🍩 Database of Original & Non-Theoretical Uses of Topology

(found 5 matches in 0.003053s)
  1. Topological Data Analysis of Single-Cell Hi-C Contact Maps (2020)

    Mathieu Carrière, Raúl Rabadán
    Abstract Due to recent breakthroughs in high-throughput sequencing, it is now possible to use chromosome conformation capture (CCC) to understand the three dimensional conformation of DNA at the whole genome level, and to characterize it with the so-called contact maps. This is very useful since many biological processes are correlated with DNA folding, such as DNA transcription. However, the methods for the analysis of such conformations are still lacking mathematical guarantees and statistical power. To handle this issue, we propose to use the Mapper, which is a standard tool of Topological Data Analysis (TDA) that allows one to efficiently encode the inherent continuity and topology of underlying biological processes in data, in the form of a graph with various features such as branches and loops. In this article, we show how recent statistical techniques developed in TDA for the Mapper algorithm can be extended and leveraged to formally define and statistically quantify the presence of topological structures coming from biological phenomena, such as the cell cyle, in datasets of CCC contact maps.
  2. Identification of Relevant Genetic Alterations in Cancer Using Topological Data Analysis (2020)

    Raúl Rabadán, Yamina Mohamedi, Udi Rubin, Tim Chu, Adam N. Alghalith, Oliver Elliott, Luis Arnés, Santiago Cal, Álvaro J. Obaya, Arnold J. Levine, Pablo G. Cámara
    Abstract Large-scale cancer genomic studies enable the systematic identification of mutations that lead to the genesis and progression of tumors, uncovering the underlying molecular mechanisms and potential therapies. While some such mutations are recurrently found in many tumors, many others exist solely within a few samples, precluding detection by conventional recurrence-based statistical approaches. Integrated analysis of somatic mutations and RNA expression data across 12 tumor types reveals that mutations of cancer genes are usually accompanied by substantial changes in expression. We use topological data analysis to leverage this observation and uncover 38 elusive candidate cancer-associated genes, including inactivating mutations of the metalloproteinase ADAMTS12 in lung adenocarcinoma. We show that ADAMTS12−/− mice have a five-fold increase in the susceptibility to develop lung tumors, confirming the role of ADAMTS12 as a tumor suppressor gene. Our results demonstrate that data integration through topological techniques can increase our ability to identify previously unreported cancer-related alterations., Rare cancer mutations are often missed using recurrence-based statistical approaches, but are usually accompanied by changes in expression. Here the authors leverage this information to uncover several elusive candidate cancer-associated genes using topological data analysis.
  3. Quantifying Genetic Innovation: Mathematical Foundations for the Topological Study of Reticulate Evolution (2020)

    Michael Lesnick, Raúl Rabadán, Daniel I. S. Rosenbloom
    Abstract A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabadán in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an evolutionary history. In this paper, we develop theoretical foundations for this approach. First, we present a novel formulation of the underlying inference problem. Specifically, we introduce and study the novelty profile, a simple, stable statistic of an evolutionary history which not only counts recombination events but also quantifies how recombination creates genetic diversity. We propose that the (hitherto implicit) goal of the topological approach to recombination is the estimation of novelty profiles. We then study the problem of obtaining a lower bound on the novelty profile using barcodes. We focus on a low-recombination regime, where the evolutionary history can be described by a directed acyclic graph called a galled tree, which differs from a tree only by isolated topological defects. We show that in this regime, under a complete sampling assumption, the \$1\textasciicircum\mathrm\st\\$ barcode yields a lower bound on the novelty profile, and hence on the number of recombination events. For \$i\textgreater1\$, the \$i\textasciicircum\\mathrm\th\\\$ barcode is empty. In addition, we use a stability principle to strengthen these results to ones which hold for any subsample of an arbitrary evolutionary history. To establish these results, we describe the topology of the Vietoris--Rips filtrations arising from evolutionary histories indexed by galled trees. As a step towards a probabilistic theory, we also show that for a random history indexed by a fixed galled tree and satisfying biologically reasonable conditions, the intervals of the \$1\textasciicircum\\mathrm\st\\\$ barcode are independent random variables. Using simulations, we explore the sensitivity of these intervals to recombination.
  4. Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis (2019)

    Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raúl Rabadán
    Abstract Glioblastoma multiforme (GBM) is an aggressive form of human brain cancer that is under active study in the field of cancer biology. Its rapid progression and the relative time cost of obtaining molecular data make other readily available forms of data, such as images, an important resource for actionable measures in patients. Our goal is to use information given by medical images taken from GBM patients in statistical settings. To do this, we design a novel statistic—the smooth Euler characteristic transform (SECT)—that quantifies magnetic resonance images of tumors. Due to its well-defined inner product structure, the SECT can be used in a wider range of functional and nonparametric modeling approaches than other previously proposed topological summary statistics. When applied to a cohort of GBM patients, we find that the SECT is a better predictor of clinical outcomes than both existing tumor shape quantifications and common molecular assays. Specifically, we demonstrate that SECT features alone explain more of the variance in GBM patient survival than gene expression, volumetric features, and morphometric features. The main takeaways from our findings are thus 2-fold. First, they suggest that images contain valuable information that can play an important role in clinical prognosis and other medical decisions. Second, they show that the SECT is a viable tool for the broader study of medical imaging informatics. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
  5. Inference of Ancestral Recombination Graphs Through Topological Data Analysis (2016)

    Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán
    Abstract The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands., Evolution occurs through different mechanisms, including point mutations, gene duplication, horizontal gene transfer, and recombinations. Some of these mechanisms cannot be captured by tree graphs. We present a framework, based on the mathematical tools of computational topology, that can explicitly accommodate both recombination and mutation events across the evolutionary history of a sample of genomic sequences. This approach generates a new type of summary graph and algebraic structures that provide quantitative information on the evolutionary scale and frequency of recombination events. The accompanying software, TARGet, is applied to several examples, including migration between sexually-reproducing populations, human recombination, and recombination in Darwin’s finches.