☆ 4.6 Review

Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer

CANCERS (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Article Biochemistry & Molecular Biology

Clinical application and detection techniques of liquid biopsy in gastric cancer

Shuo Ma et al.

Molecular Cancer (2023)

添加到收藏夹

Article Multidisciplinary Sciences

A DNA methylation atlas of normal human cell types

Netanel Loyfer et al.

Summary: DNA methylation is an important epigenetic mark that regulates gene expression and chromatin organization. This study presents a human methylome atlas based on deep whole-genome bisulfite sequencing, providing a comprehensive analysis of 39 cell types from 205 healthy tissue samples. The atlas reveals tissue-specific methylation patterns and potential biomarkers for liquid biopsies.

NATURE (2023)

添加到收藏夹

Article Medical Laboratory Technology

Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma

Stephanie C. Y. Yu et al.

Summary: Recent studies have highlighted the presence of a substantial amount of analyzable long cell-free DNA (cfDNA) in plasma through single molecule, real-time (SMRT) sequencing. In this study, the size biases of SMRT sequencing by PacBio and nanopore sequencing by ONT were evaluated. The results showed that both platforms had biases towards sequencing longer DNA fragments, with PacBio showing a stronger bias. Tissue-of-origin analysis based on single-molecule methylation patterns performed comparably on both platforms. It is important to be aware of the analytical characteristics and biases of the sequencing platforms used when analyzing the size and end motif of cfDNA.

CLINICAL CHEMISTRY (2023)

添加到收藏夹

Article Critical Care Medicine

Multidimensional Cell-Free DNA Fragmentomic Assay for Detection of Early-Stage Lung Cancer

Siwei Wang et al.

Summary: In this study, an accurate and affordable approach for early-stage lung cancer detection was established by integrating cfDNA fragmentomics and machine learning models. The stacked ensemble model achieved superior sensitivity for detecting early-stage lung cancer, which could promote early diagnosis and benefit more patients.

AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE (2023)

添加到收藏夹

Review Cell Biology

Circulating DNA fragmentomics and cancer screening

A. R. Thierry

Summary: Fragmentomics utilizes the size patterns and positioning of DNA molecules within nucleosomes to determine the origin and nature of DNA, particularly useful for cancer diagnosis and screening. In the omics era, the screening power of fragmentomics has been greatly enhanced through the development of sophisticated technologies assisted by machine learning.

CELL GENOMICS (2023)

添加到收藏夹

Review Oncology

At the dawn: cell-free DNA fragmentomics and gene regulation

Yaping Liu

Summary: Epigenetic mechanisms are essential in gene regulation, and circulating cell-free DNA (cfDNA) in peripheral blood provides a non-invasive way to monitor the genomes of inaccessible tissues. The fragment patterns of plasma cfDNA reflect gene regulation status and have the potential to identify tissue origin. Studies in this area pave the way for non-invasive monitoring of gene regulatory dynamics in both peripheral immune cells and diseased tissues.

BRITISH JOURNAL OF CANCER (2022)

添加到收藏夹

Article Oncology

Cancer statistics, 2022

Rebecca L. Siegel et al.

Summary: Each year, the American Cancer Society compiles data on cancer occurrence and outcomes in the United States. The latest data shows that breast and prostate cancer progress has stagnated, while lung cancer has shown improvements in survival rates. Lung cancer incidence for advanced disease has declined while localized-stage rates have increased, resulting in higher survival rates. Mortality patterns align with incidence trends, with lung cancer deaths declining rapidly, breast cancer deaths slowing, and prostate cancer deaths stabilizing.

CA-A CANCER JOURNAL FOR CLINICIANS (2022)

添加到收藏夹

Article Gastroenterology & Hepatology

Ultrasensitive and affordable assay for early detection of primary liver cancer using plasma cell-free DNA fragmentomics

Xiangyu Zhang et al.

Summary: This study aims to develop an accurate and affordable method for the early detection of primary liver cancer (PLC) and differentiating between its subtypes using plasma cell-free DNA (cfDNA) fragmentomic profiles, showing excellent clinical potential.

HEPATOLOGY (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

Exosomes as a new frontier of cancer liquid biopsy

Dan Yu et al.

Summary: Liquid biopsy, a revolutionary strategy for cancer diagnosis and prognosis prediction, uses minimally invasive detection through biofluids such as blood, saliva, and urine. Exosomes, a subset of extracellular vesicles, play a crucial role in intercellular communication and are considered as potential biomarkers in liquid biopsy. However, the lack of high-quality separation and component analysis methods has limited the further clinical application of exosomes.

MOLECULAR CANCER (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

Liquid biopsy in lung cancer: significance in diagnostics, prediction, and treatment monitoring

Wen Li et al.

Summary: Primary lung cancer is a common malignant tumor in China, and liquid biopsy technology plays a crucial role in early diagnosis and individualized treatment. Liquid biopsy, with advantages of being nontraumatic, easy to obtain, and allowing real-time monitoring of the overall state of the tumor, has been widely researched and applied.

MOLECULAR CANCER (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Deep cfDNA fragment end profiling enables cancer detection

Yulia V. Zhitnyuk et al.

MOLECULAR CANCER (2022)

添加到收藏夹

Article Oncology

A pipeline for copy number profiling of single circulating tumour cells to assess intrapatient tumour heterogeneity

Teoman Deger et al.

Summary: In this study, a pipeline for analyzing single circulating tumor cells (CTCs) was developed to assess intrapatient tumor heterogeneity through copy number analysis. The pipeline was optimized and successfully validated using CTCs from patients.

MOLECULAR ONCOLOGY (2022)

添加到收藏夹

Article Oncology

Genome-wide aneuploidy detected by mFast-SeqS in circulating cell-free DNA is associated with poor response to pembrolizumab in patients with advanced urothelial cancer

Pauline A. J. Mendelaar et al.

Summary: This study investigated the use of a gene testing method called mFast-SeqS to evaluate treatment response in patients with mUC. The results showed that the mFast-SeqS score correlated significantly with tissue-based scores and ctDNA levels in the plasma, and a high score was independently associated with lack of clinical benefit from pembrolizumab treatment.

MOLECULAR ONCOLOGY (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Ensembl 2022

Fiona Cunningham et al.

Summary: Ensembl is unique in its flexible infrastructure for access to genomic data and annotation. They have focused on expediting annotation of new assemblies via the Ensembl Rapid Release platform, with the greatest annual number of newly annotated genomes released. They also developed a new method for comparative analyses and annotated non-vertebrate eukaryotes for the first time.

NUCLEIC ACIDS RESEARCH (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons

Daniel Beck et al.

Summary: Genome-wide DNA methylation analysis is commonly used for genome characterization and differential DNA methylation assessment, with CpG density playing a crucial role in different molecular techniques. Observations show that most genomes have low CpG density, with MeDIP focusing on <5 CpG/100 bp regions and RRBS identifying higher CpG density areas.

