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cfRNA-seq & cfDNA-seq Tech.

See other topics of cfRNA in cfRNA Studies

I. cfRNA-seq Protocols & Technologies

  • 2022 Clin. Transl. Med. - Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids
  • ✅ Purification: 2021 bioRxiv - Performance of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study
  • ✅ Storage & Transportation: 2021 Nature Commn. - Grail - A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection
  • 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
  • Multiplex: Nature Methods 2019 - Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
  • 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

II. cfRNA and EV Purification Method

1. Exosome and EV

  • 2022 bioRxiv - Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles
  • RNP: 2021 Nature Cell Biol. - Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets
  • 2021 Nature Methods - Exosome detection via the ultrafast-isolation system: EXODUS
  • ✨ 2021 JEV - Comprehensive evaluation of methods for small extracellular vesicles separation from human plasma, urine and cell culture medium
  • Extracellular carriers: Cell minireview 2019 - Mapping Extracellular RNA Sheds Lights on Distinct Carriers
  • 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
  • Exosome PD-L1: Cell article 2019 - Suppression of Exosomal PD-L1 Induces Systemic Anti-tumor Immunity and Memory

2. EV and RNP Purification Method

  • 2022 JEV - Tetraspanins distinguish separate extracellular vesicle subpopulations in human serum and plasma – Contributions of platelet extracellular vesicles in plasma samples
  • SEC: 2020 Molecular Therapy - Simple and Fast SEC-Based Protocol to Isolate Human Plasma-Derived Extracellular Vesicles for Transcriptional Research
  • MV+sEV+RNP: 2017 Nature Communication - Coding and noncoding landscape of extracellular RNA

III. cfRNA 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
  • ✅ [Smart-seq3]2020 Nature Biotech -Single-cell RNA counting at allele and isoform resolution using Smart-seq3
  • [UMI]2012 Nature Methods -Counting absolute numbers of molecules using unique molecular identifiers
  • [Barcode]2015 Nature Methods -Simultaneous generation of many rna-seq libraries in a single reaction
  • ✅ [DASH]2016 Genome Biology -Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications
  • [Phospho‐seq]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
  • [SILVER‐seq]2019 PNAS -Extracellular RNA in a single droplet of human serum reflects physiologic and disease states
  • [CATS‐seq]2014 RNA Biology -Capture and Amplification by Tailing and Switching (CATS)
  • [Pico-similar]2013 RNA Biology -Peregrine - A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material
  • [Review]2018 NAR -Capturing the ‘ome’: the expanding molecular toolbox for RNA and DNA library construction

V. cfDNA Tech.

Nanopore

  • 2021 Mol. Cancer - Nanopore sequencing from liquid biopsy analysis of copy number variations from cell-free DNA of lung cancer patients

VI. cfDNA Methylation Tech.

  • TAPS
  • 2022 NAR - Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology
  • ✨[cfTAPS] 2021 Science Advances - Cell-free DNA TAPS provides multimodal information for early cancer detection
  • ✨[TAPS] 2019 Nature Biotech. - Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution
  • MeDIP
  • 2022 NCOMMN. - The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors
  • 2020 Nat Medicine - Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes
  • ✨[cfMeDIP] 2019 Nature Protocol - Preparation of cfMeDIP-seq libraries for methylome
  • ✨[cfMeDIP] 2018 Nature - Sensitive tumour detection and classification using plasma cell-free DNA methylomes
  • BS
  • 2022 Nature Cancer - cfDNA methylome profiling for detection and subtyping of small cell lung cancers
  • 2021 Nature Biomedical Engineering - Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning
  • ✨ [Targeted BS] 2021 Annals of Oncology - Grail and CCGA Consortium - Clinical validation of a targeted methylation-based multi-cancer early detection test using an independent validation set
  • ✨ [Targeted BS] 2020 Annals 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
  • [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
  • [WGBS] 2013 PNAS - Noninvasive detection of cancer-associated genome- wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing
  • 5Hmc
  • 2019 Gut - Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma
  • 2019 Blood Adv - Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma
  • 2017 Cell Res - 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers
  • Nanopore
  • 2022 Genome Biology - Detecting cell‐of‐origin and cancer‐specific methylation features of cell‐free DNA from Nanopore sequencing

1. More reading on cfDNAmet-seq

  • 2020 Sci Adv - Reliable tumor detection by whole-genome methylation sequencing of cell-free DNA in cerebrospinal fluid of pediatric medulloblastoma.
  • 2019 Clin Chem - Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing
  • 2017 Genomic Medicine - Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans.
  • 2015 Cell Res - Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients
  • 2014 Clin Epigenetics - Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma.

2. Validation of DNAmet

  • [mqMSP] 2021 PNAS - Efficient detection and post-surgical monitoring of colon cancer with a multi-marker DNA methylation liquid biopsy
  • [qMSP]2019 Clin Epigenetics - Promoter methylation of ADAMTS1 and BNC1 as potential biomarkers for early detection of pancreatic cancer in blood
  • [MSRE] 2016 Clin Epigenetics - Detection and monitoring of hypermethylated RASSF1A in serum from patients with metastatic breast cancer
  • [qMSP] 2019 Theranostics - Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA