scholarly journals Molecular Profiling of Malignant Pleural Effusions with Next Generation Sequencing (NGS): Evidence that Supports Its Role in Cancer Management

2020 ◽  
Vol 10 (4) ◽  
pp. 206
Author(s):  
Georgia Ι. Grigoriadou ◽  
Stepan M. Esagian ◽  
Han Suk Ryu ◽  
Ilias P. Nikas
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Advanced Cancer ◽  
Liquid Biopsy ◽  
Molecular Profiling ◽  
Pleural Effusions ◽  
Advanced Cancer Patients ◽  
Cancer Management ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Malignant pleural effusions (MPEs) often develop in advanced cancer patients and confer significant morbidity and mortality. In this review, we evaluated whether molecular profiling of MPEs with next generation sequencing (NGS) could have a role in cancer management, focusing on lung cancer. We reviewed and compared the diagnostic performance of pleural fluid liquid biopsy with other types of samples. When applied in MPEs, NGS may have comparable performance with corresponding tissue biopsies, yield higher DNA amount, and detect more genetic aberrations than blood-derived liquid biopsies. NGS in MPEs may also be preferable to plasma liquid biopsy in advanced cancer patients with a MPE and a paucicellular or difficult to obtain tissue/fine-needle aspiration biopsy. Of interest, post-centrifuge supernatant NGS may exhibit superior results compared to cell pellet, cell block or other materials. NGS in MPEs can also guide clinicians in tailoring established therapies and identifying therapy resistance. Evidence is still premature regarding the role of NGS in MPEs from patients with cancers other than lung. We concluded that MPE processing could provide useful prognostic and theranostic information, besides its diagnostic role.

Next-generation sequencing ordering trends in the cancer trajectory.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 10104-10104
Author(s):  
Joseph Ma ◽  
Chelsea Hagmann ◽  
Alexandra Dullea ◽  
Winnie S Wang ◽  
Warren Yau ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Advanced Cancer ◽  
Metastatic Disease ◽  
Primary Objective ◽  
Next Generation ◽  
Advanced Cancer Patients ◽  
The Difference ◽  
Generation Sequencing ◽  
Tumor Profiling

10104 Background: Next-generation sequencing (NGS) molecular tumor profiling is increasingly being ordered for advanced cancer patients to evaluate non-traditional therapeutic options. The timing of when NGS is ordered relative to date of diagnosis, palliative care (PC) consultation, and death remains unknown. The primary objective of this study was to examine NGS ordering patterns among cancer patients. Methods: This was a single center, retrospective data analysis in cancer patients at our institution between January 2011 and February 2016. Cancer patients ≥16 yrs of age were identified from a tumor registry and matched to an existing NGS tumor profiling database. Additional data were collected from an electronic medical record and compiled into a single database. Differences in the date of when NGS was ordered compared to date of diagnosis, PC consultation, and/or date of death were determined. A Mann-Whitney rank sum test examined differences in patients where NGS was ordered relative to the date of PC consultation. Logistic regression examined variables possibly associated with PC consultation. Results: Analysis included 1596 (807 women) cancer patients. Mean±SD age was 55.5±15.2 years, 30.8% (n = 492) of patients had metastatic disease, with breast and lung the most common cancers. The difference between date of cancer diagnosis and date of NGS order was 1053.6±1568.5 days (n = 1546). The difference between date of NGS order and date of death was 221.2.4±186.6 days. Two-hundred and fifty-one patients (15.7%) received a PC consultation, of which 82 patients had a NGS order before the PC consultation and 169 patients had a NGS order after the PC consultation. The mean difference in number of days between a NGS order before versus after a PC consultation was 147.3±216.8 vs. 179.8±169.7 days (p < 0.005). Four-hundred and sixty-six (29%) patients have died with 121 receiving a PC consultation. Metastatic disease, but not age and sex, was associated with PC completion (OR 1.7; 95%CI 1.27-2.21). Conclusions: NGS was frequently ordered near the time of death. PC consultations were completed in a minority of patients. NGS ordering in advanced cancer patients may serve as a trigger for PC consultation.

Clinical utility of profiling somatic alterations in Indian cancer patients using a multi-gene next generation sequencing (NGS) test.

