scholarly journals Next-Generation Novel Noninvasive Cancer Molecular Diagnostics Platforms Beyond Tissues

2018 ◽  
pp. 964-977 ◽  
Author(s):  
Xiaoliang Wu ◽  
Lin Zhu ◽  
Patrick C. Ma
Keyword(s):  
Molecular Diagnostics ◽  
Cancer Detection ◽  
Cancer Genomics ◽  
Cancer Diagnostics ◽  
Next Generation ◽  
Disease Response ◽  
Depth Analysis ◽  
Volatile Organic ◽  
Recent Arrival ◽  
Cancer Immunotherapies

In recent years, there has been a revolutionary expansion in technologic advances and therapeutic innovations in cancer medicine. Cancer diagnostics has begun to move away from a sole dependence on direct tumor tissue biopsy for cancer detection, diagnosis, and treatment monitoring. The need for improvement in molecular cancer diagnostics has never been more important, with not only the advent of cancer genomics and genomics-guided precision medicine but also the recent arrival of cancer immunotherapies. Owing to the practical limitations and risks associated with tissue-based biopsy diagnostics, novel noninvasive cancer diagnostics platforms have continued to evolve and expand in recent years. Examples of these platforms include the liquid biopsy, which is used to interrogate ctDNA or circulating tumor cells, proteomics, metabolomics, and exosomes; the urine biopsy, which is used to assay ctDNAs; saliva and stool biopsies, which are used for molecular genomics assays; and the breath biopsy, which measures volatile organic compounds. These next-generation noninvasive molecular diagnostics assays beyond tissues fundamentally transform the potential utilities of cancer diagnostics to enable repeat, prospective, and serial longitudinal “biopsies” to monitor disease response resistance and progression on therapies. Moreover, they allow continual interrogation and molecular in-depth analysis of the evolving tumor’s pan-canceromics under therapeutic stress. These technological and diagnostic advances have already brought about paradigm-changing next-generation cancer therapeutic strategies to enhance overall treatment efficacies. This article reviews the key noninvasive next-generation molecular diagnostics platforms beyond tissues, with emphasis on clinical utilities and applications.

Influence of Next-Generation Sequencing on Advancements in the Diagnosis of Major Psychiatric Diseases - A Review

2020 ◽  
Author(s):  
Maheen Nisar
Keyword(s):  
Next Generation Sequencing ◽  
Mental Disorders ◽  
Attention Deficit Disorder ◽  
Autism Spectrum ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
New Genes ◽  
Depth Analysis ◽  
Pubmed Search ◽  
Generation Sequencing

Rapid progress is being made in the development of next-generation sequencing (NGS) technologies, allowing repeated findings of new genes and a more in-depth analysis of genetic polymorphisms behind the pathogenesis of a disease. In a field such as psychiatry, characteristic of vague and highly variable somatic manifestations, these technologies have brought great advances towards diagnosing various psychiatric and mental disorders, identifying high-risk individuals and towards more effective corresponding treatment. Psychiatry has the difficult task of diagnosing and treating mental disorders without being able to invariably and definitively establish the properties of its illness. This calls for diagnostic technologies that go beyond the traditional ways of gene manipulation to more advanced methods mainly focusing on new gene polymorphism discoveries, one of them being NGS. This enables the identification of hundreds of common and rare genetic variations contributing to behavioral and psychological conditions. Clinical NGS has been useful to detect copy number and single nucleotide variants and to identify structural rearrangements that have been challenging for standard bioinformatics algorithms. The main objective of this article is to review the recent applications of NGS in the diagnosis of major psychiatric disorders, and hence gauge the extent of its impact in the field. A comprehensive PubMed search was conducted and papers published from 2013-2018 were included, using the keywords, “schizophrenia” or “bipolar disorder” or “depressive disorder” or “attention deficit disorder” or “autism spectrum disorder” and “next-generation sequencing”

scholarly journals INNV-17. NEXT GENERATION SEQUENCING IMPACTS OUTCOMES IN RECURRENT PRIMARY GLIOBLASTOMA: A SINGLE-CENTER RETROSPECTIVE ANALYSIS

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii120-ii120
Author(s):  
Daniel Zeitouni ◽  
Michael Catalino ◽  
Jordan Wise ◽  
Kathryn Pietrosimone ◽  
Sean McCabe ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cox Model ◽  
Objective Response ◽  
Complete Response ◽  
High Rate ◽  
Next Generation ◽  
Disease Response ◽  
Primary Glioblastoma ◽  
Generation Sequencing ◽  
Recurrent Gbm

