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circulating tumor dna

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https://www.readbyqxmd.com/read/29335459/publisher-correction-discovery-of-targetable-genetic-alterations-in-advanced-non-small-cell-lung-cancer-using-a-next-generation-sequencing-based-circulating-tumor-dna-assay
#1
Helei Hou, Xiaonan Yang, Jinping Zhang, Zhe Zhang, Xiaomei Xu, Xiaoping Zhang, Chuantao Zhang, Dong Liu, Weihua Yan, Na Zhou, Hongmei Zhu, Zhaoyang Qian, Zhuokun Li, Xiaochun Zhang
A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330207/early-assessment-of-lung-cancer-immunotherapy-response-via-circulating-tumor-dna
#2
Sarah B Goldberg, Azeet Narayan, Adam J Kole, Roy H Decker, Jimmitti Teysir, Nicholas J Carriero, Angela Lee, Roxanne Nemati, Sameer K Nath, Shrikant M Mane, Yanhong Deng, Nitin Sukumar, Daniel Zelterman, Daniel J Boffa, Katerina Politi, Scott Gettinger, Lynn D Wilson, Roy S Herbst, Abhijit A Patel
PURPOSE: Decisions to continue or suspend therapy with immune checkpoint inhibitors are commonly guided by tumor dynamics seen on serial imaging.  However, immunotherapy responses are uniquely challenging to interpret because tumors often shrink slowly or can appear transiently enlarged due to inflammation.  We hypothesized that monitoring tumor cell death in real-time by quantifying changes in circulating tumor DNA (ctDNA) levels could enable early assessment of immunotherapy efficacy...
January 12, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29326054/size-based-separation-methods-of-circulating-tumor-cells
#3
Si-Jie Hao, Yuan Wan, Yi-Qiu Xia, Xin Zou, Si-Yang Zheng
Circulating tumor cells (CTCs) originate from the primary tumor mass and enter into the peripheral bloodstream. Compared to other "liquid biopsy" portfolios such as exosome, circulating tumor DNA/RNA (ctDNA/RNA), CTCs have incomparable advantages in analyses of transcriptomics, proteomics, and signal colocalization. Hence, CTCs hold the key to understanding the biology of metastasis and play a vital role in cancer diagnosis, treatment monitoring, and prognosis. Size-based enrichment featureS prominently in CTC isolation...
January 8, 2018: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29312652/tyrosine-kinase-inhibitor-sensitive-pdgfr%C3%AE-mutations-in-gist-two-cases-and-review-of-the-literature
#4
Pieter A Boonstra, Jourik A Gietema, Albert J H Suurmeijer, Matthew R Groves, Fernando de Assis Batista, Ed Schuuring, Anna K L Reyners
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal malignancies of the gastrointestinal tract. Most GISTs harbor a c-KIT (80%) or a PDGFRα (10%) mutation that leads to constitutive activation of the tyrosine kinase receptor. Response to treatment with tyrosine kinase inhibitors (TKIs) is dependent on mutational status of the tumor. The most common mutation in PDGFRα, D842V, is known to be imatinib resistant. Almost all other PDGFRα mutations are imatinib sensitive. We describe two patients with a PDGFRα exon 18 mutated GIST responding to treatment with TKIs...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29310587/unique-dual-indexed-sequencing-adapters-with-umis-effectively-eliminate-index-cross-talk-and-significantly-improve-sensitivity-of-massively-parallel-sequencing
#5
Laura E MacConaill, Robert T Burns, Anwesha Nag, Haley A Coleman, Michael K Slevin, Kristina Giorda, Madelyn Light, Kevin Lai, Mirna Jarosz, Matthew S McNeill, Matthew D Ducar, Matthew Meyerson, Aaron R Thorner
BACKGROUND: Sample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk. RESULTS: Cross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0...
January 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29298756/adct-402-a-pbd-dimer-containing-antibody-drug-conjugate-targeting-cd19-expressing-malignancies
#6
Francesca Zammarchi, Simon Corbett, Lauren Adams, Peter C Tyrer, Konstantinos Kiakos, Narinder Janghra, Teresa Marafioti, Charles E Britten, Carin E G Havenith, Simon Chivers, Francois D'Hooge, David G Williams, Arnaud Tiberghien, Philip W Howard, John A Hartley, Patrick H van Berkel
Human CD19 antigen is a 95-kDa type I membrane glycoprotein in the immunoglobulin superfamily whose expression is limited to the various stages of B-cell development and differentiation and is maintained in the majority of B-cell malignancies, including leukemias and non-Hodgkin lymphomas of B-cell origin. Coupled with its differential and favourable expression profile, CD19 has rapid internalization kinetics and it is not shed into the circulation, making it an ideal target for the development of antibody-drug conjugates (ADCs) to treat B-cell malignancies...