2015 ◽  
Vol 33 (15_suppl) ◽  
pp. e22127-e22127
Author(s):  
Urvashi Bahadur ◽  
Aarthi Ravichandran ◽  
Shataparna Banerjee ◽  
Shreya Paliwal ◽  
Roopa Rayanur Sripathi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Clinical Utility ◽  
Next Generation ◽  
Somatic Alterations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Assessing real-world outcomes in precision oncology by linking clinical genomic testing to electronic medical records.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e18091-e18091
Author(s):  
Debajyoti Datta ◽  
Theodore Goldstein ◽  
Atul Butte
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Relational Database ◽  
Real World ◽  
Molecular Profiling ◽  
Genomic Testing ◽  
Precision Oncology ◽  
Clinical Sequencing ◽  
Clinical Genomic ◽  
Generation Sequencing

e18091 Background: With an ever-widening array of targeted therapies for cancer patients, clinical genomic testing has expanded rapidly in recent years. Tumor molecular profiling by next-generation sequencing is now considered a cornerstone of precision oncology, with the potential to offer patients with advanced cancers new therapeutic options. However, the overall impact of this testing remains unclear, and evidence demonstrating improvement in patient outcomes is lacking. The objective of this study is to assess the utility of clinical sequencing on the management of cancer patients. Methods: We present the development of a database that combines results of tumor mutation profiling using various next-generation sequencing panels (both external commercial tests and our institution’s internal sequencing panel), with a variety of data points from a de-identified representation of our institution’s electronic medical record (EMR). Assembling this data from different sources into a common relational database permits efficient retrospective analysis of real-world outcomes in patients with advanced cancers. Results: This study included over 3000 patients seen at UCSF Comprehensive Cancer Center since 2013. With this linked data set we analyzed the rate at which tumor molecular profiling affected clinical decision making, identified barriers to the efficient use of testing, and assessed for disparities in utilization. For example, by measuring patient survival relative to the clinical intervention of genomic testing for the subset of patients with a date of death recorded in our EMR, we found that a small fraction of patients died before results returned and any action could be taken, especially in cases of pancreatic cancer. Conclusions: We demonstrate that a common relational database combining clinical sequencing results with real-world EMR data provides insights into the optimal clinical use of tumor molecular profiling. This provides new opportunities for advancing precision oncology initiatives and improving patient care, such as identifying which cancer patients should get genomic testing and efficiently matching patients to clinical trials.

scholarly journals Whole exome sequencing for determination of tumor mutation load in liquid biopsy from advanced cancer patients

PLoS ONE ◽  
2017 ◽  
Vol 12 (11) ◽  
pp. e0188174 ◽  
Author(s):  
Florence Koeppel ◽  
Steven Blanchard ◽  
Cécile Jovelet ◽  
Bérengère Genin ◽  
Charles Marcaillou ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Cancer Patients ◽  
Whole Exome Sequencing ◽  
Advanced Cancer ◽  
Liquid Biopsy ◽  
Mutation Load ◽  
Advanced Cancer Patients ◽  
Whole Exome

scholarly journals Copy number alterations in cancer: detection and precision medicine

2021 ◽  
Vol 41 ◽  
pp. 02005
Author(s):  
Arief Gusnanto
Keyword(s):  
Next Generation Sequencing ◽  
Precision Medicine ◽  
Cancer Patients ◽  
Cancer Detection ◽  
Copy Number ◽  
Copy Number Alterations ◽  
Genomic Alterations ◽  
Genomic Markers ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Copy number alterations (CNAs) are genomic alterations where some regions exhibit more or less copy number than the normal two copies. In this talk, I will describe two ideas: (1) how CNAs are estimated from data generated by next generation sequencing (NGS) and what steps are required to make the data interpretable, (2) how the CNA can be utilised for precision medicine in terms of prediction of tumour subtypes and prediction of cancer patients’ survival. If time permits, I will also discuss how to estimate genomic markers from CNA profile across cancer patients.

scholarly journals Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group

2020 ◽  
Vol 66 (9) ◽  
pp. 1156-1166 ◽  
Author(s):  
James H Godsey ◽  
Angela Silvestro ◽  
J Carl Barrett ◽  
Kelli Bramlett ◽  
Darya Chudova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
Working Group ◽  
Circulating Tumor Dna ◽  
Next Generation ◽  
Analytical Validation ◽  
Consensus Recommendation ◽  
Next Generation Sequencing Ngs ◽  
Development And Validation ◽  
Generation Sequencing

Abstract Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC’s Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors’ presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

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