DiNAMIC.Duo

Finding Recurrent DNA Copy Number Alterations and Differences

In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022) can be found at <doi: 10.1093/bioinformatics/btac542>.

README

# DiNAMICDuo

DNA copy number changes (gains and losses) are commonly seen in tumor tissue.  Some copy
number changes provide a selective growth advantage, and these are observed in the same
genomic region across multiple samples.  These copy number changes are termed recurrent.
In contrast, sporadic copy number changes that occur randomly throughout the genome because
of underlying genomic instability are less likely to have biological relevance.  A number
of bioinformatics tools have been developed to identify recurrent copy number alterations
in a single cohort.  However, to the best of our knowledge, there is no currently available
method for identifying recurrent copy number differences between two cohorts.  DiNAMICDuo
was designed to address this shortcoming.

## Example

Please refer to the vignette.

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