Bioinformatics Core Unit

The Bioinformatics Laboratory has considerable expertise in experimental design, (statistical) data analysis, and information management (e.g., use of public biological databases).

Research support

The Bioinformatics Laboratory is one of the AMC core research facilities that enable excellent research. In addition, it is one of the Dutch Techcentres for Life Sciences (DTL) technology facilities to provide access to bioinformatics expertise on a national level.

The Bioinformatics Laboratory has considerable expertise in experimental design, (statistical) data analysis, and information management (e.g., use of public biological databases). We have experience with a wide variety of experimental techniques and platforms. This includes various next generation sequencing applications (RNA-seq, exome, whole genome), DNA microarrays, proteomics, and LC-MS metabolomics.

We provide support for individual (AMC) researchers and projects but have also made arrangements with several research groups for more intensive long-term support.

Selected support projects and publications

Bioinformatics analysis of exome sequencing projects:

  • Cordeddu V, Redeker B, Stellacci E, Jongejan A, Fragale A, Bradley TE, Anselmi M, Ciolfi A, Cecchetti S, Muto V, Bernardini L, Azage M, Carvalho DR, Espay AJ, Male A, Molin AM, Posmyk R, Battisti C, Casertano A, Melis D, van Kampen A, Baas F, Mannens MM, Bocchinfuso G, Stella L, Tartaglia M, Hennekam RC. Mutations in ZBTB20 cause Primrose syndrome. Nat Genet. 2014 Aug;46(8):815-7
  • Houten SM, Denis S, Te Brinke H, Jongejan A,van Kampen AH, Bradley EJ, Baas F, Hennekam RC, Millington DS, Young SP, Frazier DM,Gucsavas-Calikoglu M, Wanders RJ. Mitochondrial NADP(H) deficiency due to a mutation in NADK2 causes dienoyl-CoA reductase deficiency with hyperlysinemia. Hum. Mol. Genet.,2014, 23 (18), 5009-5016
  • Van Houdt JK, Nowakowska BA, Sousa SB, van Schaik BD, Seuntjens E, Avonce N, Sifrim A, Abdul-Rahman OA, van den Boogaard MJ, Bottani A, Castori M,Cormier-Daire V, Deardorff MA, Filges I, Fryer A, Fryns JP, Gana S, Garavelli L, Gillessen-Kaesbach G, Hall BD, Horn D, Huylebroeck D, Klapecki J, Krajewska-Walasek M, Kuechler A, Lines MA, Maas S, Macdermot KD, McKee S, Magee A, de Man SA, Moreau Y, Morice-Picard F, Obersztyn E, Pilch J, Rosser E,Shannon N, Stolte-Dijkstra I, Van Dijck P, Vilain C, Vogels A, Wakeling E, Wieczorek D, Wilson L, Zuffardi O, van Kampen AH, Devriendt K, Hennekam R,Vermeesch JR. Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome. Nat Genet. 2012;44(4):445-9

We participated in GoNL consortium in the sequencing of whole genomesof 250 Dutch parent-offspring families and constructed a haplotypemap of 20.4 millionsingle-nucleotide variants and 1.2 million insertions anddeletions:

