Thank you, next: The impact of next-generation sequencing in clinical decision making.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e13136-e13136
Author(s):  
William Davis ◽  
Gabriel Makar ◽  
Greg J. Kubicek
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Decision Making ◽  
Poor Response ◽  
Clinical Decision ◽  
Next Generation ◽  
Duration Of Treatment ◽  
Tissue Samples ◽  
Off Label ◽  
The Impact ◽  
Generation Sequencing

e13136 Background: Next Generation Sequencing (NGS) is increasingly used to identify actionable mutations for oncology treatment. We examined the results of NGS at our institution. Methods: We retrospectively reviewed the medical charts of 305 consecutive patients who had genomic testing performed on tumor samples from March 2014 to April 2017. Next Generation Sequencing was performed by Foundation One testing. Results: Of the 305 tissue samples sent to Foundation One, 189 reports were potentially usable. Reports were unusable due to an insufficient quantity of tissue (43), inadequate follow-up (32), cessation of oncologic care due to transferring to hospice or expiring (32), or a report not being generated due to the order being cancelled (4) or undocumented reasons (5). Of the 189 usable reports, 76 (40.21%) demonstrated an aberration targetable by on-label therapies, 126 (66.67%) via off-label therapies (66 of these had no available on-label treatment), and 170 (89.94%) revealed actionable aberrations via all potential avenues, including clinical trials. 19 (6.2%) yielded a change in management, 6 of these changes were utilizing on-label therapies, 6 were via off-label therapies, 3 were via enrollment in a clinical trial, and 4 involved discontinuing a medication with a predicted poor response. For the 6 patients with off-label use, median duration of treatment was 46 days and discontinued secondary to death (3 patients) or progression (3 patients). Conclusions: Only a minority of NGS assay results (6.2% percent of all tests ordered and 10% of useable tests) resulted in a management change. A small minority (6 patients, 1.9%) were started on off-label therapy based on NSG results and overall had poor responses to off-label treatment. While in theory NGS may improve oncology outcome, the results of our initial 305 patients who had NGS was poor.

scholarly journals Next-Generation Sequencing in 305 Consecutive Patients: Clinical Outcomes and Management Changes

2019 ◽  
Vol 15 (12) ◽  
pp. e1028-e1034 ◽  
Author(s):  
William Davis ◽  
Gabriel Makar ◽  
Pallav Mehta ◽  
Gord G. Zhu ◽  
Robert Somer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Poor Response ◽  
Oncologic Outcomes ◽  
Next Generation ◽  
Duration Of Treatment ◽  
Tissue Samples ◽  
Off Label ◽  
Oncology Treatment ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

PURPOSE: Next-generation sequencing (NGS) is increasingly used to identify actionable mutations for oncology treatment. We examined the results and use of NGS assays at our institution. PATIENTS AND METHODS: We retrospectively reviewed the medical records of 305 consecutive patients who had NGS testing of tumor samples from March 2014 to April 2017. NGS was performed by FoundationOne. RESULTS: Of the 305 tissue samples sent to FoundationOne, 189 reports were potentially usable. Of these reports, 76 (40.21%) demonstrated an aberration targetable by on-label therapies and 126 (66.67%) by off-label therapies, and 170 (89.94%) revealed actionable aberrations via all potential avenues, including clinical trials; 21 of these 189 potentially usable reports (11.1%) yielded a change in management, including use of on-label therapies (n = 7), use of off-label therapies (n = 6), enrollment in a clinical trial (n = 6), and discontinuation of a medication with a predicted poor response (n = 3; one report was used twice). For the six patients with off-label use, median duration of treatment was 46 days and discontinued after death (n = 3) or progression (n = 3). CONCLUSION: Only a minority of NGS assay results (6.9% percent of all tests ordered and 11.1% of useable tests) resulted in a management change. A small minority of patients started off-label therapy on the basis of NSG assay results and overall had poor responses to off-label treatment. Although in theory NGS assays may improve oncologic outcomes, the results of our initial 305 patients showed low clinical utility.

scholarly journals Impact on Clinical Decision Making of Next-Generation Sequencing in Pediatric Epilepsy in a Tertiary Epilepsy Referral Center

