Precision Medicine - I

Liquid Biopsy

0. News/Patents of Liquid Biopsy

关于液体活检技术的科普

I. Reviews of Liquid Biopsy

  • 2020 Nature Reviews - RNA delivery by extracellular vesicles in mammalian cells and its applications

  • 2020 Science - The biology, function, and biomedical applications of exosomes

  • 2020 Genome Biology - The promise and challenge of cancer microbiome research

  • 2019 Cell - Review - The Role of Non-coding RNAs in Oncology

  • 2018 Nature Reviews Genetics - Current and future perspectives of liquid biopsies in genomics-driven oncology

  • 2018 Nat Rev Clin Oncol. - Extracellular vesicles in cancer - implications for future improvements in cancer care

  • 2018 NEJM - Circulating Extracellular Vesicles in Human Disease (翻译版)

  • 2018 NEJM - Application of Cell-free DNA Analysis to Cancer Treatment (翻译版)

  • 2018 NEJM - Sequencing of circulating cell-free dna during pregnancy (翻译版)

PDFs

II. Research in Liquid Biopsy

1. Representative Studies

Comparison of different liquid biopsy tech. : Comparison Table

  • cfDNA - Fragment Size

    • 2019 Nature - Genome-wide cell-free DNA fragmentation in patients with cancer

  • ctDNA - Mutations+

    • 2020 - Nature Med. - Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

    • 2020 Nature - Integrating genomic features for noninvasive early lung cancer detection

    • 2020 Science - ctDNA+PET-CT - Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention

    • 2018 Science - ctDNA+Protein(CancerSEEK) - Detection and localization of surgically resectable cancers with a multi-analyte blood test

  • ctDNA - Methylation

    • 2020 Analysis of Oncology - Grail and CCGA Consortium - Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

    • 2018 Nature - Sensitive tumour detection and classification using plasma cell-free DNA methylomes

  • cfRNA/exRNA

    • Exosome Composition (ERCC): 2019 Cell - Reassessment of Exosome Composition

    • cfRNA: 2018 Science - Noninvasive blood tests for fetal development predict gestational age and preterm delivery

    • Platelet RNA: 2015 Cancer Cell - RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics

  • Proteomics

    • Exosomic proteins: 2020 Cell - Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers

  • PDFs of cfDNA/ctDNA

  • PDFs of cfRNA/exRNA

  • PDFs of Proteomics

2. exRNA/cfRNA

  • MISC

    • mRNA/lncRNA fragments: 2019 EMBO J. - Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

    • exRNA Components: 2017 Nature Communication - Coding and noncoding landscape of extracellular RNA

  • Lu Z.J. Lab

    • structured ncRNA domain (small cfRNA-seq): 2019 Clinical chemistry - Noncoding RNAs serve as diagnosis and prognosis biomarkers for hepatocellular carcinoma

    • lncRNA: 2017 Nature Communications - Recurrently deregulated lncRNAs in hepatocellular carcinoma.

    • Prospective Review: 2017 Noncoding RNA - RNA Biomarkers: Frontier of Precision Medicine for Cancer

  • Fudan Group (Shenglin Huang Lab + Peng Wang Lab)

    • long evRNA-seq: 2020 GUT Plasma extracellular vesicle long RNA profiling identifies a diagnostic signature for the detection of pancreatic ductal adenocarcinoma

    • long evRNA-seq: 2019 Clinical Chemistry - Extracellular Vesicles Long RNA Sequencing Reveals Abundant mRNA, circRNA, and lncRNA in Human Blood as Potential Biomarkers for Cancer Diagnosis

    • exoRBase: 2018 NAR - exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes

  • Zhong S. Lab

    • cfRNA: 2020 Current Biology - Presymptomatic increase of an extracellular RNA in blood plasma is associated with the development of Alzheimer’s disease

    • SILVER-seq: 2019 PNAS - Extracellular RNA in a single droplet of human serum reflects physiologic and disease states

  • Quake S. Lab

    • long cfRNA-seq: 2018 Science - Noninvasive blood tests for fetal development predict gestational age and preterm delivery

    • long cfRNA-seq: 2017 Clinical chemistry - Simultaneously Monitoring Immune Response and Microbial Infections during Pregnancy through Plasma cfRNA Sequencing

  • Wurdinger T. :

    • Platelet RNA: 2015 Cancer Cell - RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics

    • Platelet RNA: 2017 Cancer Cell - Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets

  • Fan J. Lab

    • miRNA7: 2011 JCO - Jia Fan - Plasma MicroRNA Panel to Diagnose Hepatitis B Virus–Related Hepatocellular Carcinoma

