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Cancer Treatment Reviews Sep 2023Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be... (Review)
Review
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.
Topics: Humans; Circulating Tumor DNA; High-Throughput Nucleotide Sequencing; Mutation; Cell-Free Nucleic Acids; Neoplasms; Biomarkers, Tumor
PubMed: 37390697
DOI: 10.1016/j.ctrv.2023.102595 -
Journal of Immunology (Baltimore, Md. :... Nov 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37844281
DOI: 10.4049/jimmunol.2390018 -
Journal of Immunology (Baltimore, Md. :... Dec 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 38048526
DOI: 10.4049/jimmunol.2390021 -
Journal of Immunology (Baltimore, Md. :... Nov 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37931211
DOI: 10.4049/jimmunol.2390019 -
Journal of Immunology (Baltimore, Md. :... Aug 2023
Topics: Software; Algorithms; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37549396
DOI: 10.4049/jimmunol.2390013 -
Journal of Immunology (Baltimore, Md. :... Jul 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37399080
DOI: 10.4049/jimmunol.2390011 -
Journal of Immunology (Baltimore, Md. :... Jul 2023
Topics: Algorithms; Software; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing
PubMed: 37339402
DOI: 10.4049/jimmunol.2390010 -
Clinica Chimica Acta; International... Nov 2023Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing... (Review)
Review
Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.
Topics: Humans; Precision Medicine; Genomics; High-Throughput Nucleotide Sequencing; Prognosis
PubMed: 37839516
DOI: 10.1016/j.cca.2023.117568 -
Journal of Clinical Microbiology Aug 2023Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection and quantification from plasma....
Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection and quantification from plasma. The Karius Test, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μL in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory quality metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 h (interquartile range [IQR] 25 to 28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD-10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374 Aspergillus spp., 258 Pneumocystis jirovecii, 196 , and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector-borne pathogens, 144 Mycobacterium spp., 80 spp., 78 systemic dimorphic fungi, 69 spp., and 57 protozoan parasites) comprised 675 (3%) of all detections. This is the largest reported cohort of patients tested using plasma mcfDNA sequencing and represents the first report of a clinical grade metagenomic test performed at scale. Data reveal new insights into the breadth and complexity of potential pathogens identified.
Topics: Adult; Humans; Fungi; Bacteria; Viruses; High-Throughput Nucleotide Sequencing; Metagenomics; Sequence Analysis, DNA
PubMed: 37439686
DOI: 10.1128/jcm.01855-22 -
Nature Protocols Feb 2024Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can be studied by deep... (Review)
Review
Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can be studied by deep sequencing of bulk DNA, very few somatic mutations expand clonally, and most are unique to each cell. We describe a detailed protocol for single-cell whole-genome sequencing to discover and analyze somatic mutations in tissues and organs. The protocol comprises single-cell multiple displacement amplification (SCMDA), which ensures efficiency and high fidelity in amplification, and the SCcaller software tool to call single-nucleotide variations and small insertions and deletions from the sequencing data by filtering out amplification artifacts. With SCMDA and SCcaller at its core, this protocol describes a complete procedure for the comprehensive analysis of somatic mutations in a single cell, covering (1) single-cell or nucleus isolation, (2) single-cell or nucleus whole-genome amplification, (3) library preparation and sequencing, and (4) computational analyses, including alignment, variant calling, and mutation burden estimation. Methods are also provided for mutation annotation, hotspot discovery and signature analysis. The protocol takes 12-15 h from single-cell isolation to library preparation and 3-7 d of data processing. Compared with other single-cell amplification methods or single-molecular sequencing, it provides high genomic coverage, high accuracy in single-nucleotide variation and small insertions and deletion calling from the same single-cell genome, and fewer processing steps. SCMDA and SCcaller require basic experience in molecular biology and bioinformatics. The protocol can be utilized for studying mutagenesis and genome mosaicism in normal and diseased human and animal tissues under various conditions.
Topics: Animals; Humans; Mutation; Whole Genome Sequencing; Mutagenesis; Sequence Analysis, DNA; High-Throughput Nucleotide Sequencing; Nucleotides
PubMed: 37996541
DOI: 10.1038/s41596-023-00914-8