2019 ◽  
Vol 51 (1) ◽  
pp. 61-69 ◽  
Author(s):  
Hannes Hoelz ◽  
Christian Herdl ◽  
Lucia Gerstl ◽  
Moritz Tacke ◽  
Katharina Vill ◽  
...  
Keyword(s):  
Decision Making ◽  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Clinical Management ◽  
Clinical Decision Making ◽  
Clinical Decision ◽  
Pediatric Epilepsy ◽  
Next Generation ◽  
The Impact ◽  
Generation Sequencing

Background. Next-generation sequencing (NGS) describes new powerful techniques of nucleic acid analysis, which allow not only disease gene identification diagnostics but also applications for transcriptome/methylation analysis and meta-genomics. NGS helps identify many monogenic epilepsy syndromes. Pediatric epilepsy patients can be tested using NGS epilepsy panels to diagnose them, thereby influencing treatment choices. The primary objective of this study was to evaluate the impact of genetic testing on clinical decision making in pediatric epilepsy patients. Methods. We completed a single-center retrospective cohort study of 91 patients (43 male) aged 19 years or less undergoing NGS with epilepsy panels differing in size ranging from 5 to 434 genes from October 2013 to September 2017. Results. During a mean time of 3.6 years between symptom onset and genetic testing, subjects most frequently showed epileptic encephalopathy (40%), focal epilepsy (33%), and generalized epilepsy (18%). In 16 patients (18% of the study population), “pathogenic” or “likely pathogenic” results according to ACMG criteria were found. Ten of the 16 patients (63%) experienced changes in clinical management regarding their medication and avoidance of further diagnostic evaluation, that is, presurgical evaluation. Conclusion. NGS epilepsy panels contribute to the diagnosis of pediatric epilepsy patients and may change their clinical management with regard to both preventing unnecessary and potentially harmful diagnostic procedures and management. Thus, the present data support the early implementation in order to adopt clinical management in selected cases and prevent further invasive investigations. Given the relatively small sample size and heterogeneous panels a larger prospective study with more homogeneous panels would be helpful to further determine the impact of NGS on clinical decision making.

Clinical benefit of next generation sequencing in soft tissue and bone sarcoma: Rush University Medical Center’s experience.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e22552-e22552
Author(s):  
Mia C. Weiss ◽  
Alan Blank ◽  
Steven Gitelis ◽  
Mary J. Fidler ◽  
Marta Batus
Keyword(s):  
Overall Survival ◽  
Next Generation Sequencing ◽  
Soft Tissue ◽  
Clinical Decision Making ◽  
Soft Tissue Sarcomas ◽  
Bone Sarcoma ◽  
Next Generation ◽  
Undifferentiated Sarcoma ◽  
The Impact ◽  
Generation Sequencing

e22552 Background: The overall survival for metastatic sarcoma has remained at only 18-20%. In the era of next generation sequencing (NGS), much research is ongoing on identifying optimal treatments. The MULTISARC trial aims to determine if NGS can lead to improved overall survival by randomizing patients with metastatic STS to receive NGS (followed by possible NGS-guided therapy) or not. We present our center’s experience with NGS in sarcomas patients. Methods: Patients with soft tissue and bone sarcomas at Rush that had the Foundation Medicine assay sent on tumor samples between August 2017 and August 2018 were analyzed retrospectively. The impact of NGS on clinical decision making was determined based on patients being prescribed off-label FDA-approved therapy targeting identified mutation. Results: Thirty-four patients with bone/soft tissue sarcomas that had NGS sent on specimens were identified. Median age at diagnosis: 43 (18-78 years); 18 males, 16 females. Histologic subtypes: synovial sarcoma, myxofibrosarcoma, leiomyosarcoma, chondrosarcoma, sclerosing epitheloid fibrosarcoma, PEcoma, pleomorphic undifferentiated sarcoma, MPNST, liposarcoma- well and de-differentiated, angiosarcoma, osteosarcoma. 16/34 patients had targetable mutations with approved therapies in tumor types other than sarcoma. Four of these patients had therapy changed based on NGS results, 1 patient with metastatic chondrosarcoma (PTEN mutation, everolimus added), 1 patient with metastatic liposarcoma (CDK4 mutation, palbociclib added), 1 patient with metastatic osteosarcoma (CCD1/CDK4 and a PDGFRA mutation for which palbociclib followed by imatinib was added), and 1 patient with metastatic pleomorphic undifferentiated sarcoma (CDK4 mutation, palbociclib added). Targetable mutations for which clinical trials are available were identified in 25/34 (73%) of the cases. Conclusions: NGS was readily able to identify actionable mutations in close to 50% of patients with clinical trial opportunities in close to 75%. Four patients had therapy changed as a result of NGS testing. Although our study size is small, our data show potential for the use of genomic profiling to identify actionable targets, tailor therapy, and hopefully improve outcomes. [Table: see text]

