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Article ; Online: Next-Generation Sequencing and Result Interpretation in Clinical Oncology: Challenges of Personalized Cancer Therapy.

Khotskaya, Yekaterina B / Mills, Gordon B / Mills Shaw, Kenna R

2017 Volume 68, Page(s) 113–125

Abstract: The tools of next-generation sequencing (NGS) technology, such as targeted sequencing of candidate cancer genes and whole-exome and -genome sequencing, coupled with encouraging clinical results based on the use of targeted therapeutics and biomarker- ... ...

Abstract	The tools of next-generation sequencing (NGS) technology, such as targeted sequencing of candidate cancer genes and whole-exome and -genome sequencing, coupled with encouraging clinical results based on the use of targeted therapeutics and biomarker-guided clinical trials, are fueling further technological advancements of NGS technology. However, NGS data interpretation is associated with challenges that must be overcome to promote the techniques' effective integration into clinical oncology practice. Specifically, sequencing of a patient's tumor often yields 30-65 somatic variants, but most of these variants are "passenger" mutations that are phenotypically neutral and thus not targetable. Therefore, NGS data must be interpreted by multidisciplinary decision-support teams to determine mutation actionability and identify potential "drivers," so that the treating physician can prioritize what clinical decisions can be pursued in order to provide cancer therapy that is personalized to the patient and his or her unique genome.
Language	English
Publishing date	2017-01-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	207930-6
ISSN	1545-326X ; 0066-4219
ISSN (online)	1545-326X
ISSN	0066-4219
DOI	10.1146/annurev-med-102115-021556
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Article ; Online: Precision oncology: neither a silver bullet nor a dream.

Sánchez, Nora S / Mills, Gordon B / Mills Shaw, Kenna R

Pharmacogenomics

2017 Volume 18, Issue 16, Page(s) 1525–1539

Abstract: Precision oncology is not an illusion, nor is it the magic bullet that will eradicate all cancers. Precision oncology is simply another weapon in our growing armament against cancer. Rather than honing in on the failures of a relatively young field, one ... ...

Abstract	Precision oncology is not an illusion, nor is it the magic bullet that will eradicate all cancers. Precision oncology is simply another weapon in our growing armament against cancer. Rather than honing in on the failures of a relatively young field, one should advocate for integrating its successes into widespread clinical practice, especially for indications, such as: ABL, ALK, BRAF, BRCA1, BRCA2, EGFR, KIT, KRAS, PDGFRA, PDGFRB, ROS1, BCR-ABL, FLT3 and ROS1, where aberrations have been shown to alter responses to US FDA approved drugs - that is, level 1 data. Moreover, to truly assess the promise of precision oncology, we must first begin by defining our expectations for this field. Importantly, we must recognize that the conception of precision oncology arose as an antithesis of the 'one-size fits all' cancer therapeutics approach. Consequently, tools used for evaluating these conventional, large-scale trials, are not directly transferable for assessing nonconventional, smaller-scale trials needed for evaluating precision oncology. Hence, a thorough vetting of precision oncology as another tool of the trade, must first begin by reassessing our expectations for this field, as well as current clinical trial designs and end point measurements. Importantly, we must recognize that most targeted therapy approaches are in their infancy, with only monotherapy approaches being assessed and combination therapies likely being necessary to fulfill the promise of precision oncology.
MeSH term(s)	Antineoplastic Agents/therapeutic use ; Clinical Trials as Topic ; Humans ; Molecular Targeted Therapy ; Neoplasms/drug therapy ; Precision Medicine/methods
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2017-11
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2019513-8
ISSN	1744-8042 ; 1462-2416
ISSN (online)	1744-8042
ISSN	1462-2416
DOI	10.2217/pgs-2017-0094
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Zs.A 5247: Show issues

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Article ; Online: Targeting TRK family proteins in cancer.

Khotskaya, Yekaterina B / Holla, Vijaykumar R / Farago, Anna F / Mills Shaw, Kenna R / Meric-Bernstam, Funda / Hong, David S

Pharmacology & therapeutics

2017 Volume 173, Page(s) 58–66

Abstract: The tropomyosin receptor kinase (TRK) family includes TRKA, TRKB, and TRKC proteins, which are encoded by NTRK1, NTRK2 and NTRK3 genes, respectively. Binding of neurotrophins to TRK proteins induces receptor dimerization, phosphorylation, and activation ... ...