EPIGENETICS (2022)

添加到收藏夹

Review Oncology

Functional analysis of circulating tumour cells: the KEY to understand the biology of the metastatic cascade

Zahra Eslami-S et al.

Summary: Metastasis formation is the main cause of cancer-related death in patients with solid tumors. This process involves the escape of cancer cells from the primary tumor to the bloodstream, where they become circulating tumor cells (CTCs). Only a small subgroup of CTCs will survive and colonize distant sites. Analyzing these metastasis-competent CTCs is challenging due to their low concentration in peripheral blood, but a few research groups have successfully expanded CTCs in vitro and in vivo to serve as models for comprehensive analysis. These models have revealed the complexity and variability of the metastatic cascade, opening new avenues for diagnostic and therapeutic advancements.

BRITISH JOURNAL OF CANCER (2022)

添加到收藏夹

Article Medical Laboratory Technology

Single-Molecule Sequencing Enables Long Cell-Free DNA Detection and Direct Methylation Analysis for Cancer Patients

L. Y. Lois Choy et al.

Summary: Background analysis of circulating tumor DNA is crucial for cancer care, but previous studies focused on short DNA fragments. Bisulfite sequencing, a traditional method for methylation analysis, causes DNA degradation. This study overcame these limitations using single-molecule sequencing and discovered a previously unknown long cfDNA population.

CLINICAL CHEMISTRY (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments

Saife N. Lone et al.

Summary: Liquid biopsies are non-invasive methods that have revolutionized cancer diagnosis and monitoring. By analyzing tumor-derived entities in body fluids, liquid biopsies provide detailed information about tumor characteristics and can be used for detection, prognosis, and treatment monitoring.

MOLECULAR CANCER (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

A clinician's handbook for using ctDNA throughout the patient journey

Samantha O. Hasenleithner et al.

Summary: The analysis of cell-free DNA from liquid biopsy, particularly circulating tumor DNA (ctDNA), has shown promise in oncology, but questions remain regarding its clinical validity and utility, necessitating further research and study.

MOLECULAR CANCER (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors

Coren A. Milbury et al.

Summary: FoundationOne (R) CDx is an FDA-approved companion diagnostic test that utilizes comprehensive genomic profiling technology to analyze 324 cancer genes in solid tumors. It accurately identifies patients who may benefit from specific drug therapies and helps improve treatment outcomes for cancer patients.

PLOS ONE (2022)

添加到收藏夹

Review Medicine, General & Internal

Cell-Free DNA Fragmentomics in Liquid Biopsy

Spencer C. Ding et al.

Summary: Cell-free DNA (cfDNA) has revolutionized the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. The study of cfDNA fragmentation patterns, known as 'fragmentomics,' has provided valuable information about the tissue of origin of cfDNA molecules. Recent advancements in understanding cfDNA fragmentation have led to the discovery of fragmentomic markers with potential clinical applications.

DIAGNOSTICS (2022)

添加到收藏夹

Review Biochemistry & Molecular Biology

Cell-Free DNA Fragmentomics: A Promising Biomarker for Diagnosis, Prognosis and Prediction of Response in Breast Cancer

Caterina Gianni et al.

Summary: This review focuses on the available research on circulating cell-free DNA integrity as a biomarker for diagnosis, prognosis, and treatment response in breast cancer, highlighting new perspectives and critical issues for future applications.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

添加到收藏夹

Review Oncology

Circulating Tumor DNA-A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques

Xiaosha Wen et al.

Summary: This article reviews the different sources of ctDNA, the mutation and methylation detection methods, and the application value of ctDNA in various stages of tumor development. ctDNA, as an ideal biomarker, has a comprehensive and accurate application in the field of cancer research.

CANCERS (2022)

添加到收藏夹

Article Biochemistry & Molecular Biology

An ultra-sensitive assay using cell-free DNA fragmentomics for multi-cancer early detection

Hua Bao et al.

Summary: This study developed a robust machine learning model for multi-cancer early detection using cell-free DNA fragmentomics. The model showed high accuracy and sensitivity in detecting early-stage and small-size tumors. This research has significant implications for the development of cancer early screening in clinical practice.

MOLECULAR CANCER (2022)

添加到收藏夹

Article Oncology

Combining variant detection and fragment length analysis improves detection of minimal residual disease in postsurgery circulating tumour DNA of stage II-IIIA NSCLC patients

Daan C. L. Vessies et al.

Summary: A study developed a method combining variant calling and ctDNA fragment length analysis to identify patients with disease recurrence or no recurrence in stage II-IIIA NSCLC patients, providing useful information for postoperative treatment.

MOLECULAR ONCOLOGY (2022)

添加到收藏夹

Article Multidisciplinary Sciences

DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies

Emanuel Goncalves et al.

Summary: The study identified diagnostic biomarkers for early HCC through DNA methylation analysis, which can accurately detect HCC in tissue and liquid biopsy samples, successfully differentiating tumor samples from healthy controls.

SCIENTIFIC REPORTS (2022)

添加到收藏夹

Article Medicine, General & Internal

Sensitive detection of stage I lung adenocarcinoma using plasma cell-free DNA breakpoint motif profiling

Wei Guo et al.

Summary: A predictive model based on cfDNA fragmentomics was developed for early-stage lung adenocarcinoma (LUAD) detection. The model showed high sensitivity for early lesions and small-sized tumors and remained effective even with reduced sequencing depth.

EBIOMEDICINE (2022)

添加到收藏夹

Review Oncology

Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis

Estela Sanchez-Herrero et al.

Summary: This article provides an overview of the biological features of circulating tumor DNA (ctDNA), including size, structure, shedding and clearance mechanisms, as well as the pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is crucial for the development of new methods for ctDNA analysis.

FRONTIERS IN ONCOLOGY (2022)

添加到收藏夹

Article Oncology

Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids

Zhongzhen Liu et al.

Summary: This article introduces a newly developed RNA sequencing strategy called PALM-Seq, which enables simultaneous quantification and characterization of cell-free messenger RNA (cf-mRNA) and long non-coding RNA (cf-lncRNA). By applying this method, differentially abundant mRNA, lncRNA, and microRNA were successfully identified in the blood plasma of pregnant women, and cfRNAs in various body fluids were characterized. The study found that the distribution and preferences of cf-mRNA and cf-lncRNA were related to the types of body fluids and the functions of the originating tissues.

CLINICAL AND TRANSLATIONAL MEDICINE (2022)

添加到收藏夹

Review Oncology

Detection of circulating tumor cells: opportunities and challenges

Siwei Ju et al.

Summary: Circulating tumor cells (CTCs) are cells that shed from a primary tumor and travel through the bloodstream. Studying CTCs can provide in-depth knowledge about lethal tumor diseases. Researchers are working on capturing and detecting CTCs with improved sensitivity and specificity. However, there are still challenges that limit the current use of this diagnostic approach.

