic P/LP variants in recessive cancer-risk genes (e.g. MUTYH) reduces the diagnostic yield to 13%. Stratified by cancer type, and removing mono-allelic recessives, positive yield was: breast 11.8%, ovarian 18%, prostate 15%, and pancreatic 16%. Conclusions: These data show that comprehensive panel testing in patients with a broad range of cancers more than doubles the diagnostic yield, providing actionable results for an additional 9,737 per 113,107 patients tested. Potential germline-based clinical actionability for these patients includes: 1) pan-cancer eligibility for PARP inhibitor clinical trials, 2) FDA approved PD1 blockade for advanced cancer of ANY type and a molecular diagnosis of Lynch syndrome, 3) cascade family variant testing.This study suggests that genetic testing guidelines should be expanded to include recommendations supporting multigene panel testing in patients with cancer to improve the care of patients and their family members.
Germline EGFR mutation and cancer predisposition in adolescent and young adult (AYA) females with adrenocortical carcinoma.
Authors: Akhavanfard Sara , Yehia Lamis , Padmanabhan Roshan , Romigh Todd , Ni Ying , Eng Charis 
Published: May 2019

e13014 Background: Adrenocortical Carcinoma (ACC) is a rare endocrine tumor with poor overall prognosis and slight overrepresentation in females. In children, ACC is associated with inherited cancers, predominantly Li-Fraumeni syndrome, with 50-80% of childhood ACC harboring TP53 germline mutations. ACC in AYA are rarely due to germline TP53 mutations; IGF2, PRKAR1A and MEN1 are other less common germline mutated genes in this age group. Methods: We analyzed exome sequencing data from 21 children (C, < 15y), 32 AYA (15-39y), and 60 adult patients ( > 39y) with ACC, originating from the Cleveland Clinic, and TCGA and St. Jude’s datasets. We utilized the Integrative Variant Analysis platform to classify variants based on the American College of Medical Genetics guidelines. We retained all pathogenic, likely pathogenic, and highly-prioritized Variants of Uncertain Significance. Results: Pathway analysis on prioritized variants showed EGFR and p53 pathways as the two top pathways among our C-AYA patients. We found that 4.8% of children and 6.2% of AYA, all female patients, harbored a non-kinase-domain germline EGFR mutation, compared to only 1.7% of adult patients with ACC. As proof-of-principle functional validation, we engineered a lentiviral-mutant stable ACC-cell line, harboring an EGFR variant from a 21 y/o female with aggressive bilateral ACC (p.Asp1080Asn), without germline TP53 mutation. We showed that mutant cells grow slower, yet migrate faster and are characterized by a stem-like phenotype compared to wildtype cells. Osimertinib, among all tested EGFR inhibitors, resulted in the highest growth inhibition of mutant cells. While EGFR inhibitors had no effect on the stemness of mutant cells, Sunitinib, a multi-receptor tyrosine kinase inhibitor, significantly reduced the stem-like behavior. Conclusions: Our data suggest that EGFR is a novel underlying germline predisposition factor for ACC, especially in the female C-AYA population. Although our pre-clinical observations need to be further validated, identifying a targetable gene for ACC has the potential to improve precision oncology management of this disease, which is known to have limited therapeutic options.
Landscape of multilocus inherited neoplasia alleles syndrome in China.
Authors: Ouyang Quchang , Gao Jie , Huang Jun , Dai Pingping , Zhang Mingming , Chen Chen , Guan Yan-Fang , Yang Ling , Yi Xin , Xia Xuefeng 
Published: May 2019

e13027 Background: Comprehensive gene panels are able to identify patients with more than one pathogenic germline mutations. This phenomenon is known as multilocus inherited neoplasia alleles syndrome (MINAS). The frequency and phenotype of double heterozygous carriers in China are still unknown. Methods: A cohort of 12514 unrelated patients with solid tumor were screened using a validated panel. DNA damage repair-associated genes ( BRCA1, BRCA2, PALB2, ATM) and DNA mismatch repair genes ( MLH1, MSH2, MSH6, PMS2, MLH3, MSH3, PMS1) are taken focused on this study. Results: 10 (2.16%) cases harboring two pathogenic/likely pathogenic mutations were identified in 464 patients with germline variant. All patients had at least one high-risk gene mutation except for G10(LC, 73y), which carried 2 ATM variants in the same allele. All patients developed tumors associated with only one of the mutation identified until now. Among 3 patients had PMS2/MSH6 mutation, G6 & G7 did not translated into recognized Lynch Syndrome due to abnormal BRCA1/2(H-risk for BC), while G8 harboring ATM (M-risk for BC) mutation developed to CRC. All of the five patients developed to breast cancer were TNBC molecular subtype. The median ages of diagnosis for BC were similar to single variation patients (44.3 vs 42, p=0.6190). Conclusions: Two double heterozygotes did not appear to have severe or different manifestations than single heterozygote. With the growing implementation of NGS based panel testing, relevant variants in two (or more) genes will be found more frequently. [Table: see text]
Discovering HPV16 and HPV18 infection status and cancer gene variations in cervical cancer patient specimens by using Next-generation sequencing.
Authors: Meng Bo , Quan Lili , Yang Wenjuan , Lang Jidong , Chen Lanyou , Dong Ruyi , Zhao Juanyu , Tian Geng 
Published: May 2019