Abstract	The tropomyosin receptor kinase (TRK) family includes TRKA, TRKB, and TRKC proteins, which are encoded by NTRK1, NTRK2 and NTRK3 genes, respectively. Binding of neurotrophins to TRK proteins induces receptor dimerization, phosphorylation, and activation of the downstream signaling cascades via PI3K, RAS/MAPK/ERK, and PLC-gamma. TRK pathway aberrations, including gene fusions, protein overexpression, and single nucleotide alterations, have been implicated in the pathogenesis of many cancer types, with NTRK gene fusions being the most well validated oncogenic events to date. Although the NTRK gene fusions are infrequent in most cancer types, certain rare tumor types are predominately driven by these events. Conversely, in more common histologies, such as lung and colorectal cancers, prevalence of the NTRK fusions is well below 5%. Selective inhibition of TRK signaling may therefore be beneficial among patients whose tumors vary in histologies, but share underlying oncogenic NTRK gene alterations. Currently, several TRK-targeting compounds are in clinical development. The ongoing Phase 2 trials with entrectinib and LOXO-101, two of the leading TRK inhibitors, are designed as 'basket trials', inclusive of patients whose tumors harbor NTRK gene fusions, independent of histology. Additional Phase 1 studies of other TRK inhibitors, including MGCD516, PLX7486, DS-6051b, and TSR-011, are underway. Interim data examining NTRK-rearranged tumors treated with entrectinib or LOXO-101 demonstrate encouraging activity, with patients achieving rapid and durable responses. Consequently, both drugs have achieved orphan designation from regulatory agencies, and efforts are underway to further expedite their development.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Benzamides/pharmacology ; Drug Design ; Humans ; Indazoles/pharmacology ; Molecular Targeted Therapy ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology ; Protein Kinase Inhibitors/pharmacology ; Pyrazoles/pharmacology ; Pyrimidines/pharmacology ; Receptor, trkA/antagonists & inhibitors ; Receptor, trkA/genetics ; Receptor, trkA/metabolism ; Receptor, trkB/antagonists & inhibitors ; Receptor, trkB/genetics ; Receptor, trkB/metabolism ; Receptor, trkC/antagonists & inhibitors ; Receptor, trkC/genetics ; Receptor, trkC/metabolism
Chemical Substances	Antineoplastic Agents ; Benzamides ; Indazoles ; Protein Kinase Inhibitors ; Pyrazoles ; Pyrimidines ; Receptor, trkA (EC 2.7.10.1) ; Receptor, trkB (EC 2.7.10.1) ; Receptor, trkC (EC 2.7.10.1) ; entrectinib (L5ORF0AN1I) ; larotrectinib (PF9462I9HX)
Language	English
Publishing date	2017-02-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	194735-7
ISSN	1879-016X ; 0163-7258
ISSN (online)	1879-016X
ISSN	0163-7258
DOI	10.1016/j.pharmthera.2017.02.006
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Article ; Online: Use of a Targeted Exome Next-Generation Sequencing Panel Offers Therapeutic Opportunity and Clinical Benefit in a Subset of Patients With Advanced Cancers.

Kopetz, Scott / Mills Shaw, Kenna R / Lee, J Jack / Zhang, Jiexin / Litzenburger, Beate / Holla, Vijaykumar / Kinyua, Walter / Broaddus, Emily / Daniels, Molly S / Meric-Bernstam, Funda / Broaddus, Russell R

JCO precision oncology

2019 Volume 3

Abstract: Purpose: Smaller hotspot-based next-generation sequencing (NGS) panels have emerged to support standard of care therapy for patients with cancer. When standard treatments fail, it is unknown whether additional testing using an expanded panel of genes ... ...

Abstract	Purpose: Smaller hotspot-based next-generation sequencing (NGS) panels have emerged to support standard of care therapy for patients with cancer. When standard treatments fail, it is unknown whether additional testing using an expanded panel of genes provides any benefit. The purpose of this study was to determine if larger sequencing panels that capture additional actionable genes, coupled with decision support, translates into treatment with matched therapy after frontline therapy has failed. Patients and methods: A prospective protocol accrued 521 patients with a wide variety of refractory cancers. NGS testing using a 46- or 50-gene hotspot assay, then a 409-gene whole-exome assay, was sequentially performed in a Clinical Laboratory Improvement Amendments-certified clinical laboratory. A decision-support team annotated somatic alterations in clinically actionable genes for function and facilitated therapeutic matching. Survival and the impact of matched therapy use were determined by Kaplan-Meier estimate, log-rank test, and Cox proportional hazards regression. Results: The larger NGS panel identified at least one alteration in an actionable gene not previously identified in the smaller sequencing panel in 214 (41%) of 521 of enrolled patients. After the application of decision support, 41% of the alterations in actionable genes were considered to affect the function of the gene and were deemed actionable. Forty patients (40 of 214 [19%]) were subsequently treated with matched therapy. Treatment with matched therapy was associated with significantly improved overall survival compared with treatment with nonmatched therapy ( Conclusion: Combining decision support with larger NGS panels that incorporate genes beyond those recommended in current treatment guidelines helped to identify patients who were eligible for matched therapy while improving overall treatment selection and survival. This survival benefit was restricted to a small subset of patients.
Language	English
Publishing date	2019-03-08
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.18.00213
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Article ; Online: OCTANE: Oncology Clinical Trial Annotation Engine.

