Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet. 2019;20:71–88.

Article  CAS  PubMed  Google Scholar 

Ignatiadis M, Sledge GW, Jeffrey SS. Liquid biopsy enters the clinic — implementation issues and future challenges. Nat Rev Clin Oncol. 2021;18:297–312.

Article  PubMed  Google Scholar 

Chen Z, Yam JWP. Recent advances in liquid biopsy in cancers: Diagnosis, disease state and treatment response monitoring. Clin Transl Discov. 2022;2: e111.

Article  Google Scholar 

Nikanjam M, Kato S, Kurzrock R. Liquid biopsy: current technology and clinical applications. J Hematol OncolJ Hematol Oncol. 2022;15:131.

Article  CAS  Google Scholar 

Cabús L, Lagarde J, Curado J, Lizano E, Pérez-Boza J. Current challenges and best practices for cell-free long RNA biomarker discovery. Biomark Res. 2022;10:62.

Article  PubMed  PubMed Central  Google Scholar 

Vorperian SK, Moufarrej MN, Quake SR. Cell types of origin of the cell-free transcriptome. Nat Biotechnol. 2022;:1–7.

Koh W, Pan W, Gawad C, Fan HC, Kerchner GA, Wyss-Coray T, et al. Noninvasive in vivo monitoring of tissue-specific global gene expression in humans. Proc Natl Acad Sci. 2014;111:7361–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zaporozhchenko IA, Ponomaryova AA, Rykova EY, Laktionov PP. The potential of circulating cell-free RNA as a cancer biomarker: challenges and opportunities. Expert Rev Mol Diagn. 2018;18:133–45.

Avila Cobos F, Alquicira-Hernandez J, Powell JE, Mestdagh P, De Preter K. Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nat Commun. 2020;11:5650.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jaakkola MK, Elo LL. Computational deconvolution to estimate cell type-specific gene expression from bulk data. NAR Genomics Bioinforma. 2021;3:lqaa110.

Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet. 2023;39:285–307.

Article  CAS  PubMed  Google Scholar 

Wang H, Zhan Q, Guo H, Zhao J, Xing S, Chen S, et al. Depletion-assisted multiplexing cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicle. bioRxiv;:2023.01.31.526408.

Metzenmacher M, Váraljai R, Hegedüs B, Cima I, Forster J, Schramm A, et al. Plasma next generation sequencing and droplet digital-qPCR-based quantification of circulating cell-free RNA for noninvasive early detection of cancer. Cancers. 2020;12:353.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin N, Kan C-M, Pei XM, Cheung WL, Ng SSM, Wong HT, et al. Cell-free circulating tumor RNAs in plasma as the potential prognostic biomarkers in colorectal cancer. Front Oncol. 2023;13.

Tosevska A, Morselli M, Basak SK, Avila L, Mehta P, Wang MB, et al. Cell-free RNA as a novel biomarker for response to therapy in head & neck cancer. Front Oncol. 2022;12.

Villanueva A. Hepatocellular carcinoma. N Engl J Med. 2019;380:1450–62.

Article  CAS  PubMed  Google Scholar 

Rumgay H, Arnold M, Ferlay J, Lesi O, Cabasag CJ, Vignat J, et al. Global burden of primary liver cancer in 2020 and predictions to 2040. J Hepatol. 2022;77:1598–606.

Article  PubMed  PubMed Central  Google Scholar 

Patel N, Yopp AC, Singal AG. Diagnostic delays are common among patients with hepatocellular carcinoma. J Natl Compr Cancer Netw JNCCN. 2015;13:543–9.

Article  PubMed  Google Scholar 

Wang W, Wei C. Advances in the early diagnosis of hepatocellular carcinoma. Genes Dis. 2020;7:308–19.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang J, Chen G, Zhang P, Zhang J, Li X, Gan D, et al. The threshold of alpha-fetoprotein (AFP) for the diagnosis of hepatocellular carcinoma: A systematic review and meta-analysis. PLoS ONE. 2020;15: e0228857.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang T, Zhang K-H. New blood biomarkers for the diagnosis of AFP-negative hepatocellular carcinoma. Front Oncol. 2020;10.

