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cfDNA NGS

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https://www.readbyqxmd.com/read/29765524/cross-platform-comparison-for-the-detection-of-ras-mutations-in-cfdna-ddpcr-biorad-detection-assay-beaming-assay-and-ngs-strategy
#1
Jessica Garcia, Julien Forestier, Eric Dusserre, Anne-Sophie Wozny, Florence Geiguer, Patrick Merle, Claire Tissot, Carole Ferraro-Peyret, Frederick S Jones, Daniel L Edelstein, Valérie Cheynet, Claire Bardel, Gaelle Vilchez, Zhenyu Xu, Pierre Paul Bringuier, Marc Barritault, Karen Brengle-Pesce, Marielle Guillet, Marion Chauvenet, Brigitte Manship, Marie Brevet, Claire Rodriguez-Lafrasse, Valérie Hervieu, Sébastien Couraud, Thomas Walter, Léa Payen
CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29719623/validation-and-comparison-of-two-ngs-assays-for-the-detection-of-egfr-t790m-resistance-mutation-in-liquid-biopsies-of-nsclc-patients
#2
Claudia Vollbrecht, Annika Lehmann, Dido Lenze, Michael Hummel
Analysis of circulating cell-free DNA (cfDNA) derived from peripheral blood ("liquid biopsy") is an attractive alternative to identify non-small cell lung cancer (NSCLC) patients with the EGFR T790M mutation eligible for 3rd generation tyrosine kinase inhibitor therapy. We evaluated two PCR-based next generation sequencing (NGS) approaches, one including unique molecular identifiers (UMI), with focus on highly sensitive EGFR T790M mutation detection. Therefore, we extracted and sequenced cfDNA from synthetic plasma samples spiked with mutated DNA at decreasing allele frequencies and from 21 diagnostic NSCLC patients...
April 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29599410/clinical-utility-of-cell-free-dna-for-the-detection-of-alk-fusions-and-genomic-mechanisms-of-alk-inhibitor-resistance-in-non-small-cell-lung-cancer
#3
Caroline E McCoach, Collin M Blakely, Kimberly C Banks, Benjamin Levy, Ben M Chue, Victoria M Raymond, Anh Le, Christine E Lee, Joseph Diaz, Saiama N Waqar, W Thomas Purcell, Dara L Aisner, Kurtis D Davies, Richard B Lanman, Alice T Shaw, Robert C Doebele
PURPOSE: Patients with advanced non-small cell lung cancer (NSCLC) whose tumors harbor anaplastic lymphoma kinase ALK gene fusions benefit from treatment with ALK inhibitors (ALKi). Analysis of cell-free circulating tumor DNA (cfDNA) may provide a non-invasive way to identify ALK fusions and actionable resistance mechanisms without biopsy. EXPERIMENTAL DESIGN: The Guardant360 (G360) de-identified database of NSCLC cases was queried to identify 88 consecutive patients with 96 plasma-detected ALK fusions...
March 29, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29573240/liquid-biopsy-by-ngs-differential-presence-of-exons-dpe-in-cell-free-dna-reveals-different-patterns-in-metastatic-and-nonmetastatic-colorectal-cancer
#4
Susana Olmedillas-López, Dolores C García-Olmo, Mariano García-Arranz, Ramón Peiró-Pastor, Begoña Aguado, Damián García-Olmo
Next-generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole-exome sequencing (WES) of cell-free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, "differential presence of exons" (DPE)...
March 23, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29567812/false-positive-plasma-genotyping-due-to-clonal-hematopoiesis
#5
Yuebi Hu, Bryan Ulrich, Julianna Supplee, Yanan Kuang, Patrick H Lizotte, Nora Feeney, Nicolas Guibert, Mark M Awad, Kwok-Kin Wong, Pasi A Janne, Cloud Peter Paweletz, Geoffrey R Oxnard
PURPOSE: Plasma cell-free DNA (cfDNA) genotyping is increasingly used in cancer care, but assay accuracy is debated. Because most cfDNA is derived from peripheral blood cells (PBC), we hypothesized that nonmalignant mutations harbored by hematopoietic cells (clonal hematopoiesis, CH) could be a cause of false positive plasma genotyping.  Experimental Design: We identified patients with advanced NSCLC with KRAS , JAK2 , or TP53 mutations identified in cfDNA. With consent, PBC DNA was tested using droplet digital PCR (ddPCR) or next-generation sequencing (NGS) to test for CH-derived mutations...
