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cfDNA NGS

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https://www.readbyqxmd.com/read/28522829/somatic-tumor-mutations-detected-by-targeted-next-generation-sequencing-in-minute-amounts-of-serum-derived-cell-free-dna
#1
Marjolein J A Weerts, Ronald van Marion, Jean C A Helmijr, Corine M Beaufort, Niels M G Krol, Anita M A C Trapman-Jansen, Winand N M Dinjens, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens
The use of blood-circulating cell-free DNA (cfDNA) as 'liquid-biopsy' is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28511612/ngs-analysis-on-tumor-tissue-and-cfdna-for-genotype-directed-therapy-in-metastatic-nsclc-patients-between-hope-and-hype
#2
Alexander T Falk, Simon Heeke, Véronique Hofman, Virginie Lespinet, Camille Ribeyre, Olivier Bordone, Michel Poudenx, Josiane Otto, Georges Garnier, Olivier Castelnau, Joël Guigay, Sylvie Leroy, Charles-Hugo Marquette, Paul Hofman, Marius Ilié
The advent of genomic based precision medicine led to the implementation of biomarker testing in metastatic non-small cell lung cancer (NSCLC) patients. Next generation sequencing (NGS) has been recently implemented to routine diagnostic requirements in lung oncology. Areas covered: Two cases of patients with metastatic NSCLC for whom NGS analysis performed on both tumor and liquid biopsy has not improved the clinical course of their disease are reported. These cases illustrate the difficulty of the so-called "personalized or precision" medicine in clinical routine practice for metastatic NSCLC...
May 17, 2017: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/28506684/study-of-preanalytic-and-analytic-variables-for-clinical-next-generation-sequencing-of-circulating-cell-free-nucleic-acid
#3
Meenakshi Mehrotra, Rajesh R Singh, Wei Chen, Richard S P Huang, Alaa A Almohammedsalim, Bedia A Barkoh, Crystal M Simien, Marcos Hernandez, Carmen Behrens, Keyur P Patel, Mark J Routbort, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Scott Kopetz, Rajyalakshmi Luthra
Detection of mutations in plasma circulating cell-free DNA (cfDNA) by next-generation sequencing (NGS) has opened up new possibilities for monitoring treatment response and disease progression in patients with solid tumors. However, implementation of cfDNA genotyping in diagnostic laboratories requires systematic assessment of preanalytical parameters and analytical performance of NGS platforms. We assessed the effects of peripheral blood collection tube and plasma separation time on cfDNA yield and integrity and performance of the Ion PGM, Proton, and MiSeq NGS platforms...
May 12, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28502728/technical-validation-of-a-next-generation-sequencing-assay-for-detecting-clinically-relevant-levels-of-breast-cancer-related-single-nucleotide-variants-and-copy-number-variants-using-simulated-cell-free-dna
#4
Xin Yang, Yuxing Chu, Rui Zhang, Yanxi Han, Lucheng Zhang, Yu Fu, Dan Li, Rongxue Peng, Dongdong Li, Jiansheng Ding, Ziyang Li, Meiru Zhao, Kuo Zhang, Tian Lu, Lang Yi, Qisheng Wu, Guigao Lin, Jiehong Xie, Tao Liu, Ling Yang, Xin Yi, Jinming Li
Next-generation sequencing (NGS) is commonly used in a clinical setting for diagnostic and prognostic testing of genetic mutations to select optimal targeted therapies. Herein, we describe the development of a custom NGS assay for detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 51 genes related to breast cancer. We designed and implemented a validation strategy in accordance with principles and guidelines developed by the Next-Generation Sequencing: Standardization of Clinical Testing work group using artificial, cell-free DNA (cfDNA) with mutant fragments prepared in a simple, rapid, and cost-effective manner...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28393575/using-circulating-cell-free-dna-to-monitor-personalized-cancer-therapy
#5
Michael Oellerich, Ekkehard Schütz, Julia Beck, Philipp Kanzow, Piers N Plowman, Glen J Weiss, Philip D Walson
High-quality genomic analysis is critical for personalized pharmacotherapy in patients with cancer. Tumor-specific genomic alterations can be identified in cell-free DNA (cfDNA) from patient blood samples and can complement biopsies for real-time molecular monitoring of treatment, detection of recurrence, and tracking resistance. cfDNA can be especially useful when tumor tissue is unavailable or insufficient for testing. For blood-based genomic profiling, next-generation sequencing (NGS) and droplet digital PCR (ddPCR) have been successfully applied...