BIOMARKER RESEARCH (2022)

添加到收藏夹

Review Oncology

Liquid biopsy: current technology and clinical applications

Mina Nikanjam et al.

Summary: Liquid biopsies, including circulating extracellular nucleic acids (cfDNA and ctDNA) and circulating tumor cells (CTCs), have important clinical applications in precision oncology, such as predicting treatment response and resistance, analyzing prognosis and tumor burden, and detecting cancer at early stages. This review provides an overview of current technologies and clinical applications for liquid biopsies, highlighting the potential of this powerful tool in multiple aspects of cancer management.

JOURNAL OF HEMATOLOGY & ONCOLOGY (2022)

添加到收藏夹

Review Oncology

Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer

Peilong Li et al.

Summary: Lung cancer is the leading cause of cancer-related deaths, with poor prognosis due to late-stage diagnosis. DNA methylation, a widely studied epigenetic modification, plays a crucial role in early tumorigenesis. Liquid biopsy has rapidly developed and shows promise for early detection of lung cancer based on DNA methylation.

CLINICAL EPIGENETICS (2022)

添加到收藏夹

Review Oncology

Current challenges and best practices for cell-free long RNA biomarker discovery

Lluc Cabus et al.

Summary: The analysis of biomarkers in biological fluids, known as liquid biopsies, has the potential to diagnose complex diseases like cancer with high sensitivity and minimal invasiveness. While liquid biopsies can target any biomolecule, most studies have focused on circulating nucleic acids. However, RNA-based liquid biopsies face challenges in terms of low reproducibility of results due to technical and biological variability, lack of standardized protocols, and insufficient cohorts. This review aims to identify these challenges and biases and propose solutions to minimize them during biomarker discovery in liquid biopsies with cfRNA.

BIOMARKER RESEARCH (2022)

添加到收藏夹

Article Medicine, General & Internal

Potential clinical utility of liquid biopsy in early-stage non-small cell lung cancer

Haifeng Shen et al.

Summary: Liquid biopsy has been evaluated for its diagnostic and prognostic value in early-stage non-small cell lung cancer (NSCLC) through a meta-analysis and systematic review. The study concludes that liquid biopsy can reliably facilitate more precise and effective management of early-stage NSCLC, but improvements in techniques and higher-quality trials are needed.

BMC MEDICINE (2022)

添加到收藏夹

Editorial Material Oncology

Understanding NSCLC, one cell at a time

Ivan Ballesteros et al.

Summary: This article provides a comprehensive analysis of lung cancer patients at the single-cell level, revealing extreme immune diversity and defining neutrophil populations associated with treatment outcomes.

CANCER CELL (2022)

添加到收藏夹

Article Oncology

Evaluation of cell-free DNA approaches for multi-cancer early detection

Arash Jamshidi et al.

Summary: In this study, we evaluated several approaches for a circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED) test and identified the most promising method, which is the use of whole-genome methylation feature. cTAF is an important predictor of classifier performance and more closely reflects tumor biology.

CANCER CELL (2022)

添加到收藏夹

Article Oncology

Clinical Potential of Circulating Cell-Free DNA (cfDNA) for Longitudinally Monitoring Clinical Outcomes in the First-Line Setting of Non-Small-Cell Lung Cancer (NSCLC): A Real-World Prospective Study

Valerio Gristina et al.

Summary: This study aims to explore the longitudinal plasma cfDNA kinetics as an early marker of therapeutic efficacy and disease relapse in patients with advanced NSCLC. The results demonstrate that quantitative changes in cfDNA values correlate with responses to therapy and relapse of disease.

CANCERS (2022)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

Efrat Katsman et al.

Summary: The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time sequencing. It has been shown that ONT shallow whole-genome sequencing can detect copy number alterations (CNAs) and other cancer-related changes, making it a potential powerful tool for liquid biopsy.

GENOME BIOLOGY (2022)

添加到收藏夹

Article Medicine, Research & Experimental

Whole-genome circulating tumor DNA methylation landscape reveals sensitive biomarkers of breast cancer

Luo Hai et al.

Summary: An improved method for extracting ctDNA and reducing background contamination in early breast cancer diagnosis has been discovered. The study identified 26 candidate ctDNA methylation biomarkers with high accuracy in breast cancer patients. These findings hold promise for translation into clinical practice.

MEDCOMM (2022)

添加到收藏夹

Review Biology

Liquid Biopsy, ctDNA Diagnosis through NGS

Chen Lin et al.

Summary: Liquid biopsy with ctDNA profiling by next-generation sequencing shows great promise in clinical oncology, with advantages of less invasiveness and sampling bias compared to tissue biopsy. NGS technologies are becoming more popular for ctDNA profiling, paving the way for precision medicine in cancer diagnosis and management.

LIFE-BASEL (2021)

添加到收藏夹

Article Pathology

Therapy Monitoring of EGFR-Positive Non-Small-Cell Lung Cancer Patients Using ddPCR Multiplex Assays

Remco de Kock et al.

Summary: This study demonstrates the importance of detecting EGFR-sensitizing and EGFR-resistance mutations in non-small-cell lung cancer patients using ddPCR on cfDNA for treatment selection and monitoring. The ddPCR multiplex assays were shown to be reliable and valuable for therapy monitoring in these patients.

JOURNAL OF MOLECULAR DIAGNOSTICS (2021)

添加到收藏夹

Review Biochemistry & Molecular Biology

Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA

Huiyan Luo et al.

Summary: Liquid biopsies, especially analysis of cell-free DNA, have emerged as a promising noninvasive diagnostic approach in oncology. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring MRD, predicting treatment response and prognosis, and tracing the tissue origin.

TRENDS IN MOLECULAR MEDICINE (2021)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Nanopore sequencing technology, bioinformatics and applications

Yunhao Wang et al.

Summary: Advancements in nanopore technologies for sequencing long DNA and RNA molecules have greatly improved accuracy, read length, and throughput. The field of nanopore sequencing continues to offer opportunities for enhancing data quality and analytical approaches through the development of new technologies tailored to specific applications.

NATURE BIOTECHNOLOGY (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma

Stephanie C. Y. Yu et al.

Summary: This study demonstrated the presence of long circulating cell-free DNA molecules and developed a sequencing technology to detect and analyze them. The proportions of long DNA molecules varied in maternal plasma across different trimesters, with potential clinical applications in predicting diseases and genetic information.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

DNA methylome profiling of circulating tumor cells in lung cancer at single base-pair resolution

Lei Zhao et al.

Summary: In this study, an efficient workflow LCM-mu WGBS was introduced to profile the DNA methylome of circulating tumor cells from lung cancer patients. A unique DNA methylation signature of CTCs distinct from primary lung cancer tissues was identified, with promoter hypermethylation of epithelial genes as a hallmark of stable epithelial-mesenchymal transition. Furthermore, CTCs may exhibit a stemness-related feature during dissemination and metastasis, providing potential noninvasive CTC DNA methylation biomarkers for clinical diagnosis.