Abstract BACKGROUND GBM is driven by various genomic alterations. Next generation sequencing (NGS) may reveal targetable alterations. The goal of this study was to describe how NGS can inform targeted therapy (TT) selection. METHODS The medical records of patients (pts) with GBM from 2017–2019 were reviewed. Pts with actionable mutations were included in the analysis. At first progression (PD1), two cohorts of pts were defined: cohort A received TT, while cohort B received physician’s choice chemotherapy (PCC). Regression analyses were used to determine OS and PFS between cohorts. A stratified cox model was utilized to assess the effect of TT, where KPS level (low vs high) was utilized as a stratification factor. A heat map was generated describing the landscape of mutations. Disease response in cohort A was graded per RANO criteria. RESULTS There were 38 GBM pts with actionable alterations. Cohort A had 15 (39%) pts and cohort B had 23 (61%) pts. Of the 26 common alterations, 11 (42%) were deemed actionable. Pts with higher KPS were more likely to receive TT. Pts with a KPS ≥ 70 had a longer PFS while on TT. Although not well powered, pts in cohort A had a longer median OS relative to cohort B (HR 0.37 CI 0.10–1.38). The objective response rate (ORR) was 93%, with afatinib and cabozantinib resulting in complete response, one pt had progressive disease while on TT. CONCLUSION NGS for recurrent GBM yields a high rate of actionable alterations. Pts that go on TT are often younger and with higher KPS. This likely plays into their improved survival; however, it is notable that the high ORR reflects the value of NGS in deciding on TT to match alterations that are likely to respond. In conclusion, patient selection and availability of NGS impacts outcomes in recurrent GBM.

scholarly journals Machine Learning Protocols in Early Cancer Detection Based on Liquid Biopsy: A Survey

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 638
Author(s):  
Linjing Liu ◽  
Xingjian Chen ◽  
Olutomilayo Olayemi Petinrin ◽  
Weitong Zhang ◽  
Saifur Rahaman ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cancer Detection ◽  
Liquid Biopsy ◽  
Cancer Diagnostics ◽  
Machine Learning Techniques ◽  
Learning Techniques ◽  
Cancer Subtype ◽  
Tumor Origin ◽  
Complex Relationships ◽  
Learning Protocols

With the advances of liquid biopsy technology, there is increasing evidence that body fluid such as blood, urine, and saliva could harbor the potential biomarkers associated with tumor origin. Traditional correlation analysis methods are no longer sufficient to capture the high-resolution complex relationships between biomarkers and cancer subtype heterogeneity. To address the challenge, researchers proposed machine learning techniques with liquid biopsy data to explore the essence of tumor origin together. In this survey, we review the machine learning protocols and provide corresponding code demos for the approaches mentioned. We discuss algorithmic principles and frameworks extensively developed to reveal cancer mechanisms and consider the future prospects in biomarker exploration and cancer diagnostics.

Next-generation sequencing and its applications in molecular diagnostics

2011 ◽  
Vol 11 (3) ◽  
pp. 333-343 ◽  
Author(s):  
Zhenqiang Su ◽  
Baitang Ning ◽  
Hong Fang ◽  
Huixiao Hong ◽  
Roger Perkins ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Next Generation ◽  
Generation Sequencing

ICT Aspects of Next-Generation-Sequencing Applied to Molecular Diagnostics

2013 ◽  
pp. 912-921
Author(s):  
Saskia Biskup
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Next Generation ◽  
Detection Rates ◽  
Genetic Causes ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-Generation-Sequencing (NGS) techniques are currently on the rise. This is seen as a revolution by (most) geneticists. The wealth of data stemming from Next-Generation-Sequencing will without a doubt lead to significant advances in the field of molecular diagnostics. On the clinical side, this will be higher detection rates of the genetic causes of particular diseases in patients. On the scientific side, NGS techniques will lead to the discovering of genes related to certain diseases (see, for example, Mardis, et al., 2009; Haack, et al., 2010; Lupski, et al., 2010). However, these advances come at a price: geneticists will be confronted with different and new ICT issues related to NGS. Because of the so far unknown amount of data stemming from NGS, these ICT issues need to be taken seriously. The purpose of this chapter is to give an overview on the different ICT aspects that come with the introduction of Next-Generation-Sequencing in molecular diagnostics.

Emerging ultrafast nucleic acid amplification technologies for next-generation molecular diagnostics

2019 ◽  
Vol 141 ◽  
pp. 111448 ◽  
Author(s):  
Sang Hun Lee ◽  
Seung-min Park ◽  
Brian N. Kim ◽  
Oh Seok Kwon ◽  
Won-Yep Rho ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Molecular Diagnostics ◽  
Nucleic Acid Amplification ◽  
Next Generation

The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics

2018 ◽  
Vol 71 (9) ◽  
pp. 767-773 ◽  
Author(s):  
Caterina Fumagalli ◽  
Davide Vacirca ◽  
Alessandra Rappa ◽  
Antonio Passaro ◽  
Juliana Guarize ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Diagnostics ◽  
Small Cell ◽  
Next Generation ◽  
Small Cell Lung ◽  
Single Institution ◽  
Lung Cancers ◽  
Targeted Next Generation Sequencing ◽  
Molecular Alterations ◽  
Generation Sequencing

BackgroundMolecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously.AimsTo evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC.MethodsA single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes.Results441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed in KRAS, TP53, EGFR, STK11 and MET genes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairing KRAS or EGFR in association with TP53 alterations.ConclusionsThe study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.

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