March 22, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29566644/the-characteristics-of-ctdna-reveal-the-high-complexity-in-matching-the-corresponding-tumor-tissues
#6
Nong Yang, Yi Li, Zhidong Liu, Hao Qin, Duanming Du, Xinkai Cao, Xiaoqing Cao, Jun Li, Dongge Li, Bo Jiang, Lincan Duan, Haiyan Yang, Zhenghua Zhang, Hao Lin, Jianying Li, Zhenhua Yang, Lei Xiong, Hua Shen, Lizhu Lin, Fugen Li
BACKGROUND: Next-generation sequencing (NGS) is an efficient and sensitive method to detect mutations from ctDNA. Many features and clinical conditions could significantly affect the concordance between ctDNA and corresponding tumor tissues. Our goal was to systematically investigate the critical factors contributing to different concordance between ctDNA and corresponding tumor tissues. METHODS: We recruited two groups of IIIB or IV lung cancer patients: The standard group to evaluate the accuracy of our method and the concordance between ctDNA and tumor tissues, and the study group with various clinical conditions...
March 23, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29535804/detection-of-somatic-mutations-in-cell-free-dna-in-plasma-and-correlation-with-overall-survival-in-patients-with-solid-tumors
#7
Meenakshi Mehrotra, Rajesh R Singh, Sanam Loghavi, Dzifa Yawa Duose, Bedia A Barkoh, Carmen Behrens, Keyur P Patel, Mark J Routbort, Scott Kopetz, Russell R Broaddus, L Jeffrey Medeiros, Ignacio I Wistuba, Rajyalakshmi Luthra
A suitable clinical-grade platform is required for detection of somatic mutations with high sensitivity in cell-free DNA (cfDNA) of patients with solid tumors. In this study, we evaluated in parallel ultra-deep NGS with MassARRAY and allele-specific droplet digital PCR (ddPCR) for cfDNA genotyping and correlated cfDNA yield and mutation status with overall survival (OS) of patients. We assessed plasma samples from 46 patients with various advanced metastatic solid tumors and known mutations by deep sequencing using an Ampliseq cancer hotspot panel V2 on Ion Proton...
February 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29523763/molecular-response-to-neoadjuvant-chemotherapy-in-high-grade-serous-ovarian-carcinoma
#8
Rebecca C Arend, Angelina I Londoño, Allison M Montgomery, Haller J Smith, Zachary C Dobbin, Ashwini A Katre, Alba Martinez, Eddy S Yang, Ronald D Alvarez, Warner K Huh, Kerri S Bevis, J Michael Straughn, Jacob M Estes, Lea Novak, David K Crossman, Sara J Cooper, Charles N Landen, Charles A Leath
While high-grade serous ovarian carcinoma (HGSOC) is the most common histologic subtype of ovarian cancer, significant tumor heterogeneity exists. In addition, chemotherapy induces changes in gene expression and alters the mutational profile. To evaluate the notion that patients with HGSOC could be better classified for optimal treatment based on gene expression, we compared genetic variants [by DNA next-generation sequencing (NGS) using a 50 gene Ion Torrent panel] and gene expression (using the NanoString PanCancer 770 gene Panel) in the tumor from 20 patients with HGSOC before and after neoadjuvant chemotherapy (NACT)...
May 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29517810/characterization-of-metastatic-urothelial-carcinoma-via-comprehensive-genomic-profiling-of-circulating-tumor-dna
#9
Neeraj Agarwal, Sumanta K Pal, Andrew W Hahn, Roberto H Nussenzveig, Gregory R Pond, Sumati V Gupta, Jue Wang, Mehmet A Bilen, Gurudatta Naik, Pooja Ghatalia, Christopher J Hoimes, Dharmesh Gopalakrishnan, Pedro C Barata, Alexandra Drakaki, Bishoy M Faltas, Lesli A Kiedrowski, Richard B Lanman, Rebecca J Nagy, Nicholas J Vogelzang, Kenneth M Boucher, Ulka N Vaishampayan, Guru Sonpavde, Petros Grivas
BACKGROUND: Biomarker-guided clinical trials are increasingly common in metastatic urothelial carcinoma (mUC), yet patients for whom contemporary tumor tissue is not available are not eligible. Technological advancements in sequencing have made cell-free circulating DNA (cfDNA) next-generation sequencing (NGS) readily available in the clinic. The objective of the current study was to determine whether the genomic profile of mUC detected by NGS of cfDNA is similar to historical tumor tissue NGS studies...
May 15, 2018: Cancer
https://www.readbyqxmd.com/read/29506987/investigating-novel-resistance-mechanisms-to-third-generation-egfr-tyrosine-kinase-inhibitor-osimertinib-in-non-small-cell-lung-cancer-patients
#10
Zhe Yang, Nong Yang, Qiuxiang Ou, Yi Xiang, Tao Jiang, Xue Wu, Hua Bao, Xiaoling Tong, Xiaonan Wang, Yang W Shao, Yunpeng Liu, Yan Wang, Caicun Zhou
Background: The third-generation EGFR tyrosine kinase inhibitor osimertinib is approved to treat patients with EGFR T790M-positive non-small cell lung cancer (NSCLC) who have developed resistance to earlier-generation drugs. Acquired EGFR C797S mutation has been reported to mediate osimertinib resistance in some patients. However, the remaining resistance mechanisms are largely unknown. Methods: We performed mutation profiling using targeted next-generation sequencing (NGS) for 416 cancer-relevant genes on 93 osimertinib-resistant lung cancer patients' samples, mainly cell-free DNAs (cfDNAs), and matched pretreatment samples of 12 patients...
March 5, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29419698/next-generation-sequencing-diagnostics-of-bacteremia-in-sepsis-next-genesis-trial-study-protocol-of-a-prospective-observational-noninterventional-multicenter-clinical-trial
#11
MULTICENTER STUDY
Thorsten Brenner, Sebastian O Decker, Silke Grumaz, Philip Stevens, Thomas Bruckner, Thomas Schmoch, Mathias W Pletz, Hendrik Bracht, Stefan Hofer, Gernot Marx, Markus A Weigand, Kai Sohn
BACKGROUND: Sepsis remains a major challenge, even in modern intensive care medicine. The identification of the causative pathogen is crucial for an early optimization of the antimicrobial treatment regime. In this context, culture-based diagnostic procedures (e.g., blood cultures) represent the standard of care, although they are associated with relevant limitations. Accordingly, culture-independent molecular diagnostic procedures might be of help for the identification of the causative pathogen in infected patients...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29416824/the-dawn-of-the-liquid-biopsy-in-the-fight-against-cancer
#12
REVIEW
Irma G Domínguez-Vigil, Ana K Moreno-Martínez, Julia Y Wang, Michael H A Roehrl, Hugo A Barrera-Saldaña
Cancer is a molecular disease associated with alterations in the genome, which, thanks to the highly improved sensitivity of mutation detection techniques, can be identified in cell-free DNA (cfDNA) circulating in blood, a method also called liquid biopsy. This is a non-invasive alternative to surgical biopsy and has the potential of revealing the molecular signature of tumors to aid in the individualization of treatments. In this review, we focus on cfDNA analysis, its advantages, and clinical applications employing genomic tools (NGS and dPCR) particularly in the field of oncology, and highlight its valuable contributions to early detection, prognosis, and prediction of treatment response...
January 5, 2018: Oncotarget
https://www.readbyqxmd.com/read/29409051/impact-of-genomic-alterations-on-lapatinib-treatment-outcome-and-cell-free-genomic-landscape-during-her2-therapy-in-her2-gastric-cancer-patients
#13
S T Kim, K C Banks, E Pectasides, S Y Kim, K Kim, R B Lanman, A Talasaz, J An, M G Choi, J H Lee, T S Sohn, J M Bae, S Kim, S H Park, J O Park, Y S Park, H Y Lim, N K D Kim, W Park, H Lee, A J Bass, K Kim, W K Kang, J Lee
Background: To identify predictive markers for responders in lapatinib-treated patients and to demonstrate molecular changes during lapatinib treatment via cell-free genomics. Patients and methods: We prospectively evaluated the efficacy of combining lapatinib with capecitabine and oxaliplatin as first line neoadjuvant therapy in patients with previously untreated, HER2-overexpressing advanced gastric cancer. A parallel biomarker study was conducted by simultaneously performing immunohistochemistry and next-generation sequencing (NGS) with tumor and blood samples...
April 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29382943/optimized-targeted-sequencing-of-cell-free-plasma-dna-from-bladder-cancer-patients
#14
Emil Christensen, Iver Nordentoft, Søren Vang, Karin Birkenkamp-Demtröder, Jørgen Bjerggaard Jensen, Mads Agerbæk, Jakob Skou Pedersen, Lars Dyrskjøt
Analysis of plasma cell-free DNA (cfDNA) may provide important information in cancer research, though the often small fraction of DNA originating from tumor cells makes the analysis technically challenging. Digital droplet PCR (ddPCR) has been utilized extensively as sufficient technical performance is easily achieved, but analysis is restricted to few mutations. Next generation sequencing (NGS) approaches have been optimized to provide comparable technical performance, especially with the introduction of unique identifiers (UIDs)...