ONCOGENE (2021)

添加到收藏夹

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Analysis at the single-cell level indicates an important role of heterogeneous global DNA methylation status on the progression of lung adenocarcinoma

Quan-Fang Chen et al.

Summary: This study investigated the impact and diversity of global DNA methylation status on lung adenocarcinoma using single-cell RNAseq data. The analysis revealed the crucial role of methylation status in tumor cell function and progression, with differentially methylated cell clusters located at the ends of putative trajectories, indicating the essential role of DNA methylation and demethylation in tumor cell progression.

SCIENTIFIC REPORTS (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Single-cell DNA and RNA sequencing of circulating tumor cells

Masato Kojima et al.

Summary: Single-cell sequencing can accurately represent tumor heterogeneity, with MDA-based WGA method showing higher amplification efficiency and coverage depth. The PCR-based WTA method accurately amplifies mRNA from a single cell, showing specific gene expression patterns.

SCIENTIFIC REPORTS (2021)

添加到收藏夹

Review Cell Biology

Emerging Role of Extracellular Vesicles and Cellular Communication in Metastasis

Aisling Forder et al.

Summary: Communication between cancer cells and stromal cells through extracellular vesicles plays a key role in promoting metastasis. Tumor-secreted EVs induce a pro-tumorigenic phenotype in non-malignant cells of the stroma, driving metastasis through various mechanisms. Targeting these EV-mediated signaling pathways may have therapeutic potential for developing biomarkers and novel treatment strategies.

CELLS (2021)

添加到收藏夹

Review Oncology

Circulating Tumor DNA and Minimal Residual Disease (MRD) in Solid Tumors: Current Horizons and Future Perspectives

Yan Peng et al.

Summary: ctDNA, as a non-invasive biomarker, has promising clinical applications for individualized cancer diagnosis and therapy in solid tumors. MRD detection aids in assessing treatment response, patient prognosis, and risk of recurrence.

FRONTIERS IN ONCOLOGY (2021)

添加到收藏夹

Review Multidisciplinary Sciences

Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies

Y. M. Dennis Lo et al.

Summary: Liquid biopsies, which analyze cell-free DNA in blood plasma, are utilized for noninvasive prenatal testing, oncology, and organ transplant monitoring. The physical and molecular features of cell-free DNA fragments, along with their distribution over the genome, contain information about their tissues of origin. These features, including DNA methylation patterns and nucleosomal organization, hold promise for noninvasive detection of tissue-specific pathologies with a variety of clinical applications.

SCIENCE (2021)

添加到收藏夹

Article Biochemical Research Methods

cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Wei Zhang et al.

Summary: cfDNApipe is an easy-to-use and systematic python package for cfDNA whole-genome sequencing and whole-genome bisulfite sequencing data analysis, covering the entire analysis pipeline, quality control, and statistical analysis.

BIOINFORMATICS (2021)

添加到收藏夹

Article Oncology

Highly sensitive fusion detection using plasma cell-free RNA in non-small-cell lung cancers

Nobuhiko Hasegawa et al.

Summary: The study demonstrated the utility of cfRNA and cfDNA in detecting fusion genes in NSCLC patients, with cfRNA showing higher sensitivity compared to cfDNA, particularly in samples collected at chemo-naive or progressive disease status. This suggests that cfRNA assay could be a valuable diagnostic tool for patients with insufficient tissues and for monitoring NSCLC progression for consideration of second-line treatments.

CANCER SCIENCE (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Integrated analysis of multimodal single-cell data

Yuhan Hao et al.

Summary: The study introduces a weighted-nearest neighbor analysis framework to learn the relative utility of each data type in each cell, enabling integrative analysis of multiple modalities. Applied to a CITE-seq dataset, the method constructs a multimodal reference atlas of the circulating immune system and successfully identifies and validates previously unreported lymphoid subpopulations.

CELL (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

Yun Zhang et al.

Summary: The paper presents HISAT-3N, a method for efficiently and accurately aligning converted sequences, showing that it outperforms other modern systems in speed, accuracy, scalability, and memory requirements.

GENOME RESEARCH (2021)

添加到收藏夹

Review Biochemistry & Molecular Biology

Using single-cell sequencing technology to detect circulating tumor cells in solid tumors

Jiasheng Xu et al.

Summary: Circulating tumor cells have high metastatic potential and single-cell sequencing provides a new perspective for understanding the biological process of tumors, avoiding interference from tumor heterogeneity.

MOLECULAR CANCER (2021)

添加到收藏夹

Review Genetics & Heredity

Navigating the DNA methylation landscape of cancer

Atsuya Nishiyama et al.

Summary: DNA methylation is a chemical modification that defines cell type and lineage through controlling gene expression and genome stability. Aberrant DNA methylation in cancer cells targets CpG islands in gene expression regulatory elements. Recent studies suggest that the classical model of DNA hypermethylation in cancer needs to be reevaluated.

TRENDS IN GENETICS (2021)

添加到收藏夹

Review Medicine, General & Internal

Liquid Biopsy: A Family of Possible Diagnostic Tools

Battistelli Michela

Summary: Liquid biopsies are excellent diagnostic tools that can be used in various physiological or pathological conditions, including non-invasive prenatal testing and evaluating disease status and treatment methods. Biomarkers in different body fluids can be utilized for assessing pathological and non-pathological conditions.

DIAGNOSTICS (2021)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Technology dictates algorithms: recent developments in read alignment

Mohammed Alser et al.

Summary: Aligning sequencing reads onto a reference is crucial in genomic analysis, with computational algorithms evolving to accommodate technological advancements, resulting in a diverse array of alignment methods today. Through a systematic survey of 107 alignment methods and rigorous evaluation of 11 read aligners, we demonstrate the impact of underlying algorithms on the speed and efficiency of read alignment, as well as their customization to meet specific needs in various biological domains.

GENOME BIOLOGY (2021)

添加到收藏夹

Article Biochemistry & Molecular Biology

ClinVar: improvements to accessing data

Melissa J. Landrum et al.

NUCLEIC ACIDS RESEARCH (2020)

添加到收藏夹

Article Genetics & Heredity

Smoking, DNA Methylation, and Lung Function: a Mendelian Randomization Analysis to Investigate Causal Pathways

Emily Jamieson et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2020)

添加到收藏夹

Review Oncology

Whole exome sequencing of cell-free DNA - A systematic review and Bayesian individual patient data meta-analysis

Manouk K. Bos et al.

CANCER TREATMENT REVIEWS (2020)

添加到收藏夹

Article Pathology

A profile on cobas® EGFR Mutation Test v2 as companion diagnostic for first-line treatment of patients with non-small cell lung cancer

Susana Torres et al.