May 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28320758/tumor-cell-free-dna-copy-number-instability-predicts-therapeutic-response-to-immunotherapy
#6
Glen J Weiss, Julia Beck, Donald P Braun, Kristen Bornemann-Kolatzki, Heather Barilla, Rhiannon Cubello, Walter Quan, Ashish Sangal, Vivek Khemka, Jordan Waypa, William M Mitchell, Howard Urnovitz, Ekkehard Schütz
PURPOSE: Chromosomal instability is a fundamental property of cancer, which can be quantified by Next Generation Sequencing (NGS) from plasma/serum derived cell-free DNA (cfDNA). We hypothesized that cfDNA could be used as a real time surrogate for imaging analysis of disease status as a function of response to immunotherapy and as a more reliable tool than tumor biomarkers. EXPERIMENTAL DESIGN: Plasma cfDNA sequences from 56 patients with diverse advanced cancers, were prospectively collected and analyzed in a single-blinded study for copy number variations, expressed as a quantitative chromosomal number instability (CNI) score versus 126 non-cancer controls in a training set of 23 and a blinded validation set of 33...
March 20, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#7
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
March 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28212557/using-high-sensitivity-sequencing-for-the-detection-of-mutations-in-btk-and-plc%C3%AE-2-genes-in-cellular-and-cell-free-dna-and-correlation-with-progression-in-patients-treated-with-btk-inhibitors
#8
Adam Albitar, Wanlong Ma, Ivan DeDios, Jeffrey Estella, Inhye Ahn, Mohammed Farooqui, Adrian Wiestner, Maher Albitar
Patients with chronic lymphocytic leukemia (CLL) that develop resistance to Bruton tyrosine kinase (BTK) inhibitors are typically positive for mutations in BTK or phospholipase c gamma 2 (PLCγ2). We developed a high sensitivity (HS) assay utilizing wild-type blocking polymerase chain reaction achieved via bridged and locked nucleic acids. We used this high sensitivity assay in combination with Sanger sequencing and next generation sequencing (NGS) and tested cellular DNA and cell-free DNA (cfDNA) from patients with CLL treated with the BTK inhibitor, ibrutinib...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28170370/development-of-a-gene-panel-for-next-generation-sequencing-of-clinically-relevant-mutations-in-cell-free-dna-from-cancer-patients
#9
Umberto Malapelle, Clara Mayo de-Las-Casas, Danilo Rocco, Monica Garzon, Pasquale Pisapia, Nuria Jordana-Ariza, Maria Russo, Roberta Sgariglia, Caterina De Luca, Francesco Pepe, Alejandro Martinez-Bueno, Daniela Morales-Espinosa, María González-Cao, Niki Karachaliou, Santiago Viteri Ramirez, Claudio Bellevicine, Miguel Angel Molina-Vila, Rafael Rosell, Giancarlo Troncone
BACKGROUND: When tumour tissue is unavailable, cell-free DNA (cfDNA)can serve as a surrogate for genetic analyses. Because mutated alleles in cfDNA are usually below 1%, next-generation sequencing (NGS)must be narrowed to target only clinically relevant genes. In this proof-of-concept study, we developed a panel to use in ultra-deep sequencing to identify such mutations in cfDNA. METHODS: Our panel ('SiRe') covers 568 mutations in six genes (EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRα)involved in non-small-cell lung cancer (NSCLC), gastrointestinal stromal tumour, colorectal carcinoma and melanoma...
March 14, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28152506/detection-fidelity-of-ar-mutations-in-plasma-derived-cell-free-dna
#10
Alexa Goldstein, Patricia Valda Toro, Justin Lee, John L Silberstein, Mary Nakazawa, Ian Waters, Karen Cravero, David Chu, Rory L Cochran, Minsoo Kim, Daniel Shinn, Samantha Torquato, Robert M Hughes, Aparna Pallavajjala, Michael A Carducci, Channing J Paller, Samuel R Denmeade, Bruce Kressel, Bruce J Trock, Mario A Eisenberger, Emmanuel S Antonarakis, Ben H Park, Paula J Hurley
Somatic genetic alterations including copy number and point mutations in the androgen receptor (AR) are associated with resistance to therapies targeting the androgen/AR axis in patients with metastatic castration resistant prostate cancer (mCRPC). Due to limitations associated with biopsying metastatic lesions, plasma derived cell-free DNA (cfDNA) is increasingly being used as substrate for genetic testing. AR mutations detected by deep next generation sequencing (NGS) of cfDNA from patients with mCRPC have been reported at allelic fractions ranging from over 25% to below 1%...