January 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29305293/beyond-screening-for-chromosomal-abnormalities-advances-in-non-invasive-diagnosis-of-single-gene-disorders-and-fetal-exome-sequencing
#15
REVIEW
Jane Hayward, Lyn S Chitty
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities...
April 2018: Seminars in Fetal & Neonatal 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-nonsmall-cell-lung-cancer
#16
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...
April 2018: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29216356/improved-egfr-mutation-detection-using-combined-exosomal-rna-and-circulating-tumor-dna-in-nsclc-patient-plasma
#17
A K Krug, D Enderle, C Karlovich, T Priewasser, S Bentink, A Spiel, K Brinkmann, J Emenegger, D G Grimm, E Castellanos-Rizaldos, J W Goldman, L V Sequist, J-C Soria, D R Camidge, S M Gadgeel, H A Wakelee, M Raponi, M Noerholm, J Skog
Background: A major limitation of circulating tumor DNA (ctDNA) for somatic mutation detection has been the low level of ctDNA found in a subset of cancer patients. We investigated whether using a combined isolation of exosomal RNA (exoRNA) and cell-free DNA (cfDNA) could improve blood-based liquid biopsy for EGFR mutation detection in NSCLC patients. Patients and methods: Matched pretreatment tumor and plasma were collected from 84 patients enrolled in TIGER-X (NCT01526928), a Ph1/2 study of rociletinib in mutant EGFR NSCLC patients...
December 5, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29184677/cell-free-dna-analysis-by-sire-%C3%A2-next-generation-sequencing-panel-in-non-small-cell-lung-cancer-patients-focus-on-basal-setting
#18
Pasquale Pisapia, Francesco Pepe, Riccardo Smeraglio, Maria Russo, Danilo Rocco, Roberta Sgariglia, Mariantonia Nacchio, Caterina De Luca, Elena Vigliar, Claudio Bellevicine, Giancarlo Troncone, Umberto Malapelle
Background: Non small cell lung cancer (NSCLC) is diagnosed in most cases on small tissue samples, such as cytological preparations and histological biopsies; these limited tissue specimens may be not always sufficient for testing epidermal growth factor receptor ( EGFR ) mutations and other relevant predictive biomarkers. Cell-free DNA (cfDNA) can be used as a surrogate for EGFR mutational testing, whenever tissue is unavailable. However, the detection of gene mutations on cfDNA is challenging; in fact, the extremely low concentration of circulating tumor DNA requires the implementation of highly sensitive and validated next generation techniques...
October 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29172773/an-update-on-liquid-biopsy-analysis-for-diagnostic-and-monitoring-applications-in-non-small-cell-lung-cancer
#19
Clara Mayo-de-Las-Casas, Mónica Garzón Ibáñez, Núria Jordana-Ariza, Beatriz García-Peláez, Ariadna Balada-Bel, Sergio Villatoro, Umberto Malapelle, Niki Karachaliou, Giancarlo Troncone, Rafael Rosell, Miguel Angel Molina-Vila
Collection of tumor samples is not always feasible in non-small cell lung cancer (NSCLC) patients, and circulating free DNA (cfDNA) extracted from blood represents a viable alternative. Different sensitive platforms have been developed for genetic cfDNA testing, some of which are already in clinical use. However, several difficulties remain, particularly the lack of standardization of these methodologies. Areas covered: Here, the authors present a review of the literature to update the applicability of cfDNA for diagnosis and monitoring of NSCLC patients...
January 2018: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/29163793/rapid-ultra-low-coverage-copy-number-profiling-of-cell-free-dna-as-a-precision-oncology-screening-strategy
#20
Daniel H Hovelson, Chia-Jen Liu, Yugang Wang, Qing Kang, James Henderson, Amy Gursky, Scott Brockman, Nithya Ramnath, John C Krauss, Moshe Talpaz, Malathi Kandarpa, Rashmi Chugh, Missy Tuck, Kirk Herman, Catherine S Grasso, Michael J Quist, Felix Y Feng, Christine Haakenson, John Langmore, Emmanuel Kamberov, Tim Tesmer, Hatim Husain, Robert J Lonigro, Dan Robinson, David C Smith, Ajjai S Alva, Maha H Hussain, Arul M Chinnaiyan, Muneesh Tewari, Ryan E Mills, Todd M Morgan, Scott A Tomlins
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling...
October 27, 2017: Oncotarget
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