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Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach.

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Summary of "Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach."

Most of the evolutionary history reconstruction approaches are based on the infinite sites assumption, which states that mutations appear once in the evolutionary history. The Perfect Phylogeny model is the result of the infinite sites assumption and has been widely used to infer cancer evolution. Nonetheless, recent results show that recurrent and back mutations are present in the evolutionary history of tumors, hence the Perfect Phylogeny model might be too restrictive. We propose an approach that allows losing previously acquired mutations and multiple acquisitions of a character. Moreover, we provide an ILP formulation for the evolutionary tree reconstruction problem. Our formulation allows us to tackle both the Incomplete Directed Phylogeny problem and the Clonal Reconstruction problem when general evolutionary models are considered. The latter problem is fundamental in cancer genomics, the goal is to study the evolutionary history of a tumor considering as input data the fraction of cells having a certain mutation in a set of cancer samples. For the Clonal Reconstruction problem, an experimental analysis shows the advantage of allowing mutation losses. Namely, by analyzing real and simulated datasets, our ILP approach provides a better interpretation of the evolutionary history than a Perfect Phylogeny. The software is at https://github.com/AlgoLab/gppf.

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This article was published in the following journal.

Name: IEEE/ACM transactions on computational biology and bioinformatics
ISSN: 1557-9964
Pages: 1410-1423

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A benign tumor, usually found in the anterior lobe of the pituitary gland, whose cells stain with acid dyes. Such pituitary tumors may give rise to excessive secretion of growth hormone, resulting in gigantism or acromegaly. A specific type of acidophil adenoma may give rise to nonpuerperal galactorrhea. (Dorland, 27th ed)

A benign, rapidly growing, deeply pigmented tumor of the jaw and occasionally of other sites, consisting of an infiltrating mass of cells arranged in an alveolar pattern, and occurring almost exclusively in infants. Its source of origin is in dispute, the various theories giving rise to its several names. (Dorland, 27th ed)

The organization, management, and assumption of risks of a business or enterprise, usually implying an element of change or challenge and a new opportunity.

A small tumor of the anterior lobe of the pituitary gland whose cells stain with basic dyes. It may give rise to excessive secretion of ACTH, resulting in CUSHING SYNDROME. (Dorland, 27th ed)

Local surface sites on antibodies which react with antigen determinant sites on antigens. They are formed from parts of the variable regions of FAB FRAGMENTS.

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