Cuppen group

Genome biology

Technological innovations soon make it possible to read the complete genetic code of an individual for an affordable price (1,000 dollar genome). However, understanding such personal genomes and the biological consequences of the enclosed genetic variation remains a large challenge. The Cuppen group studies the general mechanisms underlying genotype-phenotype relationships using systematic genomics approaches in rat genetic model systems. A diversity of high-throughput techniques and bioinformatic tools, including next-generation sequencing approaches, are employed to systematically discover and study genetic variation (SNPs, structural variation) and functional genomic elements.

About the research

Fast Facts: Unraveling the secrets of DNA from Fast Facts on Vimeo.

Key publications
Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E. (2010) Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nature Methods 7:913-915

Linsen SEV, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, Kuersten S, Tewari M, and Cuppen E. (2009) Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods 6:474-476

Guryev V, Saar K, Adamovic T, Verheul M, van Heesch S, Cook S, Pravenec M, Aitman T, Jacob H, Shull JD, Hubner N, and Cuppen E. (2008) Distribution and functional impact of DNA copy number variation in the rat. Nature Genetics 40: 538-545.

Cuppen E, Gort E, Hazendonk E, Mudde J, van de Belt J, Nijman IJ, Guryev V, and Plasterk RHA. (2007) Efficient target-selected mutagenesis in Caenorhabditis elegans: towards a knockout for every gene. Genome Research 17: 649-658.

Guryev V, Smits BMG, van de Belt J, Verheul M, Hubner N, and Cuppen E. (2006) Haplotype block structure Is conserved 
across mammals. PLoS Genetics 2: e121.

Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RHA, and Cuppen E. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.

Publication list