We are pleased to announce that the project from CeNT received funding in the Foundation for Polish Science Team call. Grant was given to prof. Dariusz Plewczyński, Centre of New Technologies, University of Warsaw.

PROJECT GOAL

The aim of the research project is to explore at the population scale the relation between the three-dimensional structure variability of Human cell nucleus, and the emergence and the nature of the genomic sequence alterations. The research team will use public and proprietary experimental results of large-scale next-generation sequencing studies, and recently developed theoretical algorithms. The project will establish novel multi-scale computer method that is able to predict the 3D structure of genome for an individual using only its 1D genomic sequence (the list of structural variants SVs) by applying biopolymer theory, statistical learning and the biophysical properties of chromatin. The results will be validated by chromatin conformation capture experiments for selected families from 1000 Genomes Project, with the additional aim to better understand both normal and pathological structural changes occurring during evolution of Human genome.

The aim of the research project is to explore both theoretically and experimentally the relationship between the sequence, three-dimensional structure and biological function of Human genome. The project will exploit proprietary experimental findings of our international collaborator Prof. Yijun Ruan (The Jackson Laboratory for Genomic Medicine, JAX GM), and further advance computational algorithms developed at the Laboratory of Functional and Structural Genomics headed by Dariusz Plewczynski, PhD (Centre of New Technologies University of Warsaw, CeNT).

The project will result in establishing 3Depigenome platform that will be able to:

1. identify a genome sequence rearrangements (i.e. structural variants SV, such as deletions, duplications, inversions, insertions, translocations) and mutations (single nucleotide polymorphisms SNP) by high-throughput analysis of NGS reads either from Illumina sequencing or long read methods (Oxford Nanopore, PacBio)
2. predict the three-dimensional structure of a genome for a given cell type using its individual 1D sequence and epigenetic data together with the reference 3D conformation for lymphoblastoid cells, and finally
3. allow for mechanistic and probabilistic reinterpretation of biological function for selected genomic regions related to autoimmune diseases according to large scale Genome-Wide Association Studies (GWAS) at the scale of populations.