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Franke Group – Functional Genomics

Disease-causing variants have now been found for hundreds of common diseases. But why do these variants cause disease? What mechanisms do they use? Which pathways do they work on?

These are questions that Lude Franke and his PhD students are trying to answer by using functional genomics. By correlating genetic variation with molecular data (such as gene expression, methylation, and histone modifications) in thousands of individuals, it is now becoming clear that most disease-associated variants primarly affect gene expression levels. This group is developing new statistical genetic methods and applying them to various large-scale molecular datasets.

NEWS
Jan 2015: Harm Jan Westra awarded an NWO Rubicon. Lude Franke awarded UMCG Research prize.

Nov 2014: Lude Franke awarded an ERC Starting grant of €1.5 million for a project entitled:  New ‘big data’ approach to identify environmental risk factors for disease.

Selected publications

Gene expression analysis identifies global gene dosage sensitivity in cancer. Fehrmann RS, Karjalainen JM, Krajewska M, Westra HJ, Maloney D, Simeonov A, Pers TH, Hirschhorn JN, Jansen RC, Schultes EA, van Haagen HH, de Vries EG, Te Meerman GJ, Wijmenga C, van Vugt MA, Franke L. Nature Genetics 2015

Luister naar een radio interview met Lude Franke over zijn werk (in Dutch) RTV Noord (ga naar 20-1-2015, en dan naar tijdslot 12.00, dan naar 12.41, en dan kom je bij het interview)

Systematic identification of trans eQTLs as putative drivers of known disease associations. Westra HJ, Peters MJ, Esko T, Yaghootkar H, Schurmann C, Kettunen J, Christiansen MW, Fairfax BP, Schramm K, Powell JE, Zhernakova A, Zhernakova DV, Veldink JH, Van den Berg LH, Karjalainen J, Withoff S, … Franke L. Systematic identification of trans eQTLs as putative drivers of known disease associations. Nature Genetics 2013

Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, Almeida R, Zhernakova A, Reinmaa E, Võsa U, Hofker MH, Fehrmann RS, Fu J, Withoff S, Metspalu A, Franke L, Wijmenga C. PLoS Genetics 2013

Unraveling the regulatory mechanisms underlying tissue-dependent genetic variation of gene expression. Fu J, Wolfs MG, Deelen P, Westra HJ, Fehrmann RS, Te Meerman GJ, Buurman WA, Rensen SS, Groen HJ, Weersma RK, van den Berg LH, Veldink J, Ophoff RA, Snieder H, van Heel D, Jansen RC, Hofker MH, Wijmenga C, Franke L. PLoS Genetics 2012

Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. Fehrmann RS, Jansen RC, Veldink JH, Westra HJ, Arends D, Bonder MJ, Fu J, Deelen P, Groen HJ, Smolonska A, Weersma RK, Hofstra RM, Buurman WA, Rensen S, Wolfs MG, Platteel M, Zhernakova A, Elbers CC, Festen EM, Trynka G, Hofker MH, Saris CG, Ophoff RA, van den Berg LH, van Heel DA, Wijmenga C, Te Meerman GJ, Franke L. PLoS Genetics 2011

MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects. Westra HJ, Jansen RC, Fehrmann RS, te Meerman GJ, van Heel D, Wijmenga C, Franke L. Bioinformatics 2011

Multiple common variants for celiac disease influencing immune gene expression. Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, … Wijmenga C, van Heel DA. Nature Genetics 2010

For all publications by Lude Franke see GoogleScholar

 

Team members

The group members include:

  • Lude Franke, PhD
  • Freerk van Dijk
  • Juha Karjalainen
  • Dasha Zhernakova
  • Marc Jan Bonder

Past member:

  • Harm Jan Westra, PhD

Associated projects

GeneNetwork: an integrated functional gene network