Two Notes On Genome Rearrangement

A central problem in genome rearrangement is nding a most parsimonious rearrangement scenario using certain rearrangement operations. An important problem of this type is sorting a signed genome by reversals and translocations (SBRT). Hannenhalli and Pevzner presented a duality theorem for SBRT which leads to a polynomial time algorithm for sorting a multi-chromosomal genome using a minimum number of reversals and translocations. However, there is one case for which their theorem and algorithm fail. We describe that case and suggest a correction to the theorem and the polynomial algorithm

An O(n 3/2 √ log(n)) algorithm for sorting by reciprocal translocations

AbstractWe prove that sorting by reciprocal translocations can be done in O(n3/2log(n)) for an n-gene genome. Our algorithm is an adaptation of the algorithm of Tannier, Bergeron and Sagot for sorting by reversals. This improves over the O(n3) algorithm for sorting by reciprocal translocations given by Bergeron, Mixtacki and Stoye (2006) [4]

R: On the frequency of genome rearrangement events in cancer karyotypes

Abstract. Chromosomal instability is a hallmark of cancer. The results of this instability can be observed in the karyotypes of many cancerous genomes, which often contain a variety of aberrations. In this study we introduce a new approach for analyzing rearrangement events in carcinogenesis. This approach builds on a new effective heuristic for computing a short sequence of rearrangement events that may have led to a given karyotype. We applied this heuristic on over 40,000 karyotypes reported in the scientific literature. Our analysis implies that these karyotypes have evolved predominantly via four principal event types: chromosomes gains and losses, reciprocal translocations, and terminal deletions. We used the frequencies of the reconstructed rearrangement events to measure similarity between karyotypes. Using clustering techniques, we demonstrate that in many cases, rearrangement event frequencies are a meaningful criterion for distinguishing between karyotypes of distinct tumor classes. Further investigations of this kind can provide insight on the scenarios by which particular cancer types have evolved.