bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circulating tumor DNA molecular profiling in rare cancer patients from the MASTER KEY Project.
Authors: Okuma Hitomi Sumiyoshi , Yonemori Kan , Seo Takuji , Noguchi Emi , Wakakuwa Keiko , Kato Ken , Ichikawa Hitoshi , Kohno Takashi , Hirakawa Akihiro , Kuchiba Aya , Shibata Taro , Sukigara Tamie , Nakamura Kenichi , Mano Hiroyuki , Nishida Toshirou , Fujiwara Yasuhiro 
Published: May 2019

e14532 Background: In April 2017, MASTER KEY Project, composed of a prospective registry study part and a multiple clinical trials part, was established to promote treatment development for rare cancers, which is lacking standard or investigational therapeutic options. Circulating tumor DNA (ctDNA) analysis by next-generation sequencing (NGS) has provided new insight into personalized medicine in a more accessible, non-invasive manner; however, most reports are focused on common cancers. We report genetic alterations detected by ctDNA NGS analysis in rare solid cancers. Methods: Prospectively consented patients (pts), also enrolled in MASTER KEY registry study, had ctDNA NGS testing at a CLIA-certified lab (Guardant360) for point mutations, indels, copy number amplifications, fusions, and microsatellite instability. Alterations were assessed for incidence according to cancer type, functional impact, therapeutic implications, and comparison with tissue NGS. Main inclusion criteria: 1) age ≥16, 2) histological diagnosis of rare cancer (annual incidence less than 6 cases per 100,000 population), cancer of unknown primary (CUP), or rare tissue subtypes of common cancers, 3) active metastatic / unresectable cancer, 4) a written consent. Results: From Nov. 2018 to Jan 2019, 50 pts had Guardant360 testing. Diseases included: soft tissue sarcoma (28), ovarian carc. (7), CUP (4), salivary gland tumor (3), thyroid carc. (2), GIST (1), adrenal cortical carc. (1), rare subtype of GI tract (1), malignant mesothelioma (1), nephroblastoma (1), NET (1), NUT carc. (1). All Japanese, male/female = 14/36, median age 61, ECOG performance status 0/1/2/3 = 30/19/0/1. 76% of pts (38/50) had ≥1 alteration detected, with median number of 2 alterations (range: 0-9), with VAF(0.1-60.3%); 87%(33/38) of those pts had a variant most likely pathogenic; 61% (20/33) of those pts had a variant potential for clinical action. Mean TAT was 10.3 days. 19 pts had tissue NGS testing and in 3 pts, alterations were detected by ctDNA NGS but not by tissue NGS. Updated results of 100 patients will be presented at the conference. Conclusions: Most rare cancer patients with advanced disease had a detectable genomic alteration by Guardant360. Clinical trial information: UMIN000034394.
Cell-free DNA methylation markers for noninvasive early detection of nasopharyngeal carcinoma.
Authors: Roy Dhruvajyoti , Taggart David J , Zheng Lianghong , Liu Dan , Li Gen , Li Mingzhen , Zhang Kang , Van Etten Richard A. 
