We discriminated three breast tumor subtypes based on genomic DNA copy number alterations.
These data have been used to identify clinically meaningful subtypes based on genomic and transcriptomic [ 9- 16] or epigenomic profiles [ 17, 18].
We establish a framework for genomic classification into one of four subtypes based on the pattern of the most prevalent significantly mutated genes: mutant BRAF, mutant RAS, mutant NF1, and Triple-WT (wild-type).
Therefore inference of the NA and HA subtypes based on the genomic prints, limited to 'core' genes, should be done with great caution.
HCV has been classified into six genotypes and a large number of subtypes based on their genomic sequences [15], [16], [17].
Influenza A viruses are enveloped RNA viruses in the family Orthomyxoviridae possessing eight negative-sense genomic segments and are classified into subtypes based on their two surface glycoproteins, the hemagglutinin (HA) and neuraminidase (NA).
The fast development of SNP array has made it possible to characterize tumor subtypes based on the genomic DNA copy number, nonetheless, the computational and statistical methods in this area is still under-developed.
Medulloblastoma (MB) is the most common malignant primary pediatric brain tumor and is currently divided into four subtypes based on different genomic alterations, gene expression profiles and response to treatment: WNT, Sonic Hedgehog (SHH), Group 3 and Group 4. This extensive heterogeneity has made it difficult to assess the functional relevance of genes to malignant progression.
We provide a bioinformatics framework to explore drug repurposing for cancer subtypes based on the available genomic profiles of tumour samples, normal cell types, cancer cell lines and data of drug sensitivity in cell lines.
(5) In this study we also found specific genomic imbalances in the non-GCB and GCB subtypes, based upon Hans' immunohistochemistry classification.