e13040 Background: Human papillomavirus (HPV) infection has been reported as an important cause of cervical cancer for many years. HPV16 and HPV18 are the two most prevalent types in cervical cancer5. Integration of HPV DNA is a crucial genetic event in cervical carcinogenesis. Therefore, it is important to know the HPV integration hot spots in human genome to predict the cervical cancer development status of patients. Although many studies have addressed the HPV integration sites in human genome, it is still a technique barrier to precisely determine the HPV integration sites of each patient, especially at early disease development stage with limited integration sites existing. Methods: To solve this problem, we first designed HPV probes to capture HPV integrated sequences of genome using next generation sequencing (NGS). And then we analyzed the integration sites by two methods with the NGS results, HPV Detector. We applied the study on 17 patient samples, 15 of them were found HPV16 positive and 2 of them were found HPV18 positive. Among them 16 were detected with HPV integration sites. Results: The results indicated that different samples showed different numbers of integration sites with limited overlapped positions in genome. The integrated positions of HPV16/18 located in all the genes of the virus, but mostly distributed in gene E1, L1 and L2. We identified integration sites HPV16 E6/GATC， E6/WWTR1， L2/DGKB, E1/EHHADH, ect. Some of the integrated sites in human genome are belong to intergenic region. We also used cancer gene panel, which cover 143 cancer related genes exon regions, to identify the mutation sites of each samples. We summed up a highly occurred mutated cancer gene list, which include ALK, NF1, PIK3R1, ROS1, TSC1, TSC2, ect. Most of them are either cancer driver genes or have been found highly related to cervical cancer. Further study is still carrying on. Conclusions: In conclusion, our HPV probe could successfully detect HPV16 and HPV18 in patient samples and enrich HPV integration sites in human genome of cervical samples significantly. It could provide detailed information for cervical cancer discovery and early detection.
Meta-analysis utilizing public data suggests role of innate immunity in the pathogenesis of hurthle cell carcinoma (HCC).
Authors: Allen David , Wanner Ross , McDermott Sean , Aljabban Jihad , Syed Saad , Elmaraghy Charles , Hadley Dexter 
Published: May 2019

e13048 Background: Hurthle Cell Carcinoma (HCC), a variant of follicular thyroid carcinoma, is a rare form of thyroid cancer. Though it accounts for 3-10% of thyroid cancer cases, very little is known about its pathogenesis. While HCC holds good survival rates, it is still vital to understand the pathogenesis of HCC in order to further optimize treatment protocols. Methods: We tagged 46 HCC samples and 90 healthy thyroid samples as a control. Gene signatures were analyzed in Ingenuity Pathway Analysis, using statistical significance p < 0.05 and absolute log ratio > 0.5 between disease and controls. Methods: Search Tag Analyze Resource was employed to conduct meta-analysis using the National Center for Biotechnologys Gene Expression Omnibus to define HCC pathogenesis. Results: Hepatic fibrosis, hepatic stellate cell activation and retinoic acid receptor (RAR) activation were the top canonical activators associated with HCC. Of the molecules involved, Defensin Beta 1 (DEFB1), Lipocalin-2 (LCN2), Aldehyde Dehydrogenase 1 Family Member A3 (ALDH1A3), and CDC28 Protein Kinase Regulatory Subunit 2 (CKS2) had the highest associations with HCC. The most down-regulated molecules were Hemoglobin Subunit Beta (HBB), Hemoglobin Subunit Alpha 1 and 2 (HBA1/HBA2), Cellular Retinoic Acid Binding Protein 1 (CRABP1), and BH3-Interacting Domain-Containing Protein 3 (HRK). Conclusions: These results suggest that there are a variety of factors at play regarding the development of HCC. Defensins are peptides made by neutrophils, however DEFB1 is specifically known for its ability to resist bacterial growth on epithelial surfaces, playing a major role in innate immunity. LCN2 is also known for resisting growth on surfaces and does so by sequestering iron-containing siderophores, thus effectively stopping growth of microorganisms. Additionally, ALDH1A3 and CRABP1 are associated with RAR activation. While the exact pathogenesis of HCC is not well known yet, we demonstrate that the two most up-regulated factors in HCC are strongly involved in innate immunity. This suggests that the dysfunction of innate immunity may play a vital role in the neoplastic pathogenesis of HCC.
The landscape of POLE/POLD1 mutations in Chinese solid tumor patients.
Authors: Pang Linrong , Xu Tao , Tao Hua , Chen Gang , Ni Bin , Zeng Daobing , Wang Aodi , Shi Weiwei , Wang Kai , Yao Ming 
Published: May 2019

