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cfRNA-seq Analysis

See other topics of cfRNA in cfRNA Studies

✅ or ✨ : recommended readings

0. Data Pre-process

  • [Pipeline of long and small cfRNA-seq] exSEEK Tutorial @ gitbook
  • [Pipeline of small cfRNA-seq] 2019 Cell Sys. - exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling
  • [Data Matrix of Multiple Variances] see more in RNA POSTAR Analysis about calculating features like editing, splicing, APA, chimeric RNA, etc
  • Learn from cfDNA features

I. RNA Code & Cell-of-Origin

I.1 RNA code: Motif and Structure

Background/Introduction

  • ✅ 2024 Cell Genomics - Revealing the grammar of small RNA secretion
  • ✅ 2023 PNAS - Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs
  • ✅ [miRNA motif/code] 2021 Nature - MicroRNA sequence codes for small extracellular vesicle release and cellular retention
  • G-quadruplex - 2020 Genome biology - RNA G-quadruplex structures exist and function in vivo in plants
  • G-quadruplex - 2016 Science - RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria

I.2 Deconvolution & Localization

  • 2025 Nature Biotechnology - Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples
  • ✅ [Deconvolution]: 2022 Nature Biotech. - Cell types of origin of the cell-free transcriptome
  • 2021 Nature Biotech. - ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin
  • 2017Genome Biology - CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA

II. cfRNA fragmentation

  • ✅2025 Genome Biology - Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential
  • Peak calling: 2022 Genome Biology - GoPeaks: histone modification peak calling for CUT\&Tag
  • 2021 PNAS - Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology
  • 2021 NAR - Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms
  • sRNA cluster: 2021 Gut - Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer
  • 2020 Mol. Cancer - Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer
  • Fragmented ribosomes: 2020 NAR - Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome
  • ✅ mRNA frag. : 2020 elife - Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling
  • tsRNA: 2019 Molecular Cancer - Exosomal tRNA-derived small RNA as a promising biomarker for cancer diagnosis
  • mRNA/lncRNA frag.: 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
  • srpRNA domain (RNA7SL1): 2019 Clinical Chem. - Noncoding RNAs serve as diagnosis and prognosis biomarkers for hepatocellular carcinoma

III. Feature Selection

III.1. Signature Genes

  • ✅ [TmS: total mRNA expression] 2022Nature Biotech. - Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression
  • ✅ 2021 Nature Biotech. - Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID
  • 2021 Nature Machine Intelligence - Integration of multiomics data with graph convolutional networks to identify new cancer genes and their associated molecular mechanisms
  • 2021 Genome Res. - NS-Forest: A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing
  • 2019 Briefings in Bioinformatics - A comprehensive evaluation of connectivity methods for L1000 data Briefings in Bioinformatics

III.2. Network Approach

  • 2022Nature Commn. - Network-based machine learning approach to predict immunotherapy response in cancer patients
  • ✅ [P-Net] 2021 Nature - Biologically informed deep neural network for prostate cancer discovery
  • 2021 Nature Computational Science - Modeling gene regulatory networks using neural network architectures
  • 2021Cell - A modular master regulator landscape controls cancer transcriptional identity
  • 2020 Bioinformatics - Varmole: A biologically drop-connect deep neural network model for prioritizing disease risk variants and genes
  • 2017Nature Methods- SCENIC: single-cell regulatory network inference and clustering
  • 2018Nature COMMN.- Pathway based subnetworks enable cross-disease biomarker discovery

IV. Data Clean - normalization, batch correction, etc

Issues for single-cell and cell-free RNA-seq data

  • (1) Dropout/Sparseness and Imputation
  • (2) Heterogeneity and Normalization
  • (3) Batch effect and Confounder
  • (Pseudo-time and Others)

Tutorial

  • ✅ Review: 2021Nature Biotech. - Computational principles and challenges in single-cell data integration
  • 2019Nature Methods - A discriminative learning approach to differential expression analysis for single-cell RNA-seq
  • ✅ 2018Nature Biotech. - Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
  • MNN: 2017Nature Biotech. - Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
  • ✅ Review: 2017Nature Methods - Normalizing single-cell RNA sequencing data: challenges and opportunities

V. Classification Models

Pre-training and Transfer Learning

  • ✅ 2023 Nature Methods - SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes
  • 2022 BIB - A universal approach for integrating super large-scale single-cell transcriptomes by exploring gene rankings
  • 2022 bioRxiv - Generative pretraining from large-scale transcriptomes: Implications for single-cell deciphering and clinical translation
  • ✅ 2021 bioRxiv - scBERT: a Large-scale Pretrained Deep Langurage Model for Cell Type Annotation of Single-cell RNA-seq Data