  • Francioli LC, Menelaou A, Pulit SL, van Dijk F, Palamara PF, Elbers CC, Neerincx PB, Ye K, Guryev V, Kloosterman WP, Deelen P, Abdellaoui A,van Leeuwen EM, van Oven M, Vermaat M, Li M, Laros JF, Karssen LC, Kanterakis A, Amin N, Hottenga JJ, Lameijer EW, Kattenberg M, Dijkstra M, Byelas H, van Setten J, van Schaik BD, Bot J, Nijman IJ, Renkens I, Marschall T, Schönhuth A, Hehir-Kwa JY, Handsaker RE, Polak P, Sohail M, Vuzman D, Hormozdiari F, van Enckevort D, Mei H, Koval V, Moed MH, van der Velde KJ, Rivadeneira F, Estrada K, Medina-Gomez C, Isaacs A, McCarroll SA, Beekman M, de Craen AJ, Suchiman HE, Hofman A, Oostra B, Uitterlinden AG, Willemsen G, Study LC, Platteel M, Veldink JH,van den Berg LH, Pitts SJ, Potluri S, Sundar P, Cox DR, Sunyaev SR, den Dunnen JT, Stoneking M, de Knijff P, Kayser M, Li Q, Li Y, Du Y, Chen R, Cao H, Li N, Cao S, Wang J, Bovenberg JA, Pe'er I, Slagboom PE, van Duijn CM, Boomsma DI, van Ommen GJ, de Bakker PI, Swertz MA,Wijmenga C + 82 other collaborators (including B.D.C. van Schaik). Whole-genome sequence variation, population structure and demographic history of the Dutch population.Nat Genet. 2014;46(8):818-25.

Investigation of T cell response upon hCMV infection. Using next-generationsequencing of the T cellreceptor to compare the clonal repertoiresof IL-7Rα(+) and IL-7Rα(-) subsets,weobservedlimitedoverlap of clones between thesesubsetsduring acute infection and after 1 year. Whenwe comparedthehCMV-specific repertoire between peripheral blood and pairedlymph-nodes,wefoundmany identical clones but also clones that wereexclusively found ineither compartment.

  • Remmerswaal EB, Klarenbeek PL, Alves NL, Doorenspleet ME, van Schaik BD, Esveldt RE, Idu MM, van Leeuwen EM, van der Bom-Baylon N, van Kampen AH, Koch SD, Pircher H, Bemelman FJ, Ten Brinke A, Baas F, Ten Berge IJ, van Lier RA, de Vries N. Clonal evolution of CD8+ T cell responses against latent viruses: relationship among phenotype, localization, and function. J Virol. 2015;89(1):568-80.

Associationof pneumococcal arginine biosynthesis geneswith theoutcome in patientswithpneumococcalmeningitis by clinical phenotyping using bacterialwhole-genomesequencing.

  • Piet JR, Geldhoff M, van Schaik BD, Brouwer MC, Valls Seron M, Jakobs ME, Schipper K, Pannekoek Y, Zwinderman AH, van der Poll T, van Kampen AH,Baas F, van der Ende A, van de Beek D. Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J Infect Dis. 2014;209(11):1781-91.

A combination of sequence unbiased amplification with next generation sequencing has been applied to discover viruses and investigate its sensitivity with regard to clinical material like blood and stool samples.

  • de Vries M, Oude Munnink BB, Deijs M, Canuti M, Koekkoek SM, Molenkamp R, Bakker M, Jurriaans S, van Schaik BD, Luyf AC, Olabarriaga SD, van Kampen AH, van der Hoek L. Performance of VIDISCA-454 in feces-suspensions and serum. Viruses. 2012;4(8):1328-34.

Applying mass-spectrometry the strong changes in lipid metabolism associated with cancer were investigated. An enhanced saturation of cardiolipin was observed in tumorous cells upon administering of betulinic acid leading to cell death.

  • Potze L, Di Franco S, Grandela C, Pras-Raves ML, Picavet DI, van Veen HA, van Lenthe H, Mullauer FB, van der Wel NN, Luyf A, van Kampen AH,Kemp S, Everts V, Kessler JH, Vaz FM, Medema JP. Betulinic acid induces a novel cell death pathway that depends on cardiolipin modification. Oncogene. 2015 Apr 20. [Epub ahead of print]

Bioinformatics Laboratory

Prof dr Antoine H.C. van Kampen
Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB)
Academic Medical Center

Visiting address
Meibergdreef 9
Location J1B-208
Amsterdam Zuidoost

Postal address
P.O. Box 22700
1100 DE Amsterdam
the Netherlands

Tel.: +31-20-5667096
Mobile: 06-41768067

Skype
antoine.van.kampen

Contact