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HAP-PHEN SIGNED

From haplotype to phenotype: a systems integration of allelic variation, chromatin state and 3D genome data

Total Cost €

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EC-Contrib. €

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Partnership

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Project "HAP-PHEN" data sheet

The following table provides information about the project.

Coordinator
STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS 

Organization address
address: PLESMANLAAN 121
city: AMSTERDAM
postcode: 1066 CX
website: www.nki.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Total cost 1˙500˙000 €
 EC max contribution 1˙500˙000 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-STG
 Funding Scheme ERC-STG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2020-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    STICHTING HET NEDERLANDS KANKER INSTITUUT-ANTONI VAN LEEUWENHOEK ZIEKENHUIS NL (AMSTERDAM) coordinator 1˙500˙000.00

Map

 Project objective

High-throughput sequencing methods are breaching the barrier of $1000 per genome. This means that it will become feasible to sequence the genomes of many individual and create a deep catalog of the bulk of human genetic variation. A great task will lie in assigning function to all this genetic variation. Genome wide association studies have already shown that 40% of all loci significantly associated with disease are found in intergenic, supposedly regulatory regions. One of the current challenges in human genetics is that variants that affect expression on a single allele cannot be directly linked, because only have genotype information, rather then haplotype information. The overarching aim of the project is to resolve haplotypes in order to identify genetic variants that affect gene expression. We will do this in three sub-projects. In the first main project we will use 3D genome information gathered from Hi-C experiments to haplotype the genomes of six lymphoblastoid cell lines. We will integrate these data with chromatin profiling and RNAseq data in order to build integrative models for the prediction of gene expression and the effect of genetic variation on gene expression. In the second project we will perform haplotyping the breast cancer genes BRCA1/2 in a large cohort of individuals that come from families with a high-risk of hereditary breast cancer. Allelic imbalance in BRCA1/2 expression levels are known to be associated with an increased risk for breast cancer. We will aim to find genetic variants that are associated with a decreased allelic expression of BRCA1/2 to improve breast cancer risk assessment. Finally, we will develop a novel tool to study 3D genome organization of single alleles, which will allow us to identify how individual alleles are organized in the nucleus and identify multi-way interactions (i.e. involving more than two genomic loci). With this we hope to better understand how complex 3D organization contributes to gene regulation.

 Publications

year authors and title journal last update
List of publications.
2017 Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
published pages: 693-707.e14, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.04.013
Cell 169/4 2019-05-28
2018 Geert Geeven, Hans Teunissen, Wouter de Laat, Elzo de Wit
peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data
published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gky443
Nucleic Acids Research 2019-05-28
2018 Lucas J.T. Kaaij, Robin H. van der Weide, René F. Ketting, Elzo de Wit
Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development
published pages: 1-10.e4, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2018.06.003
Cell Reports 24/1 2019-05-28
2016 Peter Hugo Lodewijk Krijger, Bruno Di Stefano, Elzo de Wit, Francesco Limone, Chris van Oevelen, Wouter de Laat, Thomas Graf
Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming
published pages: 597-610, ISSN: 1934-5909, DOI: 10.1016/j.stem.2016.01.007
Cell Stem Cell 18/5 2019-05-28

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