scholarly journals Next-generation Sequencing-based Test for Resectable Colorectal Cancer in Real-world Clinical Practice

2021 ◽  
Author(s):  
Masayo Ogiri ◽  
Ryo Seishima ◽  
Kohei Nakamura ◽  
Eriko Aimono ◽  
Shimpei Matsui ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Real World ◽  
Gene Panel ◽  
Stage I ◽  
Next Generation ◽  
Panel Testing ◽  
Gene Panel Testing ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Purpose: This study aimed to evaluate the significance of Next-generation sequencing (NGS)-based gene panel testing in resectable colorectal cancers (CRC)s by analyzing real-world data collected prospectively from patients. Methods: Patients with CRC who underwent surgery from July 2018 to February 2020 at our institution were included, and correlations between various NGS data and clinicopathological findings were evaluated. Results: Overall, 107 patients were included in this study. The tumor stage was I in 28 cases (26.2%), II in 40 cases (37.4%), III in 32 cases (29.9%), and IV in 7 cases (6.5%). Actionable gene alterations were found in 97.2% of the cases. Co-alteration analysis suggested that either TP53- or APC-related alterations were more frequently found in early-stage tumors (stage I). The copy number alteration count was significantly lower in right side colon tumors than in tumors in other locations (P < 0.05). Homologous recombination deficiency (HRD) was more often identified in stage IV tumors than in stage I or II tumors (P < 0.05). Moreover, high HRD status was suggested to be useful for identifying high-risk stage II tumors (P < 0.05). Conclusion: In this study, real-world NGS data represented the biological features of CRCs. HRD was identified as a useful result of gene panel testing with novel utility in clinical practice.

Outcomes of disease-specific next-generation sequencing gene panel testing in adolescents and young adults with colorectal cancer

2019 ◽  
Vol 235-236 ◽  
pp. 77-83
Author(s):  
Maureen E. Mork ◽  
Andrea Rodriguez ◽  
Sarah A. Bannon ◽  
Patrick M. Lynch ◽  
Miguel A. Rodriguez-Bigas ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Young Adults ◽  
Next Generation Sequencing ◽  
Gene Panel ◽  
Adolescents And Young Adults ◽  
Next Generation ◽  
Panel Testing ◽  
Gene Panel Testing ◽  
Generation Sequencing ◽  
Disease Specific

Utility of multi-gene panel testing with next generation sequencing in women with endometrial cancer.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 5588-5588
Author(s):  
Jing-Yi Chern ◽  
Nigel Madden ◽  
Jessica Lee ◽  
Deanna Gerber ◽  
Anna Cantor ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Family History ◽  
Gynecologic Cancer ◽  
Gene Mutations ◽  
Gene Panel ◽  
Next Generation ◽  
Mmr Genes ◽  
Panel Testing ◽  
Gene Panel Testing ◽  
Generation Sequencing

5588 Background: Lynch syndrome (LS) accounts for 2-6% of all endometrial cancers (EC), and women with a germline mutation in the mismatch repair (MMR) genes ( MLH1, MSH2, MSH6, and PMS2) have an average lifetime risk of EC of 40%. As with breast and ovarian cancer syndromes, there are likely other genes implicated in the development of EC outside of the MMR genes. Multi-gene panel testing (MGPT) with next generation sequencing (NGS) allows for simultaneous analysis of numerous genes.We sought to evaluate the characteristics and incidence of gene mutations in women with newly diagnosed EC. Methods: We conducted a review of EC patients diagnosed from 6/2013 to 12/2016 who had MGPT at our institution. Demographics, family history, genetic testing results, and tumor characteristics were collected and analyzed using χ2 tests. Results: Of the 129 patients who had MGPT, 13 (10%) had a mutation and only 5 (38%) were in patients < 50 years old. The median age of EC diagnosis is 55 (31-100) years and median BMI = 27.5 (21-59). Majority were stage 1, 76 (59%) and grade 1, 50 (39%). Patients with additional primary cancers, breast or colon were not more likely to have a mutation. However, patients with a family history of gynecologic cancer were more likely to have a mutation identified, 10 (77%) mutation vs no mutation 34 (29%), p = 0.003. Among all patients tested, 8 (6%) had a mutation in LS genes, and 6 (5%) had mutations in other genes ( BRCA1, BRCA2, RAD51C, MUTYH, CHEK2); 1 (0.8%) had both MSH2 and CHEK2 mutation. Three patients had prior testing for breast cancer; 2 were found to have a BRCA1/ 2 mutation and the other was on Tamoxifen and BRCA negative. IHC was performed on 7 of 13 patients, and 5 (71%) had a loss of MMR protein expression. Variants of uncertain significance were noted in 35/129 (27%) of patients tested. Conclusions: Majority of EC patients with a mutation detected with NGS were > age 50. We identified additional new mutations in non-LS genes including, CHEK2, RAD51C, and MUYTH with MGPT. These accounted for 29% of the mutations and would have not been not detected using classic LS gene testing. These genes are implicated in breast, ovary or colon cancer. MGPT testing is feasible and useful in identifying additional actionable gene mutations.