Zeng, Jia / Shufean, Md Abu / Khotskaya, Yekaterina / Yang, Dong / Kahle, Michael / Johnson, Amber / Holla, Vijaykumar / Sánchez, Nora / Mills Shaw, Kenna R / Bernstam, Elmer V / Meric-Bernstam, Funda

JCO clinical cancer informatics

2019 Volume 3, Page(s) 1–11

Abstract: Purpose: Many targeted therapies are currently available only via clinical trials. Therefore, routine precision oncology using biomarker-based assignment to drug depends on matching patients to clinical trials. A comprehensive and up-to-date trial ... ...

Abstract	Purpose: Many targeted therapies are currently available only via clinical trials. Therefore, routine precision oncology using biomarker-based assignment to drug depends on matching patients to clinical trials. A comprehensive and up-to-date trial database is necessary for optimal patient-trial matching. Methods: We describe processes for establishing and maintaining a clinical trial database, focusing on genomically informed trials. Furthermore, we present OCTANE (Oncology Clinical Trial Annotation Engine), an informatics framework supporting these processes in a scalable fashion. To illustrate how the framework can be applied at an institution, we describe how we implemented an instance of OCTANE at a large cancer center. OCTANE consists of three modules. The data aggregation module automates retrieval, aggregation, and update of trial information. The annotation module establishes the database schema, implements data integration necessary for automation, and provides an annotation interface. The update module monitors trial change logs, identifies critical change events, and alerts the annotators when manual intervention may be needed. Results: Using OCTANE, we annotated 5,439 oncology clinical trials (4,438 genomically informed trials) that collectively were associated with 1,453 drugs, 779 genes, and 252 cancer types. To date, we have used the database to screen 4,220 patients for trial eligibility. We compared the update module with expert review, and the module achieved 98.5% accuracy, 0% false-negative rate, and 2.3% false-positive rate. Conclusion: OCTANE is a general informatics framework that can be helpful for establishing and maintaining a comprehensive database necessary for automating patient-trial matching, which facilitates the successful delivery of personalized cancer care on a routine basis. Several OCTANE components are publically available and may be useful to other precision oncology programs.
MeSH term(s)	Clinical Trials as Topic ; Databases, Factual ; Decision Support Systems, Clinical ; Humans ; Medical Informatics/methods ; Medical Oncology/methods ; Neoplasms/diagnosis ; Neoplasms/etiology ; Neoplasms/therapy ; Precision Medicine/methods ; Search Engine ; Software ; Software Design ; Web Browser
Language	English
Publishing date	2019-08-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2473-4276
ISSN (online)	2473-4276
DOI	10.1200/CCI.18.00145
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Article ; Online: Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA.

Sánchez, Nora S / Kahle, Michael P / Bailey, Ann Marie / Wathoo, Chetna / Balaji, Kavitha / Demirhan, Mehmet Esat / Yang, Dong / Javle, Milind / Kaseb, Ahmed / Eng, Cathy / Subbiah, Vivek / Janku, Filip / Raymond, Victoria M / Lanman, Richard B / Mills Shaw, Kenna R / Meric-Bernstam, Funda

JCO precision oncology

2019 Volume 3

Abstract: Purpose: Cell-free DNA (cfDNA) next-generation sequencing is a noninvasive approach for genomic testing. We report the frequency of identifying alterations and their clinical actionability in patients with advanced/metastatic cancer.: Patients and ... ...