February 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28093244/novel-mutations-on-egfr-leu792-potentially-correlate-to-acquired-resistance-to-osimertinib-in%C3%A2-advanced-nsclc
#11
Kai Chen, Fei Zhou, Wenxiang Shen, Tao Jiang, Xue Wu, Xiaoling Tong, Yang W Shao, Songbing Qin, Caicun Zhou
No abstract text is available yet for this article.
January 16, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28029553/somatic-mutation-detection-using-various-targeted-detection-assays-in-paired-samples-of-circulating-tumor-dna-primary-tumor-and-metastases-from-patients-undergoing-resection-of-colorectal-liver-metastases
#12
Nick Beije, Jean C Helmijr, Marjolein J A Weerts, Corine M Beaufort, Matthew Wiggin, Andre Marziali, Cornelis Verhoef, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens
Assessing circulating tumor DNA (ctDNA) is a promising method to evaluate somatic mutations from solid tumors in a minimally-invasive way. In a group of twelve metastatic colorectal cancer (mCRC) patients undergoing liver metastasectomy, from each patient DNA from cell-free DNA (cfDNA), the primary tumor, metastatic liver tissue, normal tumor-adjacent colon or liver tissue, and whole blood were obtained. Investigated was the feasibility of a targeted NGS approach to identify somatic mutations in ctDNA. This targeted NGS approach was also compared with NGS preceded by mutant allele enrichment using synchronous coefficient of drag alteration technology embodied in the OnTarget assay, and for selected mutations with digital PCR (dPCR)...
October 10, 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28027320/genomic-analysis-of-uterine-lavage-fluid-detects-early-endometrial-cancers-and-reveals-a-prevalent-landscape-of-driver-mutations-in-women-without-histopathologic-evidence-of-cancer-a-prospective-cross-sectional-study
#13
Navya Nair, Olga Camacho-Vanegas, Dmitry Rykunov, Matthew Dashkoff, Sandra Catalina Camacho, Cassie A Schumacher, Jonathan C Irish, Timothy T Harkins, Elijah Freeman, Isaac Garcia, Elena Pereira, Sviatoslav Kendall, Rachel Belfer, Tamara Kalir, Robert Sebra, Boris Reva, Peter Dottino, John A Martignetti
BACKGROUND: Endometrial cancer is the most common gynecologic malignancy, and its incidence and associated mortality are increasing. Despite the immediate need to detect these cancers at an earlier stage, there is no effective screening methodology or protocol for endometrial cancer. The comprehensive, genomics-based analysis of endometrial cancer by The Cancer Genome Atlas (TCGA) revealed many of the molecular defects that define this cancer. Based on these cancer genome results, and in a prospective study, we hypothesized that the use of ultra-deep, targeted gene sequencing could detect somatic mutations in uterine lavage fluid obtained from women undergoing hysteroscopy as a means of molecular screening and diagnosis...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27940449/next-generation-sequencing-of-circulating-cell-free-dna-for-evaluating-mutations-and-gene-amplification-in-metastatic-breast-cancer
#14
Karen Page, David S Guttery, Daniel Fernandez-Garcia, Allison Hills, Robert K Hastings, Jinli Luo, Kate Goddard, Vedia Shahin, Laura Woodley-Barker, Brenda M Rosales, R Charles Coombes, Justin Stebbing, Jacqueline A Shaw
BACKGROUND: Breast cancer tissues are heterogeneous and show diverse somatic mutations and somatic copy number alterations (CNAs). We used a novel targeted next generation sequencing (NGS) panel to examine cell-free DNA (cfDNA) to detect somatic mutations and gene amplification in women with metastatic breast cancer (MBC). METHODS: cfDNA from pretreated patients (n = 42) and 9 healthy controls were compared with matched lymphocyte DNA by NGS, using a custom 158 amplicon panel covering hot-spot mutations and CNAs in 16 genes, with further validation of results by droplet digital PCR...
