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DNA Copy Number Variations

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Etiological stratification and prognostic assessment of haemophagocytic lymphohistiocytosis by machine learning on onco-mNGS data and clinical data.

Frontiers in immunology
INTRODUCTION: Hemophagocytic lymphohistiocytosis (HLH) is a rare, complicated and life threatening hyperinflammatory syndrome that maybe triggered by various infectious agents, malignancies and rheumatologic disorders. Early diagnosis and identificat...

TransCell: In Silico Characterization of Genomic Landscape and Cellular Responses by Deep Transfer Learning.

Genomics, proteomics & bioinformatics
Gene expression profiling of new or modified cell lines becomes routine today; however, obtaining comprehensive molecular characterization and cellular responses for a variety of cell lines, including those derived from underrepresented groups, is no...

CNVoyant a machine learning framework for accurate and explainable copy number variant classification.

Scientific reports
The precise classification of copy number variants (CNVs) presents a significant challenge in genomic medicine, primarily due to the complex nature of CNVs and their diverse impact on rare genetic diseases (RGDs). This complexity is compounded by the...

MMGCN: Multi-modal multi-view graph convolutional networks for cancer prognosis prediction.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: Accurate prognosis prediction for cancer patients plays a significant role in the formulation of treatment strategies, considerably impacting personalized medicine. Recent advancements in this field indicate that integrating...

Low-pass whole genome sequencing of circulating tumor cells to evaluate chromosomal instability in triple-negative breast cancer.

Scientific reports
Chromosomal Instability (CIN) is a common and evolving feature in breast cancer. Large-scale Transitions (LSTs), defined as chromosomal breakages leading to gains or losses of at least 10 Mb, have recently emerged as a metric of CIN due to their stan...

Multiomics integration and machine learning reveal prognostic programmed cell death signatures in gastric cancer.

Scientific reports
Gastric cancer (GC) is characterized by notable heterogeneity and the impact of molecular subtypes on treatment and prognosis. The role of programmed cell death (PCD) in cellular processes is critical, yet its specific function in GC is underexplored...

Optimizing sequence data analysis using convolution neural network for the prediction of CNV bait positions.

BMC bioinformatics
BACKGROUND: Accurate prediction of copy number variations (CNVs) from targeted capture next-generation sequencing (NGS) data relies on effective normalization of read coverage profiles. The normalization process is particularly challenging due to hid...

Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis.

The Journal of pathology
Tumour content plays a pivotal role in directing the bioinformatic analysis of molecular profiles such as copy number variation (CNV). In clinical application, tumour purity estimation (TPE) is achieved either through visual pathological review [conv...

Building a Risk Scoring Model for ARDS in Lung Adenocarcinoma Patients Using Machine Learning Algorithms.

Journal of cellular and molecular medicine
Lung adenocarcinoma (LUAD), the predominant form of non-small-cell lung cancer, is frequently complicated by acute respiratory distress syndrome (ARDS), which increases mortality risks. Investigating the prognostic implications of ARDS-related genes ...