Yang J-C, Hu J-J, Li Y-X, Luo W, Liu J-Z, Ye D-W. Clinical applications of liquid biopsy in hepatocellular carcinoma. Front Oncol. 2022;12.

Block T, Zezulinski D, Kaplan DE, Lu J, Zanine S, Zhan T, et al. Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma. Front Oncol. 2022;12.

Roskams-Hieter B, Kim HJ, Anur P, Wagner JT, Callahan R, Spiliotopoulos E, et al. Plasma cell-free RNA profiling distinguishes cancers from pre-malignant conditions in solid and hematologic malignancies. Npj Precis Oncol. 2022;6:28.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen S, Jin Y, Wang S, Xing S, Wu Y, Tao Y, et al. Cancer type classification using plasma cell-free RNAs derived from human and microbes. eLife. 2022;11:e75181.

Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, et al. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics. 2021;11:181–93.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen VL, Xu D, Wicha MS, Lok AS, Parikh ND. Utility of liquid biopsy analysis in detection of hepatocellular carcinoma, determination of prognosis, and disease monitoring: a systematic review. Clin Gastroenterol Hepatol. 2020;18:2879-2902.e9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

von Felden J, Garcia-Lezana T, Schulze K, Losic B, Villanueva A. Liquid biopsy in the clinical management of hepatocellular carcinoma. Gut. 2020;69:2025–34.

Article  Google Scholar 

Foda ZH, Annapragada AV, Boyapati K, Bruhm DC, Vulpescu NA, Medina JE, et al. Detecting liver cancer using cell-free DNA fragmentomes. Cancer Discov. 2023;13:616–31.

Article  CAS  PubMed  Google Scholar 

Kim SS, Baek GO, Son JA, Ahn HR, Yoon MK, Cho HJ, et al. Early detection of hepatocellular carcinoma via liquid biopsy: panel of small extracellular vesicle-derived long noncoding RNAs identified as markers. Mol Oncol. 2021;15:2715–31.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ibarra A, Zhuang J, Zhao Y, Salathia NS, Huang V, Acosta AD, et al. Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing. Nat Commun. 2020;11:400.

Article  CAS  PubMed  PubMed Central  Google Scholar 

SRA Toolkit Development Team. NCBI SRA-Toolkit.

Bushnell B. BBMap. https://sourceforge.net/projects/bbmap/.

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.

Article  CAS  PubMed  Google Scholar 

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.

Article  CAS  PubMed  Google Scholar 

R Core Team. R: A language and environment for statistical computing. 2021.

Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics. 2005;21:3439–40.

Article  CAS  PubMed  Google Scholar 

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28:882–3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.

Article  PubMed  PubMed Central  Google Scholar 

Hadley W. ggplot2: elegant graphics for data analysis. New York: Springer; 2016.

Google Scholar 

MacParland SA, Liu JC, Ma X-Z, Innes BT, Bartczak AM, Gage BK, et al. Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations. Nat Commun. 2018;9:4383.

Article  PubMed  PubMed Central  Google Scholar 

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015;12:115–21.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kassambara A. rstatix: Pipe-friendly framework for basic statistical tests. manual. 2023.

Kassambara A. ggpubr: “ggplot2” based publication ready plots. manual. 2023.

Kuhn M. Building predictive models in R using the caret package. J Stat Softw. 2008;28:1–26.

Article  Google Scholar 

Olsen LR, Zachariae HB. cvms: Cross-validation for model selection. manual. 2023.

Liaw A, Wiener M. Classification and regression by randomForest. R News. 2002;2:18–22.

Google Scholar 

Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12:77.

Article  PubMed  PubMed Central  Google Scholar 

Friedman JH, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33:1–22.

Article  PubMed  PubMed Central  Google Scholar 

Sachs MC. plotROC: A tool for plotting ROC curves. J Stat Softw. 2017;79:1–19.

Article  Google Scholar 

Stevenson M, Nunes ES with contributions from T, Heuer C, Marshall J, Sanchez J, Thornton R, et al. epiR: Tools for the analysis of epidemiological data. manual. 2023.

Jew B, Alvarez M, Rahmani E, Miao Z, Ko A, Garske KM, et al. Accurate estimation of cell composition in bulk expression through robust integration of single-cell information. Nat Commun. 2020;11:1971.

Article  CAS