scholarly journals Next Generation Sequencing (NGS) and patient pathways: What is the impact on clinical decision?

2018 ◽  
Vol 29 ◽  
pp. vi14-vi15
Author(s):  
S. Coquerelle ◽  
M. Darlington ◽  
M. Michel ◽  
M. Durand ◽  
J. Gutton ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Decision ◽  
Next Generation ◽  
Patient Pathways ◽  
Next Generation Sequencing Ngs ◽  
The Impact ◽  
Generation Sequencing

Next-generation sequencing-based BRCA testing on cytological specimens from ovarian cancer ascites reveals high concordance with tumour tissue analysis

2019 ◽  
Vol 73 (3) ◽  
pp. 168-171 ◽  
Author(s):  
Caterina Fumagalli ◽  
Alessandra Rappa ◽  
Chiara Casadio ◽  
Ilaria Betella ◽  
Nicoletta Colombo ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Next Generation Sequencing ◽  
Clinical Decision Making ◽  
Parp Inhibitor ◽  
Clinical Decision ◽  
Tumour Tissue ◽  
Next Generation ◽  
High Concordance ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

BackgroundWith the approval of the poly (ADP-ribose) polymerase (PARP) inhibitor olaparib for newly diagnosed, breast cancer gene (BRCA)1/2 mutated, ovarian cancer women, the assessment of BRCA1/2 tumour status will be shortly required at the time of diagnosis.AimTo investigate the feasibility of next-generation sequencing (NGS)-based BRCA tumour test on cytological specimens from ovarian cancer ascites.MethodsWe evaluated the BRCA1/2 status on neoplastic ascites and corresponding tumour tissue of 11 patients with ovarian cancer, using the NGS ‘Oncomine BRCA Research Assay’.ResultsThe NGS-based BRCA test on cytological samples had a success rate of 100%, with 11 of 11 concordant BRCA1/2 results between ascites and tumour tissues analyses, including two wild type samples and nine cases harbouring somatic or germline variants.ConclusionBRCA test may be performed on ovarian cancer ascites, reproducing BRCA1/2 tumour status and representing a useful tool for clinical decision-making.

scholarly journals Case Report: Fascioliasis Hepatica Precisely Diagnosed by Metagenomic Next-Generation Sequencing and Treated With Albendazole

2021 ◽  
Vol 8 ◽  
Author(s):  
Yaling Zhang ◽  
Huan Xu ◽  
Yi Liu ◽  
Juan Kang ◽  
Hairu Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Decision Making ◽  
Fasciola Hepatica ◽  
Malignant Tumors ◽  
Clinical Manifestations ◽  
Clinical Decision ◽  
The Body ◽  
Therapeutic Effects ◽  
Next Generation ◽  
Generation Sequencing

The clinical manifestations of fascioliasis hepatica in humans are unspecific. Traditional diagnosis relies on evidence of live parasites or eggs in the bile or feces. However, due to similar imaging manifestations, they are often misdiagnosed as malignant tumors. Here, we report a case of a 43-year-old woman with fever and space-occupying liver disease. Liver biopsy, parasite-specific antibody screening, and stool testing did not find any pathogens. Therefore, metagenomic next-generation sequencing (mNGS) and routine microbiological examinations were performed. Finally, Fasciola hepatica was only identified by mNGS. The body temperature of the patient and the eosinophil count remained normal, and the space-occupying liver lesions were significantly absorbed after more than 7 months of treatment with albendazole. The details of this case highlight the timely use of mNGS to identify parasites and judge therapeutic effects after treatment, providing important help for clinical decision-making.

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