Precision Medicine

Literature Recommendations

0. News/Patents of Liquid Biopsy

关于液体活检技术的科普

  • 为何投资者对癌症ctDNA液体活检依旧“信心满满,热情高涨” - NBT解析背后原因 ( Wechat link | Nature Biotech. )

  • 开启肿瘤早筛新纪元,液态活检蓄势待发 ( Everhub; Wechat link )

  • 测序中国-2019 聚焦DNA甲基化与癌症早筛专题报告Beta版 ( PDF )

  • Patents: 2019 - Nature Biotech. - Recent patents in cancer detection ( PDF )

I. Reviews of Liquid Biopsy

PDFs

II. Representative Studies of Liquid Biopsy

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

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

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

  • Platelet RNA ( PDFs ):

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

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

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

PDFs

III. Detailed Studies of Liquid Biopsy

1. Biomarker Panel Studies

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1.1 Meta-analysis Studies

  • 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

1.2 Detection and Early 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

1.3 Prognosis Studies

  • 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

2. exRNA/cfRNA Studies

2.1 Representative papers

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

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

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

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

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

PDFs

2.2 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

3. exRNA-seq Technologies

3.1 Comparison of differnt liquid biopsy tech.

3.2 exRNA-seq 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

3.3 Commercial exRNA-seq library construction kit manual

  • 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

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4. ctDNA

4.1 ctDNA Mutations/Fragments

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

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4.2 cfDNA Methylation

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

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

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

PDFs

IV. Cancer Immunology

  • 2019 - Nat Genetics - Landscape of B cell immunity and related immune evasion in human cancers. PubMed PMID: 30742113

  • 2018 - Nat Biotech - Evaluation of immune repertoire inference methods from RNA-seq data. PubMed PMID: 30412202

  • 2017 - Nat Genetics - Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA-seq data.

  • 2016 - Nature Genetics - Landscape of tumor-infiltrating T cell repertoire of human cancers

  • 2018 - JCO - Immune checkpoint molecule expression measured using circulating cell-free RNA isolated from the blood of metastatic prostate cancer patients.