Published: May 2019

e14537 Background: Nasopharyngeal carcinoma (NPC) is one of the most prevalent malignancies among populations native to Southeast Asia, the Mediterranean Basin and the Arctic. Early diagnosis of NPC is predicted to improve survival. The identification of cancer-specific DNA methylation patterns of cell-free DNA (cfDNA) isolated from blood samples is an established approach for detecting various cancers. In the present study, we evaluated the performance characteristics of a previously identified NPC methylation marker panel for the diagnosis of nasopharyngeal carcinoma. Methods: Retrospective samples were obtained for 168 subjects, including: 59 subjects diagnosed with NPC (Stage I to IV), 14 subjects diagnosed with benign nasopharyngeal disease and 43 healthy subjects. In addition, sample were obtained for 52 subjects diagnosed with breast, colorectal, liver or lung cancer. Samples were provided to the laboratory blinded for DNA methylation analysis by using the IvyGene Platform. Results: A total of 57 of the 59 samples drawn from subjects with NPC were correctly identified for an overall sensitivity of 97%, with little difference between the sensitivity of detecting Stage I to Stage IV nasopharyngeal carcinoma (range 92% to 100%). For subjects diagnosed with other cancers, 85% of colorectal cancer samples, 82% of lung cancer samples, 93% of both breast cancer and liver cancer samples, were correctly identified as negative for NPC, for a total calculated analytical specificity of 86%. Additionally, all 43 samples drawn from healthy donors and 14 samples drawn from subjects diagnosed with benign nasopharyngeal disease were correctly identified as negative for nasopharyngeal carcinoma for a combined specificity of 100%. Conclusions: The NPC methylation panel was demonstrated to be both sensitive and specific for the detection of nasopharyngeal carcinoma. The potential of cfDNA methylation markers for the early detection of nasopharyngeal carcinoma is predicted to improve patient outcomes through earlier detection of the disease.
MET amplification and exon 14 skipping in treatment naïve patients in lung cancer.
Authors: Han Yaqian , Xu Ying , Liu Chunling , Zhao Jun , Zhu Lingjun , Li Liren , Gen Lin , Liu Lianke , Cheng Yong , Ye Ke , Chen Likun , Zhang Longbo , Yu Fenglei , Du Kaiqi , Miao Liyun , Chen Rongrong , Xia Xuefeng 
Published: May 2019

e14543 Background: Somatic mutations in MET are diverse and include MET amplification, exon 14 skipping and also some functional point mutations (H1094Y, Y1230H, D1228N, etc). Generally, amplification and ex14 skipping are the two main mutation types. Methods: MET mutation profiles were analyzed using hybridization capture based next-generation sequencing (NGS), which enables the simultaneous detection of multi-mutation types of at least 59 genes (range 59-1021 genes). Results: Screening tens of thousands treatment naive patients, we found 319 patients with MET mutations, 56 patients (18%) with MET amplification, 55 patients (17%) with MET ex14 skipping, and 214 patients with other unknown functional point mutations. 39 cases with MET amplification and 52 cases with MET ex14 skipping in lung cancer. Patients with MET amplification or ex14 skipping had fewer mutations compared with patients with other MET mutations ( P < 0.0001), while there were no differences in ctDNA abundance between two groups ( P = 0.58). Further compared the MET amplification and ex14 skipping groups, we found mutation numbers and ctDNA abundance were both significant lower in ex14 skipping group (mutation numbers: P = 0.0134; ctDNA abundance: P < 0.0001). MET amplification range from 2 to 7 copies in these 39 patients, and patients with more than 3 copies had a higher ctDNA abundance than = < 3 copies patients ( P < 0.0005). Six patients with both amplification and ex 14 skipping, all of them with advanced age ( > 70 years). Of the MET amplification group, 11 patients (28%) developed EGFR driver mutation concurrently, four patients with L858R, three with ex19 del, one with G719A, one with both L858R and EGFR amplification, one with both ex19 del and amplification and one with only amplification, while no patients were found to have any EGFR driver mutation in MET ex14 skipping group. Conclusions: The cfDNA from patients with EGFR amplification or ex14 skipping was only 18% or 17% in MET mutations. Both of these two mutation types were mainly found in lung cancer. Furthermore, MET amplification group patients had fewer mutations and lower ctDNA abundance. In treatment naïve patients, MET amplification concurrent with other EGFR drive mutations, rather than ex14 skipping.
Longitudinal monitoring of cell-free DNA to predict for transarterial chemo-embolization failure in hepatocellular carcinoma.
Authors: Evans Joanne , Ward Caroline , Pai Madhava , Sharma Rohini 
Published: May 2019

e14544 Background: Transarterial chemo-embolization (TACE) is the standard of care for patients with intermediate stage hepatocellular carcinoma (HCC) with adequate synthetic function, and as bridging treatment in early stage disease. Survival outcomes are heterogeneous, and improved biomarkers are needed for detection of early relapse. Current practice relies on monitoring of alpha-foetoprotein (AFP) and serial imaging. Circulating cell-free DNA (cfDNA) is a compelling emergent biomarker. Here, we describe the first study of cfDNA as prognostic biomarker in HCC following TACE. Methods: 34 patients treated with TACE (2012-2018) who had full demographic information and longitudinal stored plasma available were identified. Samples were retrieved and cfDNA extracted using the QIAamp Circulating Nucleic Acid Kit. cfDNA yields were quantified by high-sensitivity Qubit analysis. Results: 74% of patients were male, 66% had Childs Pugh A disease, and 56% of patients secreted AFP ( > 10ng/mL). Aetiologies of liver diseases were varied: viral hepatitis (44%), alcoholic or non-alcoholic steatohepatitis/cirrhosis (29%), hereditary or auto-immune (12%), and unexplained (15%). 79% of patients saw a fall in cfDNA titre following TACE. Where no reduction was seen, patients had a poorer median overall survival than those who did: 20 months (range 5.13 – 66.7 months) compared to 37 months (9.9 – 79.3 months). Of note, 44% of patients were AFP non-secretors. Here, cfDNA had a clear advantage in disease monitoring, with mean cfDNA titres in this group falling post treatment: from 1605.1 (range 185.9 – 6830) ng/mL to 693.7 (range undetectable - 2300) ng/mL and rising again with subsequent progression (mean of 1329.2 - range 616 – 3341 - ng/mL). Conclusions: These findings support a cost-effective monitoring role for plasma cfDNA analysis following treatment with TACE, with an added advantage in AFP non-secretors. Prospective validation is suggested to fully assess clinical utility.
Identify driver mutants in lung cancer by supernatants of pleural effusion and monitor resistance to targeted therapy.
Authors: Wang Yuehong , Wang Tao , Xiao Shanshan , Mao Ruifang , Lin Rui 
Published: May 2019

e14554 Background: Malignant pleural effusion (MPE) from lung cancer is an attractive alternative for molecular testing due to advantages of non-invasiveness and less heterogeneity. Previously, cell pellet blocks of MPE are widely used. This study is to further address whether supernatants of MPE is a suitable source to identify key oncogenic mutants in lung cancer and provide more information for clinical molecular testing. Methods: MPE samples from 12 lung cancer patients were centrifuged to obtain supernatants and cell pellets, and DNA were extracted. The DNA samples were analyzed by a targeted next generation sequencing (NGS) panel using Illumina HiSeq platform. Results: In a pilot study, paired cancer tissue and MPE samples were obtained from 3 lung cancer patients and analyzed using a comprehensive 500-gene cancer panel. Nine mutants were identified both in the tissue samples and MPE samples. We then analyzed another 9 lung cancer patient samples to detect oncogenic mutants using an 18-gene panel. In total, 8 mutants including EGFR L858R, exon 19 deletion, or T790M mutants were identified in MPE samples. For the total 17 mutants from the 12 MPE samples, 10 mutants were observed in both matched supernatant and cell pellet of MPE, of which more pairs (6 out of 10) had supernatants with higher abundance of mutants than cell pellets. More importantly, 7 of the 17 mutants were only detected in the supernatants of the matched MPE. Taken together, these results suggest that supernatant of MPE is a more suitable source to detect key driver mutants of lung cancer. Interestingly, 2 patients had both tyrosine kinase inhibitor (TKI) resistant mutant T790M and TKI sensitive mutants detected in supernatants of MPE; both patients had prior treatment of EGFR TKI, consistent with the development of TKI resistant mutant and supporting the utility of supernatants of MPE in monitoring TKI resistance. Conclusions: This study suggest supernatant of MPE is a more suitable source for identifying key driver mutants for lung cancer and can also be used to monitor response to targeted therapy. The study provides evidence of using supernatant of MPE as alternative source for molecular testing and thus direct precise targeted therapy and effect surveillance.
cfDNA analysis to reveal association of genomic features with chemotherapy response and survival in patients with pulmonary large-cell neuroendocrine carcinoma.