January 3, 2018: Blood
https://www.readbyqxmd.com/read/29298118/circulating-tumor-dna-guides-prognosis-in-metastatic-triple-negative-breast-cancer
#7
Andjelija Zivanovic Bujak, Sarah-Jane Dawson
No abstract text is available yet for this article.
January 3, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29291160/a-dual-biomarker-detection-platform-for-quantitating-circulating-tumor-dna-ctdna
#8
Chunyan Cai, Zhenzhong Guo, Yiping Cao, Weiying Zhang, Yong Chen
Circulating tumor DNA (ctDNA), which includes DNA mutations, epigenetic alterations and other forms of tumor-specific abnormalities, is a promising "real-time" biomarker for noninvasive cancer assessment. Tumor DNA is of great value in the process of cancer treatment, including diagnostic and prognostic information before, during treatment and at progression. Here we introduce a peptide nucleic acids probe-gold nanoparticles (PNA-AuNPs) and lead phosphate apoferritin (LPA)-based dual biomarker detection platform, which could be used in a DNA biosensor to quantify ctDNA by detection of tumor-specific mutations and methylation of PIK3CA gene...
2018: Nanotheranostics
https://www.readbyqxmd.com/read/29290998/detection-of-somatic-variants-and-egfr-mutations-in-cell-free-dna-from-non-small-cell-lung-cancer-patients-by-ultra-deep-sequencing-using-the-ion-ampliseq-cancer-hotspot-panel-and-droplet-digital-polymerase-chain-reaction
#9
Jae Sook Sung, Hyon Yong Chong, Nak-Jung Kwon, Hae Mi Kim, Jong Won Lee, Boyeon Kim, Saet Byeol Lee, Chang Won Park, Jung Yoon Choi, Won Jin Chang, Yoon Ji Choi, Sung Yong Lee, Eun Joo Kang, Kyong Hwa Park, Yeul Hong Kim
Highly sensitive genotyping assays can detect mutations in cell-free DNA (cfDNA) from cancer patients, reflecting the biology of each patient's cancer. Because circulating tumor DNA comprises a small, variable fraction of DNA circulating in the blood, sensitive parallel multiplexing tests are required to determine mutation profiles. We prospectively examined the clinical utility of ultra-deep sequencing analysis of cfDNA from 126 non-small cell lung cancer (NSCLC) patients using the Ion AmpliSeq Cancer Hotspot Panel v2 (ICP) and validated these findings with droplet digital polymerase chain reaction (ddPCR)...
December 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/29290823/magnetic-nanowire-networks-for-dual-isolation-and-detection-of-tumor-associated-circulating-biomarkers
#10
HyungJae Lee, Mihye Choi, Jiyun Lim, Minkyung Jo, Ji-Youn Han, Tae Min Kim, Youngnam Cho
Purpose: Recent developments in genomic and molecular methods have revolutionized the range of utilities of tumor-associated circulating biomarkers in both basic and clinical research. Herein, we present a novel approach for ultrasensitive extraction of cfDNA and CTCs, at high yield and purity, via the formation of magnetic nanowire networks. Materials and Methods: We fabricated and characterized biotinylated cationic polyethylenimine and biotinylated antibody cocktail-conjugated magnetic polypyrrole NWs (PEI/mPpy NW and Ab cocktail/mPpy NW, respectively)...
2018: Theranostics
https://www.readbyqxmd.com/read/29290257/primary-resistance-to-osimertinib-due-to-sclc-transformation-issue-of-t790m-determination-on-liquid-re-biopsy
#11
R Minari, P Bordi, M Del Re, F Facchinetti, F Mazzoni, F Barbieri, A Camerini, C E Comin, L Gnetti, C Azzoni, R Nizzoli, B Bortesi, E Rofi, P Petreni, N Campanini, G Rossi, R Danesi, M Tiseo
OBJECTIVES: EGFR T790M mutation is the most common mechanism of resistance to first-/second-generation EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) and could be overcome by third-generation EGFR-TKIs, such as osimertinib. Liquid biopsy, a non-invasive technique used to test the presence of the resistant mutation, may help avoiding tissue re-biopsy. However, analysing only circulating-free DNA, information about other less frequent and coexisting resistance mechanisms may remain unrevealed...