EXPERT REVIEW OF MOLECULAR DIAGNOSTICS (2020)

添加到收藏夹

Article Biochemical Research Methods

Liquid Biopsy Based Single-Cell Transcriptome Profiling Characterizes Heterogeneity of Disseminated Tumor Cells from Lung Adenocarcinoma

Yu Dong et al.

PROTEOMICS (2020)

添加到收藏夹

Review Radiology, Nuclear Medicine & Medical Imaging

Liquid Biopsy for Cancer: Review and Implications for the Radiologist

Jacob J. Underwood et al.

RADIOLOGY (2020)

添加到收藏夹

Review Medicine, General & Internal

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Rute Pereira et al.

JOURNAL OF CLINICAL MEDICINE (2020)

添加到收藏夹

Review Oncology

Diagnostic Accuracy of Droplet Digital PCR and Amplification Refractory Mutation System PCR for Detecting EGFR Mutation in Cell-Free DNA of Lung Cancer: A Meta-Analysis

Caichen Li et al.

FRONTIERS IN ONCOLOGY (2020)

添加到收藏夹

Review Respiratory System

Current and future applications of liquid biopsy in nonsmall cell lung cancer from early to advanced stages

Nicolas Guibert et al.

EUROPEAN RESPIRATORY REVIEW (2020)

添加到收藏夹

Article Oncology

Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non-Small Cell Lung Cancer

Bin Liu et al.

CLINICAL CANCER RESEARCH (2020)

添加到收藏夹

Review Oncology

Strategies for enrichment of circulating tumor cells

Xinchun Li et al.

TRANSLATIONAL CANCER RESEARCH (2020)

添加到收藏夹

Article Multidisciplinary Sciences

Integrating genomic features for non-invasive early lung cancer detection

Jacob J. Chabon et al.

NATURE (2020)

添加到收藏夹

Review Medicine, General & Internal

Liquid Biopsy as Novel Tool in Precision Medicine: Origins, Properties, Identification and Clinical Perspective of Cancer's Biomarkers

Diego Fernandez-Lazaro et al.

DIAGNOSTICS (2020)

添加到收藏夹

Review Medicine, General & Internal

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

Rossella Bruno et al.

DIAGNOSTICS (2020)

添加到收藏夹

Article Oncology

Blood-derived DNA methylation predictors of mortality discriminate tumor and healthy tissue in multiple organs

Yan Zhang et al.

MOLECULAR ONCOLOGY (2020)

添加到收藏夹

Review Genetics & Heredity

Long-read human genome sequencing and its applications

Glennis A. Logsdon et al.

NATURE REVIEWS GENETICS (2020)

添加到收藏夹

Article Medicine, Research & Experimental

Isolation of Circulating Tumor Cells from Peripheral Blood Samples of Cancer Patients Using Microfluidic Technology

A. B. Volovetskiy et al.

SOVREMENNYE TEHNOLOGII V MEDICINE (2020)

添加到收藏夹

Review Oncology

EGFR exon 20 insertions in advanced non-small cell lung cancer: A new history begins

Jordi Remon et al.

CANCER TREATMENT REVIEWS (2020)

添加到收藏夹

Review Biochemical Research Methods

Recent advances in microfluidic technologies for circulating tumor cells: enrichment, single-cell analysis, and liquid biopsy for clinical applications

Haimeng Pei et al.

LAB ON A CHIP (2020)

添加到收藏夹

Article Biotechnology & Applied Microbiology

NanoVar: accurate characterization of patients' genomic structural variants using low-depth nanopore sequencing

Cheng Yong Tham et al.

GENOME BIOLOGY (2020)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe et al.

GENOME BIOLOGY (2020)

添加到收藏夹

Review Oncology

Circulating tumor DNA and liquid biopsy in oncology

David W. Cescon et al.

NATURE CANCER (2020)

添加到收藏夹

Review Biochemical Research Methods

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application

Gaye Lightbody et al.

BRIEFINGS IN BIOINFORMATICS (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

CellMarker: a manually curated resource of cell markers in human and mouse

Xinxin Zhang et al.

NUCLEIC ACIDS RESEARCH (2019)

添加到收藏夹

Review Oncology

Liquid biopsy and minimal residual disease - latest advances and implications for cure

Klaus Pantel et al.

NATURE REVIEWS CLINICAL ONCOLOGY (2019)

添加到收藏夹

Review Oncology

The Value of Liquid Biopsies for Guiding Therapy Decisions in Non-small Cell Lung Cancer

Jatta Saarenheimo et al.

FRONTIERS IN ONCOLOGY (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Genome-wide cell-free DNA fragmentation in patients with cancer

Stephen Cristiano et al.

NATURE (2019)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

Brian Hie et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

Samuel L. Wolock et al.

CELL SYSTEMS (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

Comprehensive Integration of Single-Cell Data

Tim Stuart et al.

CELL (2019)

添加到收藏夹

Review Oncology

Circulating tumor cells in patients with lung cancer: developments and applications for precision medicine

Bing Tong et al.

FUTURE ONCOLOGY (2019)

添加到收藏夹

Review Biochemistry & Molecular Biology

Current best practices in single-cell RNA-seq analysis: a tutorial

Malte D. Luecken et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

添加到收藏夹

Article Chemistry, Multidisciplinary

Whole Genome Sequencing of Single Circulating Tumor Cells Isolated by Applying a Pulsed Laser to Cell-Capturing Microstructures

Okju Kim et al.

SMALL (2019)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Update on liquid biopsy in clinical management of non-small cell lung cancer

Zhen Wu et al.

ONCOTARGETS AND THERAPY (2019)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

Daehwan Kim et al.

NATURE BIOTECHNOLOGY (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Addressing cellular heterogeneity in tumor and circulation for refined prognostication

Su Bin Lim et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

添加到收藏夹

Article Oncology

Matched Whole-Genome Sequencing (WGS) and Whole-Exome Sequencing (WES) of Tumor Tissue with Circulating Tumor DNA (ctDNA) Analysis: Complementary Modalities in Clinical Practice

Robin Imperial et al.

CANCERS (2019)

添加到收藏夹

Review Genetics & Heredity

Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?

Elisabetta Rossi et al.

FRONTIERS IN GENETICS (2019)

添加到收藏夹

Review Oncology

Liquid biopsies

Evi Lianidou et al.

GENES CHROMOSOMES & CANCER (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

COSMIC: the Catalogue Of Somatic Mutations In Cancer

John G. Tate et al.

NUCLEIC ACIDS RESEARCH (2019)

添加到收藏夹

Review Developmental Biology

Considerations when processing and interpreting genomics data of the placenta

Chaini Konwar et al.

PLACENTA (2019)

添加到收藏夹

Article Oncology

Circulating tumor cells in lung cancer are prognostic and predictive for worse tumor response in both targeted- and chemotherapy

Menno Tamminga et al.

