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DNA Copy Number Variations

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Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier.

Breast cancer research : BCR
BACKGROUND: BRCA1-mutated cancers exhibit deficient homologous recombination (HR) DNA repair, resulting in extensive copy number alterations and genome instability. HR deficiency can also arise in tumors without a BRCA1 mutation. Compared with other ...

Machine Learning for Better Prognostic Stratification and Driver Gene Identification Using Somatic Copy Number Variations in Anaplastic Oligodendroglioma.

The oncologist
BACKGROUND: 1p/19q-codeleted anaplastic gliomas have variable clinical behavior. We have recently shown that the common 9p21.3 allelic loss is an independent prognostic factor in this tumor type. The aim of this study is to identify less frequent gen...

Cancer type prediction based on copy number aberration and chromatin 3D structure with convolutional neural networks.

BMC genomics
BACKGROUND: With the developments of DNA sequencing technology, large amounts of sequencing data have been produced that provides unprecedented opportunities for advanced association studies between somatic mutations and cancer types/subtypes which f...

A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants.

IEEE/ACM transactions on computational biology and bioinformatics
Copy number variants (CNVs), including large deletions and duplications, represent an unbalanced change of DNA segments. Abundant in human genomes, CNVs contribute to a large proportion of human genetic diversity, with impact on many human phenotypes...