January 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29288729/extracellular-vesicles-or-free-circulating-dna-where-to-search-for-braf-and-ckit-mutations
#12
Jennifer Klump, Ulrike Philipp, Marie Follo, Anna Eremin, Hannes Lehmann, Sigrun Nestel, Nikolas von Bubnoff, Irina Nazarenko
Clinical evidence in oncology argues for the advantages of performing molecular analysis of blood biomarkers to provide information about systemic changes and tumor heterogeneity. Whereas the diagnostic value of cell-free circulating DNA (fcDNA) has successfully been demonstrated in several studies, DNA enclosed in extracellular vesicles (EV) has only recently been described, and its potential diagnostic value is unclear. We established a protocol for separation of EV and fc fractions and tested for presence of mutant BRAFV600E mediating resistance to Vemurafenib and cKITD816V mediating resistance to Imatinib in blood of patients with melanoma and mastocytosis...
December 27, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29286485/characterization-of-tumor-cells-using-a-medical-wire-for-capturing-circulating-tumor-cells-a-3d-approach-based-on-immunofluorescence-and-dna-fish
#13
Giulia Gallerani, Claudia Cocchi, Martine Bocchini, Filippo Piccinini, Francesco Fabbri
Circulating tumor cells (CTCs) are associated with poor survival in metastatic cancer. Their identification, phenotyping, and genotyping could lead to a better understanding of tumor heterogeneity and thus facilitate the selection of patients for personalized treatment. However, this is hampered because of the rarity of CTCs. We present an innovative approach for sampling a high volume of the patient blood and obtaining information about presence, phenotype, and gene translocation of CTCs. The method combines immunofluorescence staining and DNA fluorescent-in-situ-hybridization (DNA FISH) and is based on a functionalized medical wire...
December 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29285512/liquid-biopsy-for-ctdna-to-revolutionize-the-care-of-patients-with-early-stage-lung-cancers
#14
COMMENT
Bob T Li, Dennis Stephens, Jamie E Chaft, Charles M Rudin, David R Jones, Valerie W Rusch, Andreas Rimner, James M Isbell
The current standard of adjuvant therapies for patients with early stage non-small-cell lung cancers largely depends on the stage of disease. Liquid biopsy for circulating tumor DNA (ctDNA) has the potential to detect minimal residual disease, depict genomic evolution, guide precision medicine to individual patients and revolutionize the management of early stage lung cancers. In light of the seminal work published by Abbosh and colleagues, we discuss the potential paradigm changing clinical implications of ctDNA, the biological and technological challenges to consider, and the future of ctDNA driven therapeutic studies...
December 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/29277949/development-and-clinical-validation-of-a-circulating-tumor-dna-test-for-the-identification-of-clinically-actionable-mutations-in-non-small-cell-lung-cancer
#15
Liping Liu, Han Liu, Di Shao, Zu Liu, Jingjing Wang, Qiuhua Deng, Hailing Tang, Haihong Yang, Yalei Zhang, Yuan Qiu, Fei Cui, Meihua Tan, Pan Zhang, Zhilong Li, Jilong Liu, Wenhua Liang, Yuying Wang, Zhiyu Peng, Jian Wang, Huanming Yang, Mao Mao, Karsten Kristiansen, Mingzhi Ye, Jianxing He
Molecular analysis of potentially actionable mutations has become routine practice in oncological pathology. However, testing a wide range of oncogenes and mutations can be technically challenging because of limitations associated with tumor biopsy. Circulating tumor DNA (ctDNA) is a potential tool for the noninvasive profiling of tumors. In this study, we developed a next-generation sequencing (NGS)-based test for the detection of clinically relevant mutations in ctDNA and evaluated the feasibility of using this ctDNA NGS-based assay as an alternative to tissue genotyping...
