Recovering rearranged cancer chromosomes from karyotype graphs

BACKGROUND: Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to the reference genome. Recently it became possible to reconcile both of these types of large-scale variations into a karyotype graph representation of the rearranged cancer genomes. Such a representation, however, does not directly describe the linear and/or circular structure of the underlying rearranged cancer chromosomes, thus limiting possible analysis of cancer genomes somatic evolutionary process as well as functional genomic changes brought by the large-scale genome rearrangements. RESULTS: Here we address the aforementioned limitation by introducing a novel methodological framework for recovering rearranged cancer chromosomes from karyotype graphs. For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP) of finding a collection of linear and/or circular rearranged cancer chromosomes that are determined by the graph. We derive and prove computational complexities for several variations of the EDP. We then demonstrate that Eulerian decomposition of the cancer karyotype graphs is not always unique and present the Consistent Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the cancer karyotype graph, and describe a novel algorithm CCR capable of solving CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate that it is capable of consistently recovering large cancer contigs even when underlying cancer genomes are highly rearranged. CONCLUSIONS: CCR can recover rearranged cancer contigs from karyotype graphs thereby addressing existing limitation in inferring chromosomal structures of rearranged cancer genomes and advancing our understanding of both patient/cancer-specific as well as the overall genetic instability in cancer

English Mainstream Texts and Specifics of Their Discourse Expansion

The paper discusses English mainstream discourse specifics and its expanding under the lens of collocations. With discourse definition being provided, discourse vs text differences are reviewed. Based on the mainstream discourse definition, collocation examples borrowed from the authentic English sources have been collected and studied. The paper analysis is focused on featuring their semantics, with some of the examples undergoing reinterpretation of the words’ direct meaning. Other cases are emphasized as hard to reveal the direct meaning due to lack of information transparency or triviality conveyed by a marked out component of the collocation. The scientific originality of the study is expected to be found in the way the authors verbalize the information. The specific intentions are conveyed by “ packing ” them into a language structure with specific features attached. The backdrop knowledge used embraces both the language structure insights and those of the social context, social “landscape”, anthropogenic figurativeness, etc to reach the targeted addressee. The research topicality as considered by the coauthors, involves identifying the usual discourse expansion features which characterize general or specific language “landscape”. The verbs and collocations with a certain role to play in a verbal and cognitive process of discourse expanding, its dynamic changes and mainstream text organization are analyzed as a part of the respective semantic field