Authors: Zhuo Minglei , Guan Yan-Fang , Yang Xue , Hong Lingzhi , Wang Yuqi , Li Zhongwu , Chen Runzhe , Abbas Hussein , Zhong Jia , Chen Hanxiao , Dong Zhi , Zhu Xiang , Li Jianjie , Roarty Emily , Rinsurongkawong Waree , Lewis Jeff , Futreal Andrew , Xia Xuefeng , Zhang Jianjun , Zhao Jun 
Published: May 2019

e14555 Background: The optimal systemic treatment for pulmonary large-cell neuroendocrine carcinoma (LCNEC) is still under debate. Previous studies showed that LCNEC with different genomic characteristics might respond differently to different chemotherapy regimens suggesting the potential role of genomic profiling in therapeutic decision-making. Tumor biopsies are often inadequate for genomic profiling, while cell-free DNA (cfDNA) analysis has demonstrated great potential in genomic profiling. Methods: A total of 63 patients with LCNEC treated with different chemotherapy regimens (etoposide-platinum doublets, pemetrexed with platinum and gemcitabine, docetaxel, or paclitaxel with platinum, hereafter referred to as SCLC-PE, NSCLC-PEM and NSCLC-GEM/TAX) were enrolled in this study. Samples were collected and included tumor DNA only from 22 patients, cfDNA only from 18 patients and paired tumor DNA and plasma cfDNA from 23 patients. Tumor DNA and cfDNA were sequenced by target-captured 179 genes from Geneplus-Beijing or Oncomine Cancer Panel v3 or 70 genes panel from Guardant 360. Survival and response analyses were only applied to 54 patients who received first line chemotherapy. Results: The mutation landscape of frequently mutated cancer genes in LCNEC from cfDNA closely resembled that from tumor DNA, which led to a 90% concordance in genomic subtyping. We classified LCNEC harboring any of these alterations: RB1 mutation/loss, PTEN mutation/loss, FGFR1/FGFR4 mutation/amplification, TP53 loss, as “SCLC-like” tumors, otherwise as NSCLC-like. Overall, patients with SCLC-like LCNEC had a shorter overall survival (OS) than those with NSCLC-like LCNEC (10.3 vs 14.4 months, p = 0.32) despite higher response rate (RR) (41% vs 22%) to chemotherapy. Furthermore, treatment with SCLC-PE was associated with longer PFS in SCLC-like LCNEC compared to NSCLC-PEM and NSCLC-GEM/TAX (median 8.3 vs 2.3 months, p = 0.0002; median 8.3 vs 5.9 months, p = 0.05), while treatment with NSCLC-GEM/TAX led to a shorter survival compared to SCLC-PE (median 1.9 vs 4.1 months, p = 0.03) or NSCLC-PEM in NSCLC-like LCNEC patients (median 1.9 vs 4 months, p = 0.07). Conclusions: Genomic subtyping has potentials in prognostication and therapeutic decision-making for patients with LCNEC and cfDNA analysis is a reliable alternative for genomic profiling of LCNEC.
Circulating tumor DNA (ctDNA) mutation and epigenomic patterns in early-stage lung cancer patients and its utility in identifying patients at high risk for early recurrence.
