Brief summary of research over the last five years
During my PhD training at the Department of Medical Genetics, UMCU, Utrecht, I was involved in setting up the SOLiD next-generation sequencing method in clinical genetics. I have developed multiplexed targeted re-sequencing method, which became widely used in clinical practice. I have rich experiences in analysis of multiple inheritance models (X-/whole exome sequencing) and positional cloning methods (haplotype sharing/trio phasing, homozygosity mapping) in multiple patient groups. Since September 2013, I work in the lab of Prof. Folkert Asselbergs, UMCU. Here, I am studying the (epi)genetic mechanisms leading to pediatric and adult cardiomyopathies and heart failure. I am actively involved in setting up the UNRAVEL DCM patient database and an EpiGen-omics facility providing expertise in ChIPseq, RNAseq, Methyl-seq, 4C, STARRseq, and other epigenetic methods. I have already produced ChIPseq and RNAseq and 4C-seq datasets derived altogether from more than 100 human samples involving controls and patients with cardiomyopathies due to mutations in PLN, TTN, MYH7, MYBPC3, TNNI3, TNNT2, ischemic cardiomyopathies and aortic stenosis.
Since 2013 – post-doc, Department of Cardiology, UMCU
Top 5 recent publications
1. Meddens CA, Harakalova M, van den Dungen NA, Foroughi Asl H, Hijma HJ, Cuppen EP, Björkegren JL, Asselbergs FW, Nieuwenhuis EE, Mokry M.: Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease; Genome Biol. 2016 Nov 30;17(1):247.
2. Mokry M, Harakalova M, Asselbergs FW, de Bakker PI, Nieuwenhuis EE: Extensive Association of Common Disease Variants with Regulatory Sequence; PLoS One. 2016 Nov 22;11(11):e0165893.
3. Harakalova M, Kummeling G, Sammani A, Linschoten M, Baas AF, van der Smagt J, Doevendans PA, van Tintelen JP, Dooijes D, Mokry M, Asselbergs FW: A systematic analysis of genetic dilated cardiomyopathy reveals numerous ubiquitously expressed and muscle-specific genes; Eur J Heart Fail. 2015 May;17(5):484-93.
4. van Hasselt PM, Ferdinandusse S, Monroe GR, Ruiter JP, Turkenburg M, Geerlings MJ, Duran K, Harakalova M, van der Zwaag B, Monavari AA, Okur I, Sharrard MJ, Cleary M, O’Connell N, Walker V, Rubio-Gozalbo ME, de Vries MC, Visser G, Houwen RH, van der Smagt JJ, Verhoeven-Duif NM, Wanders RJ, van Haaften G: Monocarboxylate transporter 1 deficiency and ketone utilization; N Engl J Med. 2014 Nov 13;371(20):1900-7.
5. 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: Dominant missense mutations in ABCC9 cause Cantú syndrome; Nat Genet. 2012 May 18;44(7):793-6.
Selection of funded projects
2016 The (epi)genetic SWITCH of the mutated heart. NWO-VENI grant
2015 Gene2Bedside – prediction of future organ manifestations in (cardio)myopathy patients based on tissue specificity of mutated gene, WKZ funds grant
2015 The regulome and transcriptome of PLN cardiomyopathy, PLN Foundation grant
2014 The distribution pattern of cardiac fibrosis is related to the genetic type of cardiomyopathy, RAC Genetics, UMCU grant