December 26, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29260398/integrated-bioinformatics-analysis-of-potential-biomarkers-for-prostate-cancer
#16
Jiufeng Tan, Xuefei Jin, Kaichen Wang
The aim was to expound the pathogenesis of prostate cancer and to identify the potentially biomarkers for prostate cancer (PC). DNA methylation microarray data GSE38240 containing 8 prostate cancer metastases and 4 normal prostate samples as well as gene expression profile data GSE26910 containing 6 prostate primary tumors and 6 normal samples were used. Differentially expressed genes (DEGs) and differently methylated sites of PC were screened and the regulatory network was constructed with DEGs-related transcription factors (TFs)...
December 19, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/29248429/predicting-therapy-response-and-resistance-in-metastatic-prostate-cancer-with-circulating-tumor-dna
#17
REVIEW
Elie Ritch, Alexander W Wyatt
The treatment of metastatic castration-resistant prostate cancer (mCRPC) is empirical, with progress to a more precision medicine approach hampered by lack of predictive biomarkers. This is due in large part to the historical difficulty of molecularly profiling a bone-predominant metastatic disease. Focus has turned to minimally invasive sources of tumor material to better understand the molecular drivers of therapy resistance. Circulating cell-free tumor DNA (ctDNA) is highly abundant in the bloodstream of mCRPC patients and appears to provide an accurate snapshot of real-time tumor genomics...
December 13, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/29248319/phase-2-trial-of-gemcitabine-cisplatin-plus-ipilimumab-in-patients-with-metastatic-urothelial-cancer-and-impact-of-dna-damage-response-gene-mutations-on-outcomes
#18
Matthew D Galsky, Huan Wang, Noah M Hahn, Przemyslaw Twardowski, Sumanta K Pal, Costantine Albany, Mark T Fleming, Alexander Starodub, Ralph J Hauke, Menggang Yu, Qianqian Zhao, Guru Sonpavde, Michael J Donovan, Vaibhav G Patel, John P Sfakianos, Josep Domingo-Domenech, William K Oh, Nicholas Akers, Bojan Losic, Sacha Gnjatic, Eric E Schadt, Rong Chen, Seunghee Kim-Schulze, Nina Bhardwaj, Andrew V Uzilov
BACKGROUND: Chemotherapy may exert immunomodulatory effects, thereby combining favorably with the immune checkpoint blockade. The pharmacodynamic effects of such combinations, and potential predictive biomarkers, remain unexplored. OBJECTIVE: To determine the safety, efficacy, and immunomodulatory effects of gemcitabine and cisplatin (GC) plus ipilimumab and explore the impact of somatic DNA damage response gene alterations on antitumor activity. DESIGN, SETTING, AND PARTICIPANTS: Multicenter single arm phase 2 study enrolling 36 chemotherapy-naïve patients with metastatic urothelial cancer...
December 13, 2017: European Urology
https://www.readbyqxmd.com/read/29247763/nanoplasmonic-sensors-for-detecting-circulating-cancer-biomarkers
#19
Abdul Rahim Ferhan, Joshua A Jackman, Jae Hyeon Park, Nam-Joon Cho, Dong-Hwan Kim
The detection of cancer biomarkers represents an important aspect of cancer diagnosis and prognosis. Recently, the concept of liquid biopsy has been introduced whereby diagnosis and prognosis are performed by means of analyzing biological fluids obtained from patients to detect and quantify circulating cancer biomarkers. Unlike conventional biopsy whereby primary tumor cells are analyzed, liquid biopsy enables the detection of a wide variety of circulating cancer biomarkers, including microRNA (miRNA), circulating tumor DNA (ctDNA), proteins, exosomes and circulating tumor cells (CTCs)...
December 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/29246024/comparison-of-cross-platform-technologies-for-egfr-t790m-testing-in-patients-with-non-small-cell-lung-cancer
#20
REVIEW
Xuefei Li, Caicun Zhou
Somatic mutations in the gene encoding epidermal growth factor receptor (EGFR) play an important role in determining targeted treatment modalities in non-small cell lung cancer (NSCLC). The EGFR T790M mutation emerges in approximately 50% of cases who acquire resistance to tyrosine kinase inhibitors. Detecting EGFR T790M mutation in tumor tissue is challenging due to heterogeneity of the tumor, low abundance of the mutation and difficulty for re-biopsy in patients with advanced disease. Alternatively, circulating tumor DNA (ctDNA) has been proposed as a non-invasive method for mutational analysis...
November 21, 2017: Oncotarget
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