Authors: Cho Jong Ho , Kim Il-Jin , Lee Junghee , Kim Hong Kwan , Lee Jinseon , Lee Se-Hoon , Shultz Matthew , Jaimovich Ariel , Odegaard Justin , Talasaz AmirAli , Kim Jhingook 
Published: May 2019

e14557 Background: Circulating tumor DNA (ctDNA) analysis has been successfully applied to therapy selection and treatment monitoring in advanced cancer patients. However, it is not yet established whether ctDNA can be used clinically for early cancer detection or predicting tumor recurrence in early stage lung cancer patients. Methods: We analyzed pre-operative plasma samples from 55 early stage NSCLC patients (stages I-IIIA) using next-generation sequencing to detect somatic mutations and differential epigenomics patterns, including methylation signatures. Results: Using somatic mutation analysis alone, ctDNA was detected in 42% (23/55) of patients, whereas combined mutational and epigenomic analysis detected ctDNA in 71%. ctDNA detection rate also varied markedly between lung squamous cell carcinoma (SCC) and adenocarcinoma (ADC);using combined analysis of somatic mutations and epigenomic patterns, ctDNA was detected in all SCC patients, while only 55% of ADC (12/22) were ctDNA-positive (p= 0.006). Within the ADC subgroup, ctDNA detection rates using the combined approach were dependent on disease stage: 47% (8/17) in stage I, 100% (2/2) in stage II, and 100% (2/2) in stage IIIA. Importantly, pre-operative ctDNA status was correlated with tumor recurrence post-resection; three of eight (38%) ctDNA-positive stage I ADC patients recurred within 2 years of resection, while only one of nine (11%) ctDNA-negative stage I ADC patients recurred (p= 0.29). Conclusions: Taken together, we show that the combination of somatic mutation detection and epigenomic analysis outperforms each individual biomarker in the detection of ctDNA in early stage lung cancer. Importantly, we also demonstrate that pre-operative ctDNA detection may identify a high-risk population of early stage lung cancer patients that may benefit from (neo)adjuvant therapy.
Dynamic change of PD-L1 expression on circulating tumor cells in advanced breast cancer undergoing PD-1 blockade therapy.
Authors: Wang Tao , Zhou Jinmei , Zhang Shaohua , Bian Li , Hu Zhiyuan , Jiang Zefei 
Published: May 2019

e14558 Background: PD-1/PD-L1 checkpoint blockade immunotherapy is revolution- izing the therapeutic strategy of malignancies. Tumor PD-L1 levels have predictive value in PD-1/PD-L1 checkpoint blockade therapies. Whether PD-L1 expression on circulating tumor cells (CTCs) could serve as an alternative biomarker is of great interest, especially in breast cancer. Methods: We established an immunofluorescence assay for semi-quantitative assessment of the PD-L1 expression levels on CTCs with four categories (PD-L1negative, PD-L1low, PD-L1medium and PD-L1high). 20patients with advanced breast cancerwere enrolled who took PD-1 inhibitortherapy. The CTC numeration and the PD-L1 expression levels were analyzedat the begining and ending of treatment . Results: 20 patients were enrolled, 85%(17/20) were triple-negative breast cancer. 65% of patients had visceral metastases, 60% of patients had ≥3 lines of treatment. Prior the treatment of PD-1 inhibitor, 95% (19/20) patients had CTCs, ranging from1 to 53(median 5). 90% (18/20) had PD-L1positive CTCs, and 75% (15/20) had at least one PD-L1high CTCs. The clinical benefit rate(CBR) rate in PD-L1high patients (26.7%) is much higher than the others (0%). we examined the proportion of PD-L1high CTCs relative to total CTCs. The median proportion of PD-L1high CTCs was 33.3%. Patients with ≥33% PD-L1high CTCs had a significantly longer PFS (median 2.6 vs. 1.4 months( P = 0.027). 100% patients with CBR had PD-L1highCTCs decreased and 46.7% of patients without CBR decreased. Further analysis showed that the mean proportion of PD-L1highCTCs at baseline and after treatment was 56.8±20.7%, 19.0±23.7%, p = 0.005. There was no significant difference in the mean proportion of PD-L1highCTCs before and after treatment in the non-CBR group (28.0±26.2%, 30.3±31.5%, p = 0.846). Conclusions: We revealed that the abundance of PD-L1high CTCs at baseline might serve as a predictor to screen patients for PD-1/PD-L1 blockade therapies and measuring the dynamic changes of PD-L1high CTCscould indicate the therapeutic response at early time.
Clinical significance of circulating tumor cells identified by cell-surface vimentin in pancreatic cancer.
