3D genome reconstruction from partially phased Hi-C data

DOI10.1007/S11538-024-01263-7arXiv2301.11764MaRDI QIDQ6192541FDOQ6192541

Oskar Henriksson, Jan Draisma, Diego Cifuentes, Kaie Kubjas, Annachiara Korchmaros

Publication date: 11 March 2024

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Abstract: The 3-dimensional (3D) structure of the genome is of significant importance for many cellular processes. In this paper, we study the problem of reconstructing the 3D structure of chromosomes from Hi-C data of diploid organisms, which poses additional challenges compared to the better-studied haploid setting. With the help of techniques from algebraic geometry, we prove that a small amount of phased data is sufficient to ensure finite identifiability, both for noiseless and noisy data. In the light of these results, we propose a new 3D reconstruction method based on semidefinite programming, paired with numerical algebraic geometry and local optimization. The performance of this method is tested on several simulated datasets under different noise levels and with different amounts of phased data. We also apply it to a real dataset from mouse X chromosomes, and we are then able to recover previously known structural features.

Full work available at URL: https://arxiv.org/abs/2301.11764

zbMATH Keywords

numerical algebraic geometryapplied algebraic geometryHi-Cdiploid organisms3D genome organization

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20) Semidefinite programming (90C22) Real algebraic sets (14P05) Numerical algebraic geometry (65H14)

Cites Work

• HomotopyContinuation.jl: a package for homotopy continuation in Julia
• A generalized solution of the orthogonal Procrustes problem
• Euclidean Distance Geometry and Applications
• Sum of squares method for sensor network localization
• A Polyhedral Method for Solving Sparse Polynomial Systems
• The Numerical Solution of Systems of Polynomials Arising in Engineering and Science
• A partial proximal point algorithm for nuclear norm regularized matrix least squares problems
• Title not available (Why is that?)
• Solving Euclidean distance matrix completion problems via semidefinite progrmming
• The BKK root count in $\mathbf {C}^n$
• Euclidean Distance Matrices and Applications
• Euclidean distance matrix completion problems
• Likelihood equations and scattering amplitudes
• Robust Euclidean embedding via EDM optimization
• Identifying 3D Genome Organization in Diploid Organisms via Euclidean Distance Geometry

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