TRANSLATIONAL LUNG CANCER RESEARCH (2019)

添加到收藏夹

Review Oncology

Liquid biopsy: one cell at a time

Su Bin Lim et al.

NPJ PRECISION ONCOLOGY (2019)

添加到收藏夹

Review Oncology

Unravelling tumour heterogeneity by single-cell profiling of circulating tumour cells

Laura Keller et al.

NATURE REVIEWS CANCER (2019)

添加到收藏夹

Review Genetics & Heredity

Next-generation sequencing in liquid biopsy: cancer screening and early detection

Ming Chen et al.

HUMAN GENOMICS (2019)

添加到收藏夹

Article Biochemistry & Molecular Biology

Frequencies and expression levels of programmed death ligand 1 (PD-L1) in circulating tumor RNA (ctRNA) in various cancer types

Toshiyuki Ishiba et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2018)

添加到收藏夹

Review Biotechnology & Applied Microbiology

Circulating tumor cell isolation, culture, and downstream molecular analysis

Sandhya Sharma et al.

BIOTECHNOLOGY ADVANCES (2018)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Kelly Street et al.

BMC GENOMICS (2018)

添加到收藏夹

Article Oncology

Early Assessment of Lung Cancer Immunotherapy Response via Circulating Tumor DNA

Sarah B. Goldberg et al.

CLINICAL CANCER RESEARCH (2018)

添加到收藏夹

Article Oncology

Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non-Small Cell Lung Cancer

Caroline E. McCoach et al.

CLINICAL CANCER RESEARCH (2018)

添加到收藏夹

Review Biochemistry & Molecular Biology

Long reads: their purpose and place

Martin O. Pollard et al.

HUMAN MOLECULAR GENETICS (2018)

添加到收藏夹

Article Biochemical Research Methods

Isolation and genome sequencing of individual circulating tumor cells using hydrogel encapsulation and laser capture microdissection

Emily S. Park et al.

LAB ON A CHIP (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

Xinyi Guo et al.

NATURE MEDICINE (2018)

添加到收藏夹

Article Biochemical Research Methods

scmap: projection of single-cell RNA -seq data across data sets

Vladimir Yu Kiselev et al.

NATURE METHODS (2018)

添加到收藏夹

Article Biochemical Research Methods

Strelka2: fast and accurate calling of germline and somatic variants

Sangtae Kim et al.

NATURE METHODS (2018)

添加到收藏夹

Article Biochemistry & Molecular Biology

GeneMANIA update 2018

Max Franz et al.

NUCLEIC ACIDS RESEARCH (2018)

添加到收藏夹

Review Oncology

The Present and Future of Liquid Biopsies in Non-Small Cell Lung Cancer: Combining Four Biosources for Diagnosis, Prognosis, Prediction, and Disease Monitoring

Jillian Wilhelmina Paulina Bracht et al.

CURRENT ONCOLOGY REPORTS (2018)

添加到收藏夹

Article Multidisciplinary Sciences

Tumor-derived exosomal miR-1247-3p induces cancer-associated fibroblast activation to foster lung metastasis of liver cancer

Tian Fang et al.

NATURE COMMUNICATIONS (2018)

添加到收藏夹

Article Multidisciplinary Sciences

An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters

Neha Bhagwat et al.

SCIENTIFIC REPORTS (2018)

添加到收藏夹

Article Chemistry, Analytical

Developing Ultrasensitive Library-Aliquot-Based Droplet Digital PCR for Detecting T790M in Plasma-Circulating Tumor DNA of Non-small-Cell-Lung-Cancer Patients

Ke Yang et al.

ANALYTICAL CHEMISTRY (2018)

添加到收藏夹

Article Cell Biology

Enhanced detection of circulating tumor DNA by fragment size analysis

Florent Mouliere et al.

SCIENCE TRANSLATIONAL MEDICINE (2018)

添加到收藏夹

Article Oncology

Peripheral blood biomarkers correlate with outcomes in advanced non-small cell lung Cancer patients treated with anti-PD-1 antibodies

Aixa E. Soyano et al.

JOURNAL FOR IMMUNOTHERAPY OF CANCER (2018)

添加到收藏夹

Article Cell Biology

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines

Clotilde Thery et al.

JOURNAL OF EXTRACELLULAR VESICLES (2018)

添加到收藏夹

Article Biotechnology & Applied Microbiology

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf et al.

GENOME BIOLOGY (2018)

添加到收藏夹

Review Oncology

Liquid biopsy of cancer: a multimodal diagnostic tool in clinical oncology

Raffaele Palmirotta et al.

THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY (2018)

添加到收藏夹

Review Medicine, General & Internal

Cancer Diagnosis Using a Liquid Biopsy: Challenges and Expectations

Francesc Castro-Giner et al.

DIAGNOSTICS (2018)

添加到收藏夹

Article Oncology

A Comparison of ddPCR and ARMS for detecting EGFR T790M status in ctDNA from advanced NSCLC patients with acquired EGFR-TKI resistance

Wenxian Wang et al.

CANCER MEDICINE (2017)

添加到收藏夹

Article Multidisciplinary Sciences

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Christopher Abbosh et al.

NATURE (2017)

添加到收藏夹

Article Biochemical Research Methods

chromVAR : inferring transcription-factor-associated accessibility from single-cell epigenomic data

Alicia N. Schep et al.

NATURE METHODS (2017)

添加到收藏夹

Article Biochemical Research Methods

Simultaneous epitope and transcriptome measurement in single cells

Marlon Stoeckius et al.

NATURE METHODS (2017)

添加到收藏夹

Article Biochemical Research Methods

Single-cell mRNA quantification and differential analysis with Census

Xiaojie Qiu et al.

NATURE METHODS (2017)

添加到收藏夹

Article Biochemical Research Methods

Reversed graph embedding resolves complex single-cell trajectories

Xiaojie Qiu et al.

NATURE METHODS (2017)

添加到收藏夹

Review Oncology

Integrating liquid biopsies into the management of cancer

Giulia Siravegna et al.

NATURE REVIEWS CLINICAL ONCOLOGY (2017)

添加到收藏夹

Review Pharmacology & Pharmacy

Exosomes: Therapy delivery tools and biomarkers of diseases

Lucio Barile et al.

PHARMACOLOGY & THERAPEUTICS (2017)

添加到收藏夹

Article Cell Biology

Direct detection of early-stage cancers using circulating tumor DNA

Jillian Phallen et al.

SCIENCE TRANSLATIONAL MEDICINE (2017)

添加到收藏夹

Article Biology

The Human Cell Atlas

Aviv Regev et al.

ELIFE (2017)

添加到收藏夹

Editorial Material Respiratory System

Sputum-based DNA methylation biomarkers to guide lung cancer screening decisions

Delphine Lissa et al.

JOURNAL OF THORACIC DISEASE (2017)

添加到收藏夹

Article Multidisciplinary Sciences

Whole exome sequencing for determination of tumor mutation load in liquid biopsy from advanced cancer patients

Florence Koeppel et al.

