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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
#1
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...
February 13, 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
#2
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...
February 7, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28152506/detection-fidelity-of-ar-mutations-in-plasma-derived-cell-free-dna
#3
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%...
January 31, 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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...
August 30, 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
#12
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
#13
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
https://www.readbyqxmd.com/read/27270325/cell-free-dna-mutations-as-biomarkers-in-breast-cancer-patients-receiving-tamoxifen
#14
Maurice Phm Jansen, John Wm Martens, Jean Ca Helmijr, Corine M Beaufort, Ronald van Marion, Niels Mg Krol, Kim Monkhorst, Anita Mac Trapman-Jansen, Marion E Meijer-van Gelder, Marjolein Ja Weerts, Diana E Ramirez-Ardila, Hendrikus Jan Dubbink, John A Foekens, Stefan Sleijfer, Els Mjj Berns
The aim was to identify mutations in serum cell-free DNA (cfDNA) associated with disease progression on tamoxifen treatment in metastatic breast cancer (MBC). Sera available at start of therapy, during therapy and at disease progression were selected from 10 estrogen receptor (ER)-positive breast cancer patients. DNA from primary tumor and normal tissue and cfDNA from minute amounts of sera were analyzed by targeted next generation sequencing (NGS) of 45 genes (1,242 exons). At disease progression, stop-gain single nucleotide variants (SNVs) for CREBBP (1 patient) and SMAD4 (1 patient) and non-synonymous SNVs for AKAP9 (1 patient), PIK3CA (2 patients) and TP53 (2 patients) were found...
July 12, 2016: Oncotarget
https://www.readbyqxmd.com/read/27180141/circulating-cell-free-nucleic-acids-and-platelets-as-a-liquid-biopsy-in-the-provision-of-personalized-therapy-for-lung-cancer-patients
#15
L Sorber, K Zwaenepoel, V Deschoolmeester, P E Y Van Schil, J Van Meerbeeck, F Lardon, C Rolfo, P Pauwels
Lung cancer is the predominant cause of cancer-related mortality in the world. The majority of patients present with locally advanced or metastatic non-small-cell lung cancer (NSCLC). Treatment for NSCLC is evolving from the use of cytotoxic chemotherapy to personalized treatment based on molecular alterations. Unfortunately, the quality of the available tumor biopsy and/or cytology material is not always adequate to perform the necessary molecular testing, which has prompted the search for alternatives. This review examines the use of circulating cell-free nucleic acids (cfNA), consisting of both circulating cell-free (tumoral) DNA (cfDNA-ctDNA) and RNA (cfRNA), as a liquid biopsy in lung cancer...
May 4, 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/26883583/digital-pcr-for-quantification-of-recurrent-and-potentially-actionable-somatic-mutations-in-circulating-free-dna-from-patients-with-diffuse-large-b-cell-lymphoma
#16
Vincent Camus, Nasrin Sarafan-Vasseur, Elodie Bohers, Sydney Dubois, Sylvain Mareschal, Philippe Bertrand, Pierre-Julien Viailly, Philippe Ruminy, Catherine Maingonnat, Emilie Lemasle, Aspasia Stamatoullas, Jean-Michel Picquenot, Marie Cornic, Ludivine Beaussire, Christian Bastard, Thierry Frebourg, Hervé Tilly, Fabrice Jardin
Diffuse large B-cell lymphoma (DLBCL) is an aggressive and heterogeneous malignancy harboring frequent targetable activating somatic mutations. Emerging evidence suggests that circulating cell-free DNA (cfDNA) can be used to detect somatic variants in DLBCL using Next-Generation Sequencing (NGS) experiments. In this proof-of-concept study, we chose to develop simple and valuable digital PCR (dPCR) assays for the detection of recurrent exportin-1 (XPO1) E571K, EZH2 Y641N, and MYD88 L265P mutations in DLBCL patients, thereby identifying patients most likely to potentially benefit from targeted therapies...
