AIMC Topic: Cell-Free Nucleic Acids

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Multimodal analysis of cell-free DNA enhances differentiation of early-stage breast cancer from benign lesions and healthy individuals.

BMC biology Aug 20, 2025
BACKGROUND: Breast cancer (BC) remains the second leading cause of cancer-related mortality among women worldwide. Liquid biopsy based on circulating tumor DNA (ctDNA) offers a promising noninvasive approach for early detection; however, differentiat...
Humans Female Middle Aged DNA Methylation Cell-Free Nucleic Acids Early Detection of Cancer Aged Adult Breast Neoplasms Biomarkers, Tumor
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Circulating cell-free RNA signatures for the characterization and diagnosis of myalgic encephalomyelitis/chronic fatigue syndrome.

Proceedings of the National Academy of Sciences of the United States of America Aug 11, 2025
People living with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) experience heterogeneous and debilitating symptoms that lack sufficient biological explanation, compounded by the absence of accurate, noninvasive diagnostic tools. To add...
Case-Control Studies Cell-Free Nucleic Acids Humans Adult Machine Learning Male Fatigue Syndrome, Chronic Middle Aged Biomarkers Female
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Raised Leptin and Pappalysin2 cell-free RNAs are the hallmarks of pregnancies complicated by preeclampsia with fetal growth restriction.

Nature communications Jul 18, 2025
Preeclampsia (PE) and fetal growth restriction (FGR) complicate 5-10% of pregnancies and are major causes of maternal and fetal morbidity and mortality. Here we demonstrate that measuring circulating cell-free RNAs (cfRNAs) from maternal plasma can a...
Humans Machine Learning Biomarkers Pregnancy Pre-Eclampsia ROC Curve Fetal Growth Retardation Cell-Free Nucleic Acids Pregnancy-Associated Plasma Protein-A Female Proteoglycans Adult Leptin Case-Control Studies
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Prediction of Cerebrospinal Fluid (CSF) Pressure with Generative Adversarial Network Synthetic Plasma-CSF Biomarker Pairing.

Neuroinformatics Jul 10, 2025
Non-invasive intracranial pressure (ICP) monitoring can help clinicians safely and efficiently monitor spaceflight-associated neuro-ocular syndrome (SANS), idiopathic intracranial hypertension, and traumatic brain injury in astronauts. Current invasi...
Humans Neural Networks, Computer Biomarkers Cell-Free Nucleic Acids Generative Adversarial Networks Cerebrospinal Fluid Pressure
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Evaluating cell-free DNA integrity index as a non-invasive biomarker for neoadjuvant chemotherapy in colorectal cancer patients.

BMC cancer Jul 8, 2025
BACKGROUND: Neoadjuvant chemotherapy (NAC) is gaining attention as a treatment for advanced colorectal cancer owing to its potential to improve surgical outcomes and prognosis. However, reliable biomarkers to predict the response to NAC are lacking. ...
Cell-Free Nucleic Acids Chemotherapy, Adjuvant Middle Aged Antineoplastic Combined Chemotherapy Protocols Neoadjuvant Therapy Prognosis Retrospective Studies Female Aged Adult Colorectal Neoplasms Biomarkers, Tumor Male Humans Machine Learning
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Inflammation-related 5-hydroxymethylation signatures as markers for clinical presentations of coronary artery disease.

Cardiovascular diabetology Jun 23, 2025
BACKGROUND: Coronary angiography remains the gold standard for diagnosing coronary artery disease (CAD), but its invasive nature limits its applicability for widespread screening. Identifying non-invasive molecular markers could improve CAD classific...
Inflammation Mediators 5-Methylcytosine Predictive Value of Tests ST Elevation Myocardial Infarction Coronary Artery Disease Humans Middle Aged Machine Learning Risk Assessment Female Inflammation Biomarkers Severity of Illness Index Reproducibility of Results DNA Methylation Prognosis Epigenesis, Genetic Aged Cell-Free Nucleic Acids Male Non-ST Elevated Myocardial Infarction
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A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.

Genome biology May 23, 2025
Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from ...
Humans Machine Learning Software Sequence Analysis, DNA Cell-Free Nucleic Acids Whole Genome Sequencing High-Throughput Nucleotide Sequencing
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Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.

mSystems Apr 29, 2025
Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbio...
Colorectal Neoplasms Male Middle Aged Feces Humans Adenoma Female Microbiota Aged Proof of Concept Study Gastrointestinal Microbiome Adult Metagenome Dysbiosis Cell-Free Nucleic Acids
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Exploring the potential of cell-free RNA and Pyramid Scene Parsing Network for early preeclampsia screening.

BMC pregnancy and childbirth Apr 14, 2025
BACKGROUND: Circulating cell-free RNA (cfRNA) is gaining recognition as an effective biomarker for the early detection of preeclampsia (PE). However, the current methods for selecting disease-specific biomarkers are often inefficient and typically on...
Risk Assessment Biomarkers Humans Early Diagnosis Case-Control Studies Pregnancy Neural Networks, Computer Cell-Free Nucleic Acids Algorithms Female Pre-Eclampsia Adult
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Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing.

Communications biology Apr 14, 2025
We had previously reported a convolutional neural network (CNN) based approach, called the holistic kinetic model (HK model 1), for detecting 5-methylcytosine (5mC) by single molecule real-time sequencing (Pacific Biosciences). In this study, we cons...
DNA Methylation Cell-Free Nucleic Acids Humans Adenine Liver Neoplasms Neural Networks, Computer 5-Methylcytosine Carcinoma, Hepatocellular Deep Learning Sequence Analysis, DNA
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