Magdalena Harakalova is a PhD student supervised by Prof. Edwin Cuppen and working on "Next generation sequencing challenges in human genetics". Her research period will run from August 2009 - August 2013. She works with Dr. Wigard Kloosterman on oncological projects, and with Dr. Annette Baas on thoracic aortic aneurysm (TAA) and abdominal aortic aneurysm (AAA) projects together with research technicians Jelena Medic and Ivo Renkens."
"Despite my huge interest in neurosurgery during my medical studies in Slovakia (I first wanted to become a neuro¬surgeon), I realised being a scientist offered very interesting opportunities too. Routine hospital work and the helplessness you often feel when you run into the limits of present medical possibilities pushed me into a new aspect of medicine – research. During one of my voluntary research internships in the Netherlands in Prof. Edwin Cuppen’s lab, I soon fell in love with genetics, sequencing technologies and his challenging work. Full of enthusiasm, I applied for a PhD position in his group at the Hubrecht Institute in Utrecht, whatever the topic might be.
While I was finishing my studies, Edwin was appointed head of the Department of Medical Genetics, University Medical Centre (UMC) in Utrecht, and this was an even more surprising challenge for me as a PhD student with a medical background. In August 2009 I started my PhD in this department working with the “hottest” technology in human genetics: next-generation sequencing. His group in the Hubrecht Institute started using the SOLID next-generation sequencing platform from Applied Biosystems in 2007 as one of the first worldwide and I was lucky to have the best colleagues to teach me everything they know. Edwin has also built up a professional bioinformatics facility in his group, which gives us fantastic possibilities for analysing huge amounts of sequencing data with precision and leads to results we can confirm by other sequencing methods. These guys are gold.
Edwin has also bought a SOLID sequencer for the Department of Genetics in the UMC, which, in collaboration with the Hubrecht group, gives us great possibilities to apply this efficient sequencing by ligation and unique colour coding to our patients’ genomes. Fragment libraries, mate-paired libraries, bar coding, various slide array or in-solution enrichment techniques, exome sequencing and many more new challenging strategies should help us find “the mutation” – novel base changes, SNPs, small indels or huge copy number variations in DNA or RNA, in much shorter periods of time than ever before. Following up linkage analyses from problematic family cases, peaks from genome-wide association studies (GWAS) or using tissue samples with this sequencing platform shows promising results so far. This makes me even more enthusiastic about my work and the need to learn at least the basics of bioinformatics to better understand how to analyse my data.
As a doctor, I swore by the Hippocratic Oath to help patients – this is probably the most interesting and challenging way I could have imagined doing this."
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