Abstract	Purpose: Cell-free DNA (cfDNA) next-generation sequencing is a noninvasive approach for genomic testing. We report the frequency of identifying alterations and their clinical actionability in patients with advanced/metastatic cancer. Patients and methods: Prospectively consented patients had cfDNA testing performed. Alterations were assessed for therapeutic implications. Results: We enrolled 575 patients with 37 tumor types. Of these patients, 438 (76.2%) had at least one alteration detected, and 205 (35.7%) had one or more alterations of high potential for clinical action. In diseases with 10 or more patients enrolled, 50% or more had at least one alteration deemed of high potential for clinical action. Trials were identified in 80% of patients (286 of 357) with any alteration and in 92% of patients (188 of 205) with one or more alterations of high potential for clinical action of whom 57.6% (118 of 205) had 6 or more months of follow-up available. Of these patients, 10% (12 of 118) had received genomically matched therapy through enrollment in clinical trials (n = 8), off-label drug use (n = 3), or standard of care (n = 1). Although 88.6% of all patients had a performance status of 0 or 1 upon enrollment, the primary reason for not acting on alterations was poor performance status at next treatment change (28.1%; 27 of 96). Conclusion: cfDNA testing represents a readily accessible method for genomic testing and allows for detection of genomic alterations in most patients with advanced disease. Utility may be higher in patients interested in investigational therapeutics with adequate performance status. Additional study is needed to determine whether utility is enhanced by testing earlier in the treatment course.
Language	English
Publishing date	2019-09-24
Publishing country	United States
Document type	Journal Article
ISSN	2473-4284
ISSN (online)	2473-4284
DOI	10.1200/PO.19.00017
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Article ; Online: Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer.

Pairawan, Seyed / Hess, Kenneth R / Janku, Filip / Sanchez, Nora S / Mills Shaw, Kenna R / Eng, Cathy / Damodaran, Senthilkumar / Javle, Milind / Kaseb, Ahmed O / Hong, David S / Subbiah, Vivek / Fu, Siqing / Fogelman, David R / Raymond, Victoria M / Lanman, Richard B / Meric-Bernstam, Funda

Clinical cancer research : an official journal of the American Association for Cancer Research

2019 Volume 26, Issue 8, Page(s) 1924–1931

Abstract: Purpose: Physicians are expected to assess prognosis both for patient counseling and for determining suitability for clinical trials. Increasingly, cell-free circulating tumor DNA (cfDNA) sequencing is being performed for clinical decision making. We ... ...

Abstract	Purpose: Physicians are expected to assess prognosis both for patient counseling and for determining suitability for clinical trials. Increasingly, cell-free circulating tumor DNA (cfDNA) sequencing is being performed for clinical decision making. We sought to determine whether variant allele frequency (VAF) in cfDNA is associated with prognosis. Experimental design: We performed a retrospective analysis of 298 patients with metastatic disease who underwent clinical comprehensive cfDNA analysis and assessed association between VAF and overall survival. Results: cfDNA mutations were detected in 240 patients (80.5%). Median overall survival (OS) was 11.5 months. cfDNA mutation detection and number of nonsynonymous mutations (NSM) significantly differed between tumor types, being lowest in appendiceal cancer and highest in colon cancer. Having more than one NSM detected was associated with significantly worse OS (HR = 2.3; Conclusions: Higher levels of cfDNA VAF and a higher number of NSMs were associated with worse OS in patients with metastatic disease. Further study is needed to determine optimal VAF thresholds for clinical decision making and the utility of cfDNA VAF as a prognostic marker in different tumor types.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Cell-Free Nucleic Acids/blood ; Cell-Free Nucleic Acids/genetics ; Child ; Female ; Gene Frequency ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Middle Aged ; Mutation ; Neoplasm Metastasis ; Neoplasms/blood ; Neoplasms/genetics ; Neoplasms/mortality ; Neoplasms/pathology ; Prognosis ; Retrospective Studies ; Survival Rate ; Young Adult
Chemical Substances	Biomarkers, Tumor ; Cell-Free Nucleic Acids
Language	English
Publishing date	2019-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-19-0306
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Article ; Online: Characteristics of percutaneous core biopsies adequate for next generation genomic sequencing.

Sabir, Sharjeel H / Krishnamurthy, Savitri / Gupta, Sanjay / Mills, Gordon B / Wei, Wei / Cortes, Andrea C / Mills Shaw, Kenna R / Luthra, Rajyalakshmi / Wallace, Michael J

PloS one

2017 Volume 12, Issue 12, Page(s) e0189651

Abstract: Purpose: Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel.: Materials and methods: All patients undergoing percutaneous core biopsies in interventional radiology (IR) ... ...

