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Cuppen group

Genome biology

Next-generation sequencing has made it possible to read the complete genetic code of an individual for an affordable price (several thousands of dollars per genome). However, understanding such personal genomes and the biological consequences of the enclosed genetic variation remains a major challenge. The Cuppen group studies the general mechanisms underlying genotype-phenotype relationships using systematic genetical-genomics approaches in rat model systems and patient cases (orphan diseases and cancer). 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

Low TY, van Heesch S, van den Toorn H, Giansanti P, Cristobal A, Toonen P, Schafer S, Hübner N, van Breukelen B, Mohammed S, Cuppen E*, Heck AJ*, Guryev V (2013). Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis. Cell Reports, 5(5):1469-78

Rat Genome Sequencing and Mapping Consortium (2013). From sequence to phenotype variation in the laboratory rat. Writing group: Baud A, Hermsen R, Guryev V, Gauguier D, Stridh P, Olsson T, Holmdahl R, Graham D, McBride MW, Foroud T, Fernandez-Teruel A, Hubner N, Cuppen E, Mott R, Flint J. Sequencing group: Hermsen R, Hummel O, Lansu N, Patone G, Ruzius FP, de Bruijn E, Hauser H, Atanur SS, Aitman TJ, Flicek P, Adams DJ, Keane T, Saar K, Hubner N, Guryev V, Cuppen E. Nature Genetics, 45:767-775

Kettleborough RNW*, Busch-Nentwich EM*, Harvey SA*, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E*, Stemple DL* (2013). A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature, 496:494–497

Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CA, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V, Poot M, Cuppen E (2012). Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Reports 1:648-55
(commented in Nat Rev Cancer 12:510-511)

Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL, Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA, Asselbergs FW, Breur HM, Swinkels ME, Scurr IJ, Smithson SF, Knoers NV, van der Smagt JJ, Nijman IJ, Kloosterman WP, van Haelst MM, van Haaften G, Cuppen E. (2012). Dominant missense mutations in ABCC9 cause Cantú syndrome. Nature Genetics 44:793-6.

Simonis M, Atanur SS, Linsen S, Guryev V, Ruzius FP, Game L, Lansu N, de Bruijn E, van Heesch S, Jones SJ, Pravenec M, Aitman TJ, Cuppen E. (2012). Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel. Genome Biology 13(4):r31

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.

Publication list