e13050 Background: DNA polymerase epsilon and polymerase delta encoded by the POLE and POLD1 gene are the major components participating in DNA replication, which both carry a proofreading (exonuclease) domain allowing error correction during replication. In case of POLE/POLD1 mutation, a deficient DNA repair activity results in a hypermutated phenotype of cancer, which would be a promising biomarker for immune checkpoint inhibitors (ICPIs). However, the prevalence of POLE and POLD1 in Chinese patients (pts) with solid tumors remained unknown. Methods: Targeted panel sequencing of 450 cancer genes were performed on FFPE tissues and matched blood samples obtained from 6313 Chinese pts with 23 different types of solid tumors. In our cohort, 41% were female pts with a median age of 56-year-old (range: 1-91), while 59% were male with a median age of 59-year-old (range: 1-96). The major cancer types were NSCLC (29%), HCC (11%), CRC (11%), gastric cancer (GC, 7%), soft tissure sarcoma (6%), pancreatic cancer (5%), intrahepatic cholangiocarcinoma (5%), and others. Somatic genomic alterations (sGAs) including single base substitutions, short and long insertions/deletions (indels), copy number alterations (CNA), rearrangements, TMB and MSI status were assessed by NGS. Results: Clinical relevant genomic alterations (CRGAs) were defined as known loss-of-function mutations, truncations, mutations on splicing sites and confirmed somatic mutations in COSMIC. CRGAs of POLE and POLD1 accounted for 2.1% and 1.3% of Chinese solid tumors respectively. Tumors with highest frequency of POLE CRGAs in Chinese cohort were endometrial cancer (8.3%), urothelial cancer (4.8%), CRC (4.3%), GC (3.2%), breast cancer (2.9%), cancer of unknown primary (CUP, 2.5%), ovarian cancer (2.1%) and NSCLC (2.0%), which tumors with highest frequency of POLD1 CRGAs were endometrial cancer (8.3%), urothelial cancer (4.8%), GC (3.0%), CRC (2.8%), SCLC (2.1%), HCC (1.9%), cervical cancer (1.6%), CUP (1.2%) and pancreatic cancer (1.2%). In addition, 1.6% and 1.2% of Chinese solid tumors harbored variants of unknown significance of POLE and POLD1, respectively. Conclusions: For the first time, our study reported prevalence of somatic mutations of POLE and POLD1 in large samples of Chinese population. Comparing with large cohort study of western population (ESMO 2017, 1170P), more CRGAs of POLE were identified in Chinese solid tumors (2.1% vs. 0.6%, p < 0.0001) indicating ethnic differences of ICPIs potential candidates between Chinese and western populations.
Detect and visualize tumor microsatellite instability status from next-generation sequencing data by simulating PCR techniques.
Authors: Chen Shifu , Qu Hongyue , Yang Bo , Huang Tanxiao , Zhang Xiaoni , Liu Yuanyuan , Zhou Yanqing , You Qin , Ivanov Kamen , Gu Jia 
Published: May 2019

e13052 Background: Although multiplex PCR is still the golden standard technology for detecting microsatellite instability (MSI), it has some disadvantages. Firstly, its results are not quantized, and the interpretation of results can be varying for different operators. Secondly, PCR requires extra sample amount and may affect the sample amount for next-generation sequencing (NGS). So we developed a method to detect MSI status from NGS data. Methods: We developed a tool called VisualMSI, which simulates the PCR behaviors to detect the instability level of microsatellite loci. For each microsatellite locus, a pair of PCR primers are simulated by extracting the sequence from reference genome. The read pairs covering this microsatellite locus will be merged first, and then the simulated PCR primers will be mapped to the merged sequences to evaluate the inserted length. For paired tumor/normal samples, VisualMSI evaluates the earth mover's distance (EMD) between the inserted length distributions of tumor and normal. MSI status is determined by the EMD value, and is also visualized on a HTML page for manual validation. As a comparison, the MSI was also evaluated using a multiplex PCR comprising 5 loci (NR27, NR21, NR24, BAT25, and BAT26). Results: To evaluate the concordance of VisualMSI results and PCR-based results, we enrolled a group of 92 patients (39 lung cancers, 33 colorectal cancers and 20 others). For each patient, a tumor tissue sample and a blood sample were collected. White blood cells from the blood samples were also sequenced as normal control. For each patient, the 5 major MSI loci, including BAT-25, BAT-26, NR-21, NR-24 and NR-27 were evaluated by VisualMSI from NGS data, and by PCR. MSI status was categorized as MSI-H or MSI-L for each MSI locus. Finally, for the total 460 MSI loci, the VisualMSI and PCR results were concordant for 425 of them (92.39%), and were not concordant for the rest 35 (7.61%). The sensitivity is 89% (95% CI) and the specificity is 95% (95% CI), indicating that they were highly consistent. Conclusions: We developed a tool for detecting and visualizing MSI status from NGS data. The data shows that results of VisualMSI and PCR are highly concordant. This tool is now open-sourced at: https://github.com/OpenGene/VisualMSI.
A new method towards calculating the cancer cell fraction in cell-free DNA.
Authors: Han Tiancheng , Yu Jianing , Lin Xiaojing , Xie Hongyu , Song Xue , He Ji , Chen Weizhi 
Published: May 2019