Abstract	Purpose: Determine the characteristics of percutaneous core biopsies that are adequate for a next generation sequencing (NGS) genomic panel. Materials and methods: All patients undergoing percutaneous core biopsies in interventional radiology (IR) with samples evaluated for a 46-gene NGS panel during 1-year were included in this retrospective study. Patient and procedure variables were collected. An imaging-based likelihood of adequacy score incorporating targeting and sampling factors was assigned to each biopsied lesion. Univariate and multivariate logistic regression was performed. Results: 153 patients were included (58.2% female, average age 59.5 years). The most common malignancy was lung cancer (40.5%), most common biopsied site was lung (36%), and average size of biopsied lesions was 3.8 cm (+/- 2.7). Adequacy for NGS was 69.9%. Univariate analysis showed higher likelihood of adequacy score (p = 0.004), primary malignancy type (p = 0.03), and absence of prior systemic therapy (p = 0.018) were associated with adequacy for NGS. Multivariate analysis showed higher adequacy for lesions with likelihood of adequacy scored 3 (high) versus lesions scored 1 (low) (OR, 7.82; p = 0.002). Melanoma lesions had higher adequacy for NGS versus breast cancer lesions (OR 9.5; p = 0.01). Absence of prior systemic therapy (OR, 6.1; p = 0.02) and systemic therapy </ = 3 months (OR 3.24; p = 0.01) compared to systemic therapy >3 months before biopsy yielded greater adequacy for NGS. Lesions <3 cm had greater adequacy for NGS than larger lesions (OR 2.72, p = 0.02). Conclusion: As targeted therapy becomes standard for more cancers, percutaneous biopsy specimens adequate for NGS genomic testing will be needed. An imaging-based likelihood of adequacy score assigned by IR physicians and other pre-procedure variables can help predict the likelihood of biopsy adequacy for NGS.
MeSH term(s)	Biopsy, Large-Core Needle/methods ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung Neoplasms/diagnostic imaging ; Lung Neoplasms/pathology ; Male ; Middle Aged ; Multimodal Imaging
Language	English
Publishing date	2017-12-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0189651
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Article ; Online: Targeted next generation sequencing of well-differentiated/dedifferentiated liposarcoma reveals novel gene amplifications and mutations.

Somaiah, Neeta / Beird, Hannah C / Barbo, Andrea / Song, Juhee / Mills Shaw, Kenna R / Wang, Wei-Lien / Eterovic, Karina / Chen, Ken / Lazar, Alexander / Conley, Anthony P / Ravi, Vinod / Hwu, Patrick / Futreal, Andrew / Simon, George / Meric-Bernstam, Funda / Hong, David

Oncotarget

2018 Volume 9, Issue 28, Page(s) 19891–19899

Abstract: Well-differentiated/dedifferentiated liposarcoma is a common soft tissue sarcoma with approximately 1500 new cases per year. Surgery is the mainstay of treatment but recurrences are frequent and systemic options are limited. 'Tumor genotyping' is ... ...

Abstract	Well-differentiated/dedifferentiated liposarcoma is a common soft tissue sarcoma with approximately 1500 new cases per year. Surgery is the mainstay of treatment but recurrences are frequent and systemic options are limited. 'Tumor genotyping' is becoming more common in clinical practice as it offers the hope of personalized targeted therapy. We wanted to evaluate the results and the clinical utility of available next-generation sequencing panels in WD/DD liposarcoma. Patients who had their tumor sequenced by either FoundationOne (
Language	English
Publishing date	2018-04-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.24924
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Article ; Online: A Deep Learning Framework for Predicting Response to Therapy in Cancer.

Sakellaropoulos, Theodore / Vougas, Konstantinos / Narang, Sonali / Koinis, Filippos / Kotsinas, Athanassios / Polyzos, Alexander / Moss, Tyler J / Piha-Paul, Sarina / Zhou, Hua / Kardala, Eleni / Damianidou, Eleni / Alexopoulos, Leonidas G / Aifantis, Iannis / Townsend, Paul A / Panayiotidis, Mihalis I / Sfikakis, Petros / Bartek, Jiri / Fitzgerald, Rebecca C / Thanos, Dimitris /

Mills Shaw, Kenna R / Petty, Russell / Tsirigos, Aristotelis / Gorgoulis, Vassilis G

Cell reports

2019 Volume 29, Issue 11, Page(s) 3367–3373.e4

Abstract: A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed ...

Abstract	A major challenge in cancer treatment is predicting clinical response to anti-cancer drugs on a personalized basis. Using a pharmacogenomics database of 1,001 cancer cell lines, we trained deep neural networks for prediction of drug response and assessed their performance on multiple clinical cohorts. We demonstrate that deep neural networks outperform the current state in machine learning frameworks. We provide a proof of concept for the use of deep neural network-based frameworks to aid precision oncology strategies.
MeSH term(s)	Cell Line, Tumor ; Deep Learning ; Drug Resistance, Neoplasm ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Precision Medicine/methods ; Survival Analysis
Language	English
Publishing date	2019-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2019.11.017
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