  • ERCC (2019 Cell papers)

    • exceRpt: Cell system 2019 - exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling

    • Extracellular carriers: Cell minireview 2019 - Mapping Extracellular RNA Sheds Lights on Distinct Carriers

    • ERCC perspective: Cell perspective 2019 - The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research

    • Exosome preview: Cell preview 2019 - Explicating Exosomes: Reclassifying the Rising Stars of Intercellular Communication

    • Exosome composition: Cell article 2019 - Reassessment of Exosome Composition

    • exRNA carriers: Cell resource 2019 - exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

    • Small exRNA-seq: Cell resource 2019 - Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

    • Exosome PD-L1: Cell article 2019 - Suppression of Exosomal PD-L1 Induces Systemic Anti-tumor Immunity and Memory

  • PDFs of exRNA/cfRNA papers

3. ctDNA/cfDNA

  • cfDNA - mbDNA (Microbiome of cfDNA)

    • 2020 Nature - Microbiome analyses of blood and tissues suggest cancer diagnostic approach

  • cfDNA - Fragment-Size

    • 2019 Nature - Genome-wide cell-free DNA fragmentation in patients with cancer

  • ctDNA - Mutations+ ( PDFs )

    • Papadopoulos N Lab

      • 2020 Science - ctDNA+PET-CT - Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention

      • 2018 Science - ctDNA+Protein(CancerSEEK) - Detection and localization of surgically resectable cancers with a multi-analyte blood test

    • 2020 Nature - Integrating genomic features for noninvasive early lung cancer detection

    • 2019 Nature Medicine - Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

  • ctDNA - Methylation ( PDF )

    • 2020 Analysis of Oncology - Grail and CCGA Consortium - Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

    • chips: 2018 Nature - DNA methylation-based classification of central nervous system tumours

    • meDIP: 2018 Nature - Sensitive tumour detection and classification using plasma cell-free DNA methylomes

    • WGBS: 2017 Nature Genetics - Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA

  • PDFs of ctDNA/cfDNA papers

III. exRNA-seq Technologies

1. Protocols & Technologies

  • Comparison: RNA biology 2018 - Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

  • Barcode: Nature Methods 2015 - Simultaneous generation of many RNA-seq libraries in a single reaction

  • UMI: Nature Methods 2012 - Counting absolute numbers of molecules using unique molecular identifiers, Nature Methods 2014 - Quantitative single-cell RNA-seq with unique molecular identifiers

  • SMART-seq2(TSO): Nature Protocol 2014 - Full length RNA-seq from single cells using Smart-seq2

  • Pico-seq:

    • DASH/CRISPR: Genome Biology 2016 - Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

    • Pico Patent: Pico Patent Application Publication

  • SILVER-seq: 2019 PNAS - Extracellular RNA in a single droplet of human serum reflects physiologic and disease states

PDFs

2. Commercial Kit

  • V1-NEB: E7300-NEB small RNA kit

  • V2-SMART: SMARTer smRNA-Seq Kit for Illumina User Manual

  • V2-SMART: SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual

  • V3-Pico: Long cfRNA-seq Kit

    • Clontech technology-low input RNA library kit

    • Clontech technology-pico kit

PDFs

IV. Biomarker Panel Studies

PDFs

1. Meta-analysis

  • protein markers: 2016 Lancet Neurol - CSF and blood biomarkers for the diagnosis of Alzheimer's disease- a systematic review and meta-analysis

  • DNA markers: 2014 Nat Genetics - Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk

  • lncRNA markers: 2005 Cancer Res. - Identification of GATA3 as a Breast Cancer Prognostic Marker by Global Gene Expression Meta-analysis

2. Detection and Diagnosis

  • ctDNA+Protein (CancerSEEK): 2018 - Science - Detection and localization of surgically resectable cancers with a multi-analyte blood test

  • ctDNA+Protein+Clinical Info: 2019 - PNAS - Detection of early-stage hepatocellular carcinoma in asymptomatic HBsAg-seropositive individuals by liquid biopsy

3. Prognosis

  • Progosis ctDNA: 2019 JCO - Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

  • Prognosis ctDNA: 2019 JAMA Oncology - Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

  • Prognosis ctDNA: 2019 Translational Med. - Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer

  • Prognosis ctDNA:2019 JAMA Oncology - Circulating Tumor DNA Analyses as Markers of Recurrence Risk and Benefit of Adjuvant Therapy for Stage III Colon Cancer

  • Liquid vs. tissue biopsy: 2019 Nature Medicine - Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers