AIMC Topic: Circulating Tumor DNA

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A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.

BMC cancer
BACKGROUND: Cell-free DNA's (cfDNA) use as a biomarker in cancer is challenging due to genetic heterogeneity of malignancies and rarity of tumor-derived molecules. Here we describe and demonstrate a novel machine-learning guided panel design strategy...

Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA.

BMC cancer
BACKGROUND: Blood-based methods using cell-free DNA (cfDNA) are under development as an alternative to existing screening tests. However, early-stage detection of cancer using tumor-derived cfDNA has proven challenging because of the small proportion...

Predicting high confidence ctDNA somatic variants with ensemble machine learning models.

Scientific reports
Circulating tumour DNA (ctDNA) is a minimally invasive cancer biomarker that can be used to inform treatment of cancer patients. The utility of ctDNA as a cancer biomarker depends on the ability to accurately detect somatic variants associated with c...

Personalized surveillance in colorectal cancer: Integrating circulating tumor DNA and artificial intelligence into post-treatment follow-up.

World journal of gastroenterology
Given the growing burden of colorectal cancer (CRC) as a global health challenge, it becomes imperative to focus on strategies that can mitigate its impact. Post-treatment surveillance has emerged as essential for early detection of recurrence, signi...

Improving Prediction of Survival and Progression in Metastatic Non-Small Cell Lung Cancer After Immunotherapy Through Machine Learning of Circulating Tumor DNA.

JCO precision oncology
PURPOSE: To use modern machine learning approaches to enhance and automate the feature extraction from the longitudinal circulating tumor DNA (ctDNA) data and to improve the prediction of survival and disease progression, risk stratification, and tre...

Role of Machine Learning in Liquid Biopsy of Brain Tumours.

JPMA. The Journal of the Pakistan Medical Association
Liquid biopsy has multiple benefits and is used extensively in other fields of oncology, but its role in neuro-oncology has been limited so far. Multiple tumour-derived materials like circulating tumour cells (CTCs), tumour-educated platelets (TEPs),...

Unlocking Early Cancer Detection: Leveraging Machine Learning in Cell-Free DNA Analysis for Precision Oncology.

AMIA ... Annual Symposium proceedings. AMIA Symposium
This study introduces a groundbreaking approach to early cancer detection through the analysis of cell-free DNA (cfDNA), utilizing machine learning algorithms to navigate the complexities of low circulating tumor DNA (ctDNA) fractions and genetic het...

MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data.

Briefings in bioinformatics
MOTIVATION: Microsatellite instability (MSI) is a promising biomarker for cancer prognosis and chemosensitivity. Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues a...