PLOS ONE (2017)

添加到收藏夹

Review Oncology

Liquid biopsies in lung cancer-time to implement research technologies in routine care?

Linda Kohn et al.

ANNALS OF TRANSLATIONAL MEDICINE (2017)

添加到收藏夹

Article Oncology

A prospective examination of circulating tumor cell profiles in non-small-cell lung cancer molecular subgroups

C. R. Lindsay et al.

ANNALS OF ONCOLOGY (2017)

添加到收藏夹

Review Cell Biology

Recent progress in single-cell cancer genomics

Daphne Tsoucas et al.

CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)

添加到收藏夹

Article Biochemical Research Methods

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R

Davis J. McCarthy et al.

BIOINFORMATICS (2017)

添加到收藏夹

Review Oncology

Liquid biopsies come of age: towards implementation of circulating tumour DNA

Jonathan C. M. Wan et al.

NATURE REVIEWS CANCER (2017)

添加到收藏夹

Article Oncology

Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients

Cloud P. Paweletz et al.

CLINICAL CANCER RESEARCH (2016)

添加到收藏夹

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

添加到收藏夹

Article Respiratory System

EGFR Mutation Analysis of Circulating Tumor DNA Using an Improved PNA-LNA PCR Clamp Method

Kana Watanabe et al.

CANADIAN RESPIRATORY JOURNAL (2016)

添加到收藏夹

Article Cell & Tissue Engineering

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

Dominic Grun et al.

CELL STEM CELL (2016)

添加到收藏夹

Article Medical Laboratory Technology

SOX17 promoter methylation in plasma circulating tumor DNA of patients with non-small cell lung cancer

Ioanna Balgkouranidou et al.

CLINICAL CHEMISTRY AND LABORATORY MEDICINE (2016)

添加到收藏夹

Article Hematology

Ultra-deep sequencing leads to earlier and more sensitive detection of the tyrosine kinase inhibitor resistance mutation T315I in chronic myeloid leukemia

Constance Baer et al.

HAEMATOLOGICA (2016)

添加到收藏夹

Article Pathology

Ultrasensitive Detection of Multiplexed Somatic Mutations Using MALDI-TOF Mass Spectrometry

Michael J. Mosko et al.

JOURNAL OF MOLECULAR DIAGNOSTICS (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

Grace X. Y. Zheng et al.

NATURE BIOTECHNOLOGY (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Integrated digital error suppression for improved detection of circulating tumor DNA

Aaron M. Newman et al.

NATURE BIOTECHNOLOGY (2016)

添加到收藏夹

Article Biochemical Research Methods

Monovar: single-nucleotide variant detection in single cells

Hamim Zafar et al.

NATURE METHODS (2016)

添加到收藏夹

Article Biochemistry & Molecular Biology

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramirez et al.

NUCLEIC ACIDS RESEARCH (2016)

添加到收藏夹

Article Biochemistry & Molecular Biology

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Zhongwu Lai et al.

NUCLEIC ACIDS RESEARCH (2016)

添加到收藏夹

Article Multidisciplinary Sciences

Molecular profiling of single circulating tumor cells from lung cancer patients

Seung-min Park et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Review Genetics & Heredity

Profiling genome-wide DNA methylation

Wai-Shin Yong et al.

EPIGENETICS & CHROMATIN (2016)

添加到收藏夹

Article Genetics & Heredity

Fragment Length of Circulating Tumor DNA

Hunter R. Underhill et al.

PLOS GENETICS (2016)

添加到收藏夹

Article Medicine, General & Internal

Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study

Christine A. Parkinson et al.

PLOS MEDICINE (2016)

添加到收藏夹

Article Hematology

Ultra-deep sequencing leads to earlier and more sensitive detection of the tyrosine kinase inhibitor resistance mutation T315I in chronic myeloid leukemia

Constance Baer et al.

HAEMATOLOGICA (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Tree inference for single-cell data

Katharina Jahn et al.

GENOME BIOLOGY (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

OncoNEM: inferring tumor evolution from single-cell sequencing data

Edith M. Ross et al.

GENOME BIOLOGY (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Miten Jain et al.

GENOME BIOLOGY (2016)

添加到收藏夹

Article Biotechnology & Applied Microbiology

The Ensembl Variant Effect Predictor

William McLaren et al.

GENOME BIOLOGY (2016)

添加到收藏夹

Review Genetics & Heredity

Alignment of Next-Generation Sequencing Reads

Knut Reinert et al.

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 16 (2015)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

Maxim Ivanov et al.

BMC GENOMICS (2015)

添加到收藏夹

Article Medical Laboratory Technology

Rapid Identification of Plasma DNA Samples with Increased ctDNA Levels by a Modified FAST-SeqS Approach

Jelena Belic et al.

CLINICAL CHEMISTRY (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Glypican-1 identifies cancer exosomes and detects early pancreatic cancer

Sonia A. Melo et al.

NATURE (2015)

添加到收藏夹

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

添加到收藏夹

Article Biochemical Research Methods

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber et al.

NATURE METHODS (2015)

添加到收藏夹

Article Biochemical Research Methods

Interactive analysis and assessment of single-cell copy-number variations

Tyler Garvin et al.

NATURE METHODS (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

Yusi Fu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

添加到收藏夹

Review Genetics & Heredity

PacBio Sequencing and Its Applications

Anthony Rhoads et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2015)

添加到收藏夹

Article Multidisciplinary Sciences

Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

Richard B. Lanman et al.

PLOS ONE (2015)

添加到收藏夹

Article

Insights into therapeutic resistance from whole-genome analyses of circulating tumor DNA

Luis A. Diaz et al.

Oncotarget (2015)

添加到收藏夹

Article Oncology

Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer

F. Rothe et al.

ANNALS OF ONCOLOGY (2014)

添加到收藏夹

Article Biochemistry & Molecular Biology

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

Sean C. Bendall et al.

CELL (2014)

添加到收藏夹

Article Medical Laboratory Technology

Prognostic Relevance of Viable Circulating Tumor Cells Detected by EPISPOT in Metastatic Breast Cancer Patients

Jean-Marie Ramirez et al.

CLINICAL CHEMISTRY (2014)

添加到收藏夹

Article Biochemical Research Methods

Microfluidic device (ExoChip) for on-chip isolation, quantification and characterization of circulating exosomes

Shailender Singh Kanwar et al.

LAB ON A CHIP (2014)

添加到收藏夹

Article Oncology

Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer

Florent Mouliere et al.

MOLECULAR ONCOLOGY (2014)

添加到收藏夹

Article Biotechnology & Applied Microbiology

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2014)

添加到收藏夹

Article Biochemistry & Molecular Biology

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

Aaron M. Newman et al.