Authors: Wei Tao , Zhang Qi , Liang Tingbo , Bai Xueli 
Published: May 2019

e14562 Background: Identification of circulating tumor cells (CTCs) largely rely on epithelial tumor cell marker. Here we sought to interrogate whether cell-surface vimentin could be a biomarker for isolating CTCs potentially with mesenchymal phenotype in pancreatic ductal adenocarcinoma (PDAC). Methods: In total, 100 PDAC patients, 16 patients with intraductal papillary mucinous neoplasm (IPMN), and 30 healthy individuals were enrolled between December 2016 and November 2017. Potential CTCs were captured in 4 ml blood samples by vimentin antibody-coated microfluidic chip. CTCs were defined as vimentin+CD45-Hoechst+. Results: In vitro experiment showed that vimentin was highly expressed on the surface of pancreatic tumor cells with mesenchymal phenotype. Overall, vimentin+ CTCs were detected in 76% of patients with PDAC, but only in 2 out 30 healthy donors. Besides, five patients (31.3%) with IPMN had vimentin+ CTCs, and 10 CTCs were identified in one case. Using a cut-off value of two cells/4 ml of blood, 65% PDAC patients were positive for vimentin+ CTCs , while the positivity rates for the patients with IPMN and the healthy controls were 25% and 0%, respectively. Combined vimentin+ CTCs and CA19-9 offered a favorable diagnostic potency with area under curve of 0.968. Vimentin+ CTCs counts correlated with change of tumor burden for patients undergoing resection ( P < 0.01). Significant reduction of CTCs counts was observed after chemotherapy for subjects responding to treatment ( P < 0.05). The paired analysis showed that CTC counts was higher in portal vein blood than peripheral blood for 10 patients with available samples ( P < 0.05). Patients with 2 or more CTCs detected had more advanced disease and poorer differentiated tumor. In addition, preoperative higher CTCs counts correlated with shortened recurrence-free survival (Log-rank test: P = 0.02). Conclusions: Vimentin+ CTCs serves as a reliable biomarker in pancreatic cancer. The enrichment of potential mesenchymal CTCs could complement the strategy capturing epithelial CTCs, and provides a way to more thoroughly interrogate the biology and clinical significance of CTCs in PDAC.
Analysis of circulating tumor DNA to monitor metastatic breast cancer patients treated with first-line chemotherapy (CAMELLIA study).
Authors: Yi Zongbi , Ma Fei , Rong Guohua , Li Jin , Chang Lianpeng , Guan Yanfang , Liu Binliang , Guan Xiuwen , Li Lixi , Li Chunxiao , Zhai Jingtong , Qian Haili , Xu Binghe 
Published: May 2019

e14568 Background: Our precious study indicated that the dynamic changes in circulating tumor DNA (ctDNA) could reflect changes in tumor burden. We conduct this study to validate the role of ctDNA as a therapeutic response biomarker in a larger cohort prospective phase III randomized multicenter study. Methods: In this study, we collected 292 serial ctDNA samples from 125 metastatic breast cancer patients treated with first line chemotherapy. Target-capture deep sequencing of 1021 genes was performed to detect somatic variants in ctDNA. Results: 81.4% patients had detectable ctDNA at baseline. An undetectable ctDNA at baseline was associated with a lower disease volume (p < 0.05). The commonly mutated genes were PIK3CA (35.0%), TP53 (34.2%), MLL3 (9.4%) and ESR1 (9.4%). Kaplan–Meier analysis showed that TP53 gene mutations and remaining C2 (detected at base line and remaining at the second cycle of chemotherapy) were significantly associated with poor PFS. Longitudinal monitoring of 27 patients during treatment showed that the molecular tumor burden index ([mTBI] a measure of the percentage of ctDNA in samples) was positively correlated with tumor size as evaluated by computed tomography (P < 0.05). The evaluations based on mTBI values were consistent with those based on CT scans in 87.5% of cases at the endpoint of clinical observation. Conclusions: ctDNA could be used to predict treatment outcomes and the mTBI is a potential method to assess therapeutic response in metastatic breast cancer. Clinical trial information: NCT01917279.