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arXiv · 1310.3291

Identification of cromosomal translocation hotspots via scan statistics

Israel T. Silva·Rafael A. Rosales·Adriano J. Holanda·Michel C. Nussenzweig·Mila Jankovic
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Abstract

The detection of genomic regions unusually rich in a given pattern is an important undertaking in the analysis of next generation sequencing data. Recent studies of chromosomal translocations in activated B lymphocytes have identified regions that are frequently translocated to c-myc oncogene. A quantitative method for the identification of translocation hotspots was crucial to this study. Here we improve this analysis by using a simple probabilistic model and the framework provided by scan statistics to define the number and location of translocation breakpoint hotspots. A key feature of our method is that it provides a global chromosome-wide significance level to clustering, as opposed to previous methods based on local criteria. Whilst being motivated by a specific application, the detection of unusual clusters is a widespread problem in bioinformatics. We expect our method to be useful in the analysis of data from other experimental approaches such as of ChIP-seq and 4C-seq.

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Israel T. Silva, Rafael A. Rosales, Adriano J. Holanda, Michel C. Nussenzweig, Mila Jankovic. 2013-10-11. Identification of cromosomal translocation hotspots via scan statistics. https://doi.org/10.1093/bioinformatics%2Fbtu351

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