February 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/27926526/use-of-capture-based-next-generation-sequencing-to-detect-alk-fusion-in-plasma-cell-free-dna-of-patients-with-non-small-cell-lung-cancer
#15
Shaohua Cui, Wei Zhang, Liwen Xiong, Feng Pan, Yanjie Niu, Tianqing Chu, Huimin Wang, Yizhuo Zhao, Liyan Jiang
Capture-based next-generation sequencing (NGS) is a potentially useful diagnostic method to measure tumor tissue DNA in blood as it can identify concordant mutations between cell-free DNA (cfDNA) and primary tumor DNA in lung cancer patients. In this study, the sensitivity, specificity and accuracy of capture-based NGS for detecting ALK fusion in plasma cfDNA was assessed. 24 patients with tissue ALK-positivity and 15 who did not harbor ALK fusion were enrolled. 13 ALK-positive samples were identified by capture-based NGS among the 24 samples with tissue ALK-positivity...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/27833075/a-pilot-study-evaluating-concordance-between-blood-based-and-patient-matched-tumor-molecular-testing-within-pancreatic-cancer-patients-participating-in-the-know-your-tumor-kyt-initiative
#16
Michael J Pishvaian, R Joseph Bender, Lynn M Matrisian, Lola Rahib, Andrew Hendifar, William A Hoos, Sam Mikhail, Vincent Chung, Vincent Picozzi, Craig Heartwell, Kimberly Mason, Katelyn Varieur, Metasebia Aberra, Subha Madhavan, Emanuel Petricoin, Jonathan R Brody
Recent improvements in next-generation sequencing (NGS) technology have enabled detection of biomarkers in cell-free DNA in blood and may ultimately replace invasive tissue biopsies. However, a better understanding of the performance of blood-based NGS assays is needed prior to routine clinical use. As part of an IRB-approved molecular profiling registry trial of pancreatic ductal adenocarcinoma (PDA) patients, we facilitated blood-based NGS testing of 34 patients from multiple community-based and high-volume academic oncology practices...
November 8, 2016: Oncotarget
https://www.readbyqxmd.com/read/27826531/next-generation-sequencing-techniques-in-liquid-biopsy-focus-on-non-small-cell-lung-cancer-patients
#17
REVIEW
Umberto Malapelle, Pasquale Pisapia, Danilo Rocco, Riccardo Smeraglio, Maria di Spirito, Claudio Bellevicine, Giancarlo Troncone
The advent of genomic based personalized medicine has led to multiple advances in the molecular characterization of many tumor types, such as non-small cell lung cancer (NSCLC). NSCLC is diagnosed in most cases on small tissue samples that may be not always sufficient for EGFR mutational assessment to select patients for first and second generations' tyrosine kinase inhibitors (TKIs) therapy. In patients without tissue availability at presentation, the analysis of cell free DNA (cfDNA) derived from liquid biopsy samples, in particular from plasma, represent an established alternative to provide EGFR mutational testing for treatment decision making...
October 2016: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/27589834/cell-free-dna-and-next-generation-sequencing-in-the-service-of-personalized-medicine-for-lung-cancer
#18
REVIEW
Catherine W Bennett, Guy Berchem, Yeoun Jin Kim, Victoria El-Khoury
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer...
October 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27575703/tumor-volume-determines-the-feasibility-of-cell-free-dna-sequencing-for-mutation-detection-in-non-small-cell-lung-cancer
#19
Tatsuo Ohira, Kazuko Sakai, Jun Matsubayashi, Naohiro Kajiwara, Masatoshi Kakihana, Masaru Hagiwara, Masaaki Hibi, Koichi Yoshida, Junichi Maeda, Keishi Ohtani, Toshitaka Nagao, Kazuto Nishio, Norihiko Ikeda
Next-generation sequencing (NGS) and digital PCR technologies allow analysis of the mutational profile of circulating cell-free DNA (cfDNA) in individuals with advanced lung cancer. We have now evaluated the feasibility of cfDNA sequencing for mutation detection in patients with non-small cell lung cancer at earlier stages. A total of 150 matched tumor and serum samples were collected from non-small cell lung cancer patients at stages IA-IIIA. Amplicon sequencing with DNA extracted from tumor tissue detected frequent mutations in EGFR (37% of patients), TP53 (39%), and KRAS (10%), consistent with previous findings...
November 2016: Cancer Science
https://www.readbyqxmd.com/read/27334837/mutation-analysis-of-cell-free-dna-and-single-circulating-tumor-cells-in-metastatic-breast-cancer-patients-with-high-circulating-tumor-cell-counts
#20
Jacqueline A Shaw, David S Guttery, Allison Hills, Daniel Fernandez-Garcia, Karen Page, Brenda M Rosales, Kate S Goddard, Robert K Hastings, Jinli Luo, Olivia Ogle, Laura Woodley, Simak Ali, Justin Stebbing, R Charles Coombes
PURPOSE: The purpose of this study was to directly compare mutation profiles in multiple single circulating tumor cells (CTC) and cell-free DNA (cfDNA) isolated from the same blood samples taken from patients with metastatic breast cancer (MBC). We aimed to determine whether cfDNA would reflect the heterogeneity observed in 40 single CTCs. EXPERIMENTAL DESIGN: CTCs were enumerated by CELLSEARCH. CTC count was compared with the quantity of matched cfDNA and serum CA15-3 and alkaline phosphatase (ALP) in 112 patients with MBC...
January 1, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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