e13053 Background: Circulating tumor DNA (ctDNA) has been applied and showed potential in cancer early/late-stage detection, tumor genotyping and post-operation recurrence monitoring. The fraction of ctDNA in cell-free DNA (noted as ccf hereby), in addition to standard SNV/INDEL/CNV analysis, has also been showed to associate with the tumor progression and prognosis. In theory, accurate ccf can further be useful in correcting and improving given SNV/INDEL/CNV results. Existing tools capable for calculating ccf (PureCN, FACETS, Sequenza, etc.) use coverage data in targeted regions and SNP allele frequency to calculate the tumor fraction, which fail to give accurate estimation at relatively low ctDNA concentrations. Methods: A Maximum Likelihood model was built to estimate ccf. We first select informative SNPs with significantly different VAF in the case and paired-control samples. The mutation type of an informative SNP is determined by the variant allele frequency (VAF) in the paired samples and the copy number of the case sample. Likelihood of each SNP given a specific ccf was then calculated. After clustering SNPs into clones, the ccf of each clone was estimated using a global likelihood. Results: Performance of the method was validated by ctDNA dilution series analysis. 6 cfDNA from cancer patient was diluted (concentrations: 1/3 - 1/81). Detection limit of the method is ~2%, and correlation between estimated and expected ccf ranged from 0.93 to 0.98. Conclusions: We have developed a novel method to better estimate cancer cell fractions in cell-free DNA. Results showed our method is able to calculate ccf at lower ctDNA concentrations with higher accuracy and stability than benchmarked tools. We describe here a method for target-sequencing data that is more sensible, accurate and stable than currently available tools.
Diagnosis of lung cancer by canine olfactory detection in urine and breath samples.
Authors: Feil Charlotte , Stein Thorsten , Forster Andreas , Schmidtmann Irene , Riemann-Seibert Thomas , Berger Martin , Owen Robert , Schimanski Carl Christoph 
Published: May 2019

e13067 Background: Lung cancer is the leading oncological cause of death in western countries. The WHO estimated 2.09 million newly diagnosed lung cancer patients in 2018 worldwide. Although early detection is crucial for patients outcome, no surveillance tools exist. Dogs have a highly sensitive olfactory system which is already used in several ways, such as drug and ketone detection. The aim of the study was to evaluate the capability of a classically conditioned domestic dog to accurately distinguish samples of lung cancer patients of all tumor stages in urine and breath from healthy controls. Methods: This monocentric clinical trial was an original study and approved by the local ethics committee. After conditioning a domestic dog with samples of 186 patients (36 cancer patients and 150 control patients), further 246 patients aged between 45 and 80 entered into the study: 41 patients with a histologically proven lung cancer comprising all different stages and 205 control samples of healthy individuals with no cancer history. Two urine and two breath samples were collected of each patient and immediately shock frozen at -80°C. Urine and breath samples were separately exposed to the dog in a randomized, double-blinded manner, resulting in a specific conditioned reaction indicating the cancer sample. Results: The dog correctly predicted cancer in 36 of 41 urine samples, corresponding to a sensitivity of 87.8% and a specificity of 97.6%. Concerning the breath samples, the dog correctly predicted cancer in 32 of 41 samples, corresponding to a sensitivity of 78% and a specificity of 95.6%. Combining both techniques, the dog correctly identified 40 of 41 cancer samples, leading to an overall sensitivity of 97.6%. The specificity is not evaluable. Conclusions: Urine and breath carry volatile organic compounds indicating cancer growth, as previously reported. Canine olfactory detection of lung cancer is a simple tool to detect lung cancer non-invasively. Further identification of target compounds for technical translation of this approach is under way, with the potential for the development of a bionic electronic nose.