NATURE MEDICINE (2014)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

添加到收藏夹

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

添加到收藏夹

Article Biochemical Research Methods

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

Edward Y. Chen et al.

BMC BIOINFORMATICS (2013)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Genomic insights into cancer-associated aberrant CpG island hypermethylation

Duncan Sproul et al.

BRIEFINGS IN FUNCTIONAL GENOMICS (2013)

添加到收藏夹

Article Medical Laboratory Technology

Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

K. C. Allen Chan et al.

CLINICAL CHEMISTRY (2013)

添加到收藏夹

Article Medical Laboratory Technology

Multiplex Picodroplet Digital PCR to Detect KRAS Mutations in Circulating DNA from the Plasma of Colorectal Cancer Patients

Valerie Taly et al.

CLINICAL CHEMISTRY (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA

Muhammed Murtaza et al.

NATURE (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

Xiaohui Ni et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

添加到收藏夹

Article Oncology

Circulating Cell-Free DNA from Colorectal Cancer Patients May Reveal High KRAS or BRAF Mutation Load

Florent Mouliere et al.

TRANSLATIONAL ONCOLOGY (2013)

添加到收藏夹

Article Oncology

Amplification of the MET Receptor Drives Resistance to Anti-EGFR Therapies in Colorectal Cancer

Alberto Bardelli et al.

CANCER DISCOVERY (2013)

添加到收藏夹

Article Biotechnology & Applied Microbiology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim et al.

GENOME BIOLOGY (2013)

添加到收藏夹

Article Pathology

Circulating Tumor Cells in Lung Cancer

Rachel Young et al.

ACTA CYTOLOGICA (2012)

添加到收藏夹

Article Oncology

Quantitative Cell-Free DNA, KRAS, and BRAF Mutations in Plasma from Patients with Metastatic Colorectal Cancer during Treatment with Cetuximab and Irinotecan

Karen-Lise Garm Spindler et al.

CLINICAL CANCER RESEARCH (2012)

添加到收藏夹

Article Biochemistry & Molecular Biology

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

Pablo Cingolani et al.

FLY (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

Brock A. Peters et al.

NATURE (2012)

添加到收藏夹

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

添加到收藏夹

Article Biochemical Research Methods

Methylome analysis using MeDIP-seq with low DNA concentrations

Oluwatosin Taiwo et al.

NATURE PROTOCOLS (2012)

添加到收藏夹

Article Multidisciplinary Sciences

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

Ravi K. Patel et al.

PLOS ONE (2012)

添加到收藏夹

Article Multidisciplinary Sciences

FAST-SeqS: A Simple and Efficient Method for the Detection of Aneuploidy by Massively Parallel Sequencing

Isaac Kinde et al.

PLOS ONE (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

Chenghang Zong et al.

SCIENCE (2012)

添加到收藏夹

Article Cell Biology

Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

Tim Forshew et al.

SCIENCE TRANSLATIONAL MEDICINE (2012)

添加到收藏夹

Article Cell Biology

Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

Rebecca J. Leary et al.

SCIENCE TRANSLATIONAL MEDICINE (2012)

添加到收藏夹

Article Chemistry, Analytical

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

Benjamin J. Hindson et al.

ANALYTICAL CHEMISTRY (2011)

添加到收藏夹

Article Oncology

Recovering circulating extracellular or cell-free RNA from bodily fluids

Georgios Tzimagiorgis et al.

CANCER EPIDEMIOLOGY (2011)

添加到收藏夹

Article Pathology

Multiplex Amplification Coupled with COLD-PCR and High Resolution Melting Enables Identification of Low-Abundance Mutations in Cancer Samples with Low DNA Content

Coren A. Milbury et al.

JOURNAL OF MOLECULAR DIAGNOSTICS (2011)

添加到收藏夹

Article Multidisciplinary Sciences

Detection and quantification of rare mutations with massively parallel sequencing

Isaac Kinde et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

添加到收藏夹

Review Oncology

Cell-free nucleic acids as biomarkers in cancer patients

Heidi Schwarzenbach et al.

NATURE REVIEWS CANCER (2011)

添加到收藏夹

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

添加到收藏夹

Article Biochemical Research Methods

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

Pan Du et al.

BMC BIOINFORMATICS (2010)

添加到收藏夹

Article Oncology

Use of Cancer-Specific Genomic Rearrangements to Quantify Disease Burden in Plasma from Patients with Solid Tumors

David J. McBride et al.

GENES CHROMOSOMES & CANCER (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

添加到收藏夹

Article Pathology

Detection of Low-Level KRAS Mutations Using PNA-Mediated Asymmetric PCR Clamping and Melting Curve Analysis with Unlabeled Probes

Ji Eun Oh et al.

JOURNAL OF MOLECULAR DIAGNOSTICS (2010)

添加到收藏夹

Article Biotechnology & Applied Microbiology

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

R. Alan Harris et al.

NATURE BIOTECHNOLOGY (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Peter J. A. Cock et al.

NUCLEIC ACIDS RESEARCH (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

Kai Wang et al.

NUCLEIC ACIDS RESEARCH (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

David Warde-Farley et al.

NUCLEIC ACIDS RESEARCH (2010)

添加到收藏夹

Article Cell Biology

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

Rebecca J. Leary et al.

SCIENCE TRANSLATIONAL MEDICINE (2010)

添加到收藏夹

Article Biochemical Research Methods

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

Daniel C. Koboldt et al.

BIOINFORMATICS (2009)

添加到收藏夹

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

添加到收藏夹

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

添加到收藏夹

Article Biotechnology & Applied Microbiology

How to map billions of short reads onto genomes

Cole Trapnell et al.

NATURE BIOTECHNOLOGY (2009)

添加到收藏夹

Article Multidisciplinary Sciences

Real-Time DNA Sequencing from Single Polymerase Molecules

John Eid et al.

SCIENCE (2009)

添加到收藏夹

Article Biotechnology & Applied Microbiology

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

Da Wei Huang et al.

GENOME BIOLOGY (2007)

添加到收藏夹

Article Biochemical Research Methods

BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions

Frank Diehl et al.

NATURE METHODS (2006)

添加到收藏夹

Article Multidisciplinary Sciences

Detection and quantification of mutations in the plasma of patients with colorectal tumors

F Diehl et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

添加到收藏夹

Article Multidisciplinary Sciences

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

A Subramanian et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

添加到收藏夹

Article Multidisciplinary Sciences

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

D Dressman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

添加到收藏夹

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

添加到收藏夹

Article Multidisciplinary Sciences

Digital karyotyping

TL Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

添加到收藏夹

Article Biochemistry & Molecular Biology

The human genome browser at UCSC

WJ Kent et al.

GENOME RESEARCH (2002)

添加到收藏夹

Article Biochemistry & Molecular Biology

dbSNP: the NCBI database of genetic variation

ST Sherry et al.

NUCLEIC ACIDS RESEARCH (2001)

添加到收藏夹

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.