AIMC Topic: DNA Copy Number Variations

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Discovering the gene-brain-behavior link in autism via generative machine learning.

Science advances Jun 12, 2024
Autism is traditionally diagnosed behaviorally but has a strong genetic basis. A genetics-first approach could transform understanding and treatment of autism. However, isolating the gene-brain-behavior relationship from confounding sources of variab...
Adult Male Adolescent Machine Learning Brain Female DNA Copy Number Variations Autistic Disorder Endophenotypes Chromosomes, Human, Pair 16 Child Genetic Predisposition to Disease Humans Magnetic Resonance Imaging
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Development and validation of a reliable DNA copy-number-based machine learning algorithm (CopyClust) for breast cancer integrative cluster classification.

Scientific reports May 24, 2024
The Integrative Cluster subtypes (IntClusts) provide a framework for the classification of breast cancer tumors into 10 distinct groups based on copy number and gene expression, each with unique biological drivers of disease and clinical prognoses. G...
DNA Copy Number Variations Machine Learning Algorithms Female Breast Neoplasms Gene Expression Profiling Cluster Analysis Humans
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Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment.

PLoS computational biology May 10, 2024
The heterogeneity of Hepatocellular Carcinoma (HCC) poses a barrier to effective treatment. Stratifying highly heterogeneous HCC into molecular subtypes with similar features is crucial for personalized anti-tumor therapies. Although driver genes pla...
Algorithms Precision Medicine Prognosis Humans Machine Learning Carcinoma, Hepatocellular Genomics Computational Biology Multiomics Biomarkers, Tumor Gene Expression Profiling Liver Neoplasms Gene Expression Regulation, Neoplastic DNA Copy Number Variations Mutation
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Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning.

BMC bioinformatics May 9, 2024
BACKGROUND: The prediction of drug sensitivity plays a crucial role in improving the therapeutic effect of drugs. However, testing the effectiveness of drugs is challenging due to the complex mechanism of drug reactions and the lack of interpretabili...
Antineoplastic Agents Humans Deep Learning Computational Biology Neural Networks, Computer Cell Line, Tumor DNA Copy Number Variations Neoplasms
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GlioPredictor: a deep learning model for identification of high-risk adult IDH-mutant glioma towards adjuvant treatment planning.

Scientific reports Jan 25, 2024
Identification of isocitrate dehydrogenase (IDH)-mutant glioma patients at high risk of early progression is critical for radiotherapy treatment planning. Currently tools to stratify risk of early progression are lacking. We sought to identify a comb...
Deep Learning Glioma DNA Copy Number Variations Adjuvants, Immunologic Adjuvants, Pharmaceutic ErbB Receptors Humans Adult Isocitrate Dehydrogenase Cyclin-Dependent Kinase Inhibitor Proteins
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Integrating Machine Learning and Mendelian Randomization Determined a Functional Neurotrophin-Related Gene Signature in Patients with Lower-Grade Glioma.

Molecular biotechnology Jan 23, 2024
Recent researches reported that neurotrophins can promote glioma growth/invasion but the relevant model for predicting patients' survival in Lower-Grade Gliomas (LGGs) lacked. In this study, we adopted univariate Cox analysis, LASSO regression, and m...
Nerve Growth Factors Sulfotransferases Neoplasm Grading Proportional Hazards Models Homeodomain Proteins Brain Neoplasms Male Polymorphism, Single Nucleotide DNA Copy Number Variations Mendelian Randomization Analysis Gene Expression Regulation, Neoplastic Machine Learning Glioma Prognosis Female Humans
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Deep learning-based multiomics integration model for predicting axillary lymph node metastasis in breast cancer.

Future oncology (London, England) Jul 25, 2023
To develop a deep learning-based multiomics integration model. Five types of omics data (mRNA, DNA methylation, miRNA, copy number variation and protein expression) were used to build a deep learning-based multiomics integration model a deep neura...
Breast Neoplasms Lymph Nodes Humans Deep Learning Lymphatic Metastasis Female Multiomics DNA Copy Number Variations
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DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants.

PLoS computational biology Jul 24, 2023
The genetic etiology of brain disorders is highly heterogeneous, characterized by abnormalities in the development of the central nervous system that lead to diminished physical or intellectual capabilities. The process of determining which gene driv...
Brain Autistic Disorder Mice Animals Genetic Predisposition to Disease Deep Learning DNA Copy Number Variations
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Biologically Interpretable Deep Learning To Predict Response to Immunotherapy In Advanced Melanoma Using Mutations and Copy Number Variations.

Journal of immunotherapy (Hagerstown, Md. : 1997) May 24, 2023
Only 30-40% of advanced melanoma patients respond effectively to immunotherapy in clinical practice, so it is necessary to accurately identify the response of patients to immunotherapy pre-clinically. Here, we develop KP-NET, a deep learning model th...
Mutation Humans Melanoma Deep Learning B7-H1 Antigen Immunotherapy DNA Copy Number Variations
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Deep learning and multi-omics approach to predict drug responses in cancer.

BMC bioinformatics Nov 28, 2022
BACKGROUND: Cancers are genetically heterogeneous, so anticancer drugs show varying degrees of effectiveness on patients due to their differing genetic profiles. Knowing patient's responses to numerous cancer drugs are needed for personalized treatme...
Genomics Humans DNA Copy Number Variations Neoplasms Mutation Deep Learning
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