Next‐generation sequencing through multi‐gene panel testing for diagnosis of hereditary ichthyosis in Chinese

2020 ◽  
Vol 97 (5) ◽  
pp. 770-778 ◽  
Author(s):  
Ruhong Cheng ◽  
Jianying Liang ◽  
Yue Li ◽  
Jia Zhang ◽  
Cheng Ni ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gene Panel ◽  
Next Generation ◽  
Panel Testing ◽  
Gene Panel Testing ◽  
Generation Sequencing

Real-world application of next generation sequencing to guide therapeutic options in lymphoma.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e14645-e14645
Author(s):  
Molly Tokaz ◽  
Anthony Scott ◽  
Maryann Shango ◽  
Sumana Devata ◽  
Shannon Carty ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Precision Medicine ◽  
Real World ◽  
Local Treatment ◽  
Therapeutic Targets ◽  
Therapeutic Options ◽  
Next Generation ◽  
Considerable Uncertainty ◽  
Generation Sequencing

e14645 Background: Despite the increasing availability of targeted and novel therapies, successful treatment of many relapsed/refractory lymphomas remains a challenge. Tumor sequencing is becoming an increasingly available technique to identify potential therapeutic targets; however, there remains considerable uncertainty about the successful application of this data in a “real world” clinical setting. Methods: Herein, we describe 91 lymphoma patients who underwent DNA & RNA sequencing of tumor biopsies via the MIONCOSEQ protocol to identify actionable therapeutic targets. Their charts were reviewed for the clinical use of MIONCOSEQ recommendations. Results: Among the 91 patients were 13 Lymphoma subtypes. Most patients had Stage III/IV disease (68%) at diagnosis, underwent an average of 4 treatments before sequencing (range 0-16) and had approximately 47 distinct molecular alterations (range 2-447). Of the cohort, 60 patients (65%) had actionable targets identified of which 11 ultimately received treatment based on MIONCOSEQ recommendations. The remaining patients did not receive treatment due to multiple reasons: prior CR or on surveillance not requiring treatment (10); death (12); trial ineligibility (4); trial unavailability at the institution (8); patient preference for local treatment (6); and already on alternative treatments (9). Taken as a whole, sequencing late in the disease course and a lack of available clinical trials were identified as barriers for the incorporation of MIONCOSEQ data into clinical practice. Therefore, earlier sequencing and strategies to bolster the availability of targeted therapies may significantly increase the application of genomic data and precision medicine in clinical practice. Conclusions: While next generation sequencing (NGS) is a powerful tool for advancing precision medicine, meaningful clinical application of these results remains a challenge. Our study indicates that early sequencing and improved trial availability could be beneficial in increasing real-world therapeutic options for relapsed/refractory lymphoma. Further research is needed to determine the extent to which a personalized approach, informed by NGS data, improves outcomes.

scholarly journals Next-Generation Sequencing (NGS) in COVID-19: A Tool for SARS-CoV-2 Diagnosis, Monitoring New Strains and Phylodynamic Modeling in Molecular Epidemiology

2021 ◽  
Vol 43 (2) ◽  
pp. 845-867
Author(s):  
Goldin John ◽  
Nikhil Shri Sahajpal ◽  
Ashis K. Mondal ◽  
Sudha Ananth ◽  
Colin Williams ◽  
...  
Keyword(s):  
Quality Control ◽  
Next Generation Sequencing ◽  
Real World ◽  
Next Generation ◽  
Comprehensive Review ◽  
Current Testing ◽  
Phylogenetic Evolution ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

This review discusses the current testing methodologies for COVID-19 diagnosis and explores next-generation sequencing (NGS) technology for the detection of SARS-CoV-2 and monitoring phylogenetic evolution in the current COVID-19 pandemic. The review addresses the development, fundamentals, assay quality control and bioinformatics processing of the NGS data. This article provides a comprehensive review of the obstacles and opportunities facing the application of NGS technologies for the diagnosis, surveillance, and study of SARS-CoV-2 and other infectious diseases. Further, we have contemplated the opportunities and challenges inherent in the adoption of NGS technology as a diagnostic test with real-world examples of its utility in the fight against COVID-19.

scholarly journals NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data

2021 ◽  
Author(s):  
Anne Krogh Nøhr ◽  
Kristian Hanghøj ◽  
Genis Garcia Erill ◽  
Zilong Li ◽  
Ida Moltke ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Research ◽  
Likelihood Estimation ◽  
Software Tool ◽  
Estimation Methods ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Estimation of relatedness between pairs of individuals is important in many genetic research areas. When estimating relatedness, it is important to account for admixture if this is present. However, the methods that can account for admixture are all based on genotype data as input, which is a problem for low-depth next-generation sequencing (NGS) data from which genotypes are called with high uncertainty. Here we present a software tool, NGSremix, for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods. Using both simulated and real NGS data for admixed individuals with an average depth of 4x or below we show that our method works well and clearly outperforms all the commonly used state-of-the-art relatedness estimation methods PLINK, KING, relateAdmix, and ngsRelate that all perform quite poorly. Hence, NGSremix is a useful new tool for estimating relatedness in admixed populations from low-depth NGS data. NGSremix is implemented in C/C ++ in a multi-threaded software and is freely available on Github https://github.com/KHanghoj/NGSremix.

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