scholarly journals High Sensitivity and Specificity of Chromosomal Pertubations in Human Invasive Breast Cancer (BrCa) Associated with Circulating Nucleic Acids (CNA) Using Concatemers of Short Sequence DNA Tags in Next Generation Sequencing (NGS)

2011 ◽  
Vol 25 (S1) ◽  
Author(s):  
William Marvin Mitchell ◽  
Julia Beck ◽  
Howard B Urnovitz ◽  
Ekkehard Schuetz
Keyword(s):  
Breast Cancer ◽  
Next Generation Sequencing ◽  
Nucleic Acids ◽  
Sensitivity And Specificity ◽  
Invasive Breast Cancer ◽  
High Sensitivity ◽  
Short Sequence ◽  
Circulating Nucleic Acids ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

scholarly journals k-mer-Based Metagenomics Tools Provide a Fast and Sensitive Approach for the Detection of Viral Contaminants in Biopharmaceutical and Vaccine Manufacturing Applications Using Next-Generation Sequencing

mSphere ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Madolyn L. MacDonald ◽  
Shawn W. Polson ◽  
Kelvin H. Lee
Keyword(s):  
Next Generation Sequencing ◽  
Sensitivity And Specificity ◽  
Data Sets ◽  
Next Generation ◽  
Viral Detection ◽  
Read Alignment ◽  
Ensure Patient Safety ◽  
Hela Cell Lines ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

ABSTRACT Adventitious agent detection during the production of vaccines and biotechnology-based medicines is of critical importance to ensure the final product is free from any possible viral contamination. Increasing the speed and accuracy of viral detection is beneficial as a means to accelerate development timelines and to ensure patient safety. Here, several rapid viral metagenomics approaches were tested on simulated next-generation sequencing (NGS) data sets and existing data sets from virus spike-in studies done in CHO-K1 and HeLa cell lines. It was observed that these rapid methods had comparable sensitivity to full-read alignment methods used for NGS viral detection for these data sets, but their specificity could be improved. A method that first filters host reads using KrakenUniq and then selects the virus classification tool based on the number of remaining reads is suggested as the preferred approach among those tested to detect nonlatent and nonendogenous viruses. Such an approach shows reasonable sensitivity and specificity for the data sets examined and requires less time and memory as full-read alignment methods. IMPORTANCE Next-generation sequencing (NGS) has been proposed as a complementary method to detect adventitious viruses in the production of biotherapeutics and vaccines to current in vivo and in vitro methods. Before NGS can be established in industry as a main viral detection technology, further investigation into the various aspects of bioinformatics analyses required to identify and classify viral NGS reads is needed. In this study, the ability of rapid metagenomics tools to detect viruses in biopharmaceutical relevant samples is tested and compared to recommend an efficient approach. The results showed that KrakenUniq can quickly and accurately filter host sequences and classify viral reads and had comparable sensitivity and specificity to slower full read alignment approaches, such as BLASTn, for the data sets examined.

Concordance of genomic alterations by next generation sequencing (NGS) in tumor tissue vs. cell-free DNA in advanced breast cancer.

2016 ◽  
Vol 34 (15_suppl) ◽  
pp. 11528-11528
Author(s):  
Andrew Davis ◽  
Young Kwang Chae ◽  
Sarika Jain ◽  
Cesar Augusto Santa-Maria ◽  
Lisa E. Flaum ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Next Generation Sequencing ◽  
Advanced Breast Cancer ◽  
Tumor Tissue ◽  
Next Generation ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Free Dna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) for personalized therapy in metastatic breast cancer: Selection of therapy and outcomes.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e23166-e23166
Author(s):  
Jessica Ribeiro Gomes ◽  
Raphael Brandao Moreira ◽  
Matheus Bongers Alessandretti ◽  
Marcelo Rocha De Sousa Cruz
Keyword(s):  
Breast Cancer ◽  
Metastatic Breast Cancer ◽  
Next Generation Sequencing ◽  
Clinical Benefit ◽  
Metastatic Breast ◽  
Personalized Therapy ◽  
Genomic Alterations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

e23166 Background: Treatment for metastatic breast cancer (MBC) has been driven by hormone receptors, HER2 expressions or their absence. Resistance to therapy and progressive disease will occur and empirical chemotherapy lines usually are the next steps. We aim to analyze the role of next-generation sequencing (NGS) for a personalized therapy in metastatic breast cancer and its potential clinical benefit. Methods: We included patients diagnosed with MBC treated at Centro Oncologico Antonio Ermirio de Moraes – Brazil from April 2013 to December 2016. All patients had metastasis accessible for biopsy. The tumor tissue was stored in paraffin and then analyzed by NGS-based assay that identifies genomic alterations within 236 genes. Results: 19 patients with MBC were evaluated (10 triple-negative; 4 HER2-positive; 5 hormonal receptor positive/HER2-negative). The most frequent and relevant genomic alterations identified by NGS assay were in the following genes: 13 TP53 (68.4%); 4 ERBB2 (21%); 4 PTEN (21%); 4 FGFR (21%); 3 PIK3CA (15.8%); 2 BRCA (10.5%); 2 ATM (10.5%); 2 AKT (10.5%); 2 MYC (10.5%); 1 CCND1 (5.3%); and 1 KRAS (5.3%). The NGS assay was able to suggest further therapy in 16/19 patients (84%). The suggested therapies would not be an empirical option according to the cancer’s subtype in 12/16 patients (75%). Therapy could be personalized in nine patients, across multiple lines of therapies (median of 5th line, with a range of 1-14). Median PFS was 6 months, and 8/9 patients (90%) achieved an objective response with the treatment indicated by NGS. Therefore, the assay provided clinical benefit in 42% of patients. Conclusions: NGS panel identified potentially actionable alterations in the majority of patients with MBC (84%). The overall clinical benefit with use of NGS-based assay was 42%. Further studies are necessary to better evaluate the role of NGS for a personalized therapy in MBC.

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