September 2016: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/26823523/detection-of-ubiquitous-and-heterogeneous-mutations-in-cell-free-dna-from-patients-with-early-stage-non-small-cell-lung-cancer
#17
M Jamal-Hanjani, G A Wilson, S Horswell, R Mitter, O Sakarya, T Constantin, R Salari, E Kirkizlar, S Sigurjonsson, R Pelham, S Kareht, B Zimmermann, C Swanton
BACKGROUND: The aim of this pilot study was to assess whether both ubiquitous and heterogeneous somatic mutations could be detected in cell-free DNA (cfDNA) from patients with early-stage non-small-cell lung cancer (NSCLC). PATIENTS AND METHODS: Three stage I and one stage II primary NSCLC tumors were subjected to multiregion whole-exome sequencing (WES) and validated with AmpliSeq. A subset of ubiquitous and heterogeneous single-nucleotide variants (SNVs) were chosen...
May 2016: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/26758560/circulating-cell-free-tumor-dna-analysis-of-50-genes-by-next-generation-sequencing-in-the-prospective-moscato-trial
#18
Cécile Jovelet, Ecaterina Ileana, Marie-Cécile Le Deley, Nelly Motté, Silvia Rosellini, Alfredo Romero, Celine Lefebvre, Marion Pedrero, Noémie Pata-Merci, Nathalie Droin, Marc Deloger, Christophe Massard, Antoine Hollebecque, Charles Ferté, Amélie Boichard, Sophie Postel-Vinay, Maud Ngo-Camus, Thierry De Baere, Philippe Vielh, Jean-Yves Scoazec, Gilles Vassal, Alexander Eggermont, Fabrice André, Jean-Charles Soria, Ludovic Lacroix
PURPOSE: Liquid biopsies based on circulating cell-free DNA (cfDNA) analysis are described as surrogate samples for molecular analysis. We evaluated the concordance between tumor DNA (tDNA) and cfDNA analysis on a large cohort of patients with advanced or metastatic solid tumor, eligible for phase I trial and with good performance status, enrolled in MOSCATO 01 trial (clinical trial NCT01566019). EXPERIMENTAL DESIGN: Blood samples were collected at inclusion and cfDNA was extracted from plasma for 334 patients...
June 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/26639657/genetic-profiling-of-tumours-using-both-circulating-free-dna-and-circulating-tumour-cells-isolated-from-the-same-preserved-whole-blood-sample
#19
Dominic G Rothwell, Nigel Smith, Daniel Morris, Hui Sun Leong, Yaoyong Li, Antoine Hollebecque, Mahmood Ayub, Louise Carter, Jenny Antonello, Lynsey Franklin, Crispin Miller, Fiona Blackhall, Caroline Dive, Ged Brady
Molecular information obtained from cancer patients' blood is an emerging and powerful research tool with immense potential as a companion diagnostic for patient stratification and monitoring. Blood, which can be sampled routinely, provides a means of inferring the current genetic status of patients' tumours via analysis of circulating tumour cells (CTCs) or circulating tumour DNA (ctDNA). However, accurate assessment of both CTCs and ctDNA requires all blood cells to be maintained intact until samples are processed...
April 2016: Molecular Oncology
https://www.readbyqxmd.com/read/26633390/next-generation-sequencing-workflow-for-nsclc-critical-samples-using-a-targeted-sequencing-approach-by-ion-torrent-pgm%C3%A2-platform
#20
Irene Vanni, Simona Coco, Anna Truini, Marta Rusmini, Maria Giovanna Dal Bello, Angela Alama, Barbara Banelli, Marco Mora, Erika Rijavec, Giulia Barletta, Carlo Genova, Federica Biello, Claudia Maggioni, Francesco Grossi
Next-generation sequencing (NGS) is a cost-effective technology capable of screening several genes simultaneously; however, its application in a clinical context requires an established workflow to acquire reliable sequencing results. Here, we report an optimized NGS workflow analyzing 22 lung cancer-related genes to sequence critical samples such as DNA from formalin-fixed paraffin-embedded (FFPE) blocks and circulating free DNA (cfDNA). Snap frozen and matched FFPE gDNA from 12 non-small cell lung cancer (NSCLC) patients, whose gDNA fragmentation status was previously evaluated using a multiplex PCR-based quality control, were successfully sequenced with Ion Torrent PGM™...
2015: International Journal of Molecular Sciences
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