3D Genome Reconstruction from Partially Phased Hi-C Data

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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.

TidsskriftBulletin of Mathematical Biology
Udgave nummer4
Sider (fra-til)1.30
StatusUdgivet - 2024

Bibliografisk note

Funding Information:
We thank Anastasiya Belyaeva, Gesine Cauer, AmirHossein Sadegemanesh, Luca Sodomaco, and Caroline Uhler for very helpful discussions and answers to our questions.

Funding Information:
Open Access funding provided by Aalto University. Oskar Henriksson and Kaie Kubjas were partially supported by the Academy of Finland Grant No. 323416. Oskar Henriksson was also partially funded by the Novo Nordisk project with grant reference number NNF20OC0065582.

Publisher Copyright:
© The Author(s) 2024.

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