"Hello, I’m Yvette Alblas. I’m a 25-year old student doing the Selective Utrecht Medical Master’s course (SUMMA) in Utrecht. For the research part of my study I did a 6-month internship in the research section of the Dept. of Medical Genetics, University Medical Centre Utrecht.
In my project I sequenced the PCDH19-gene of 85 females with Dravet syndrome. This is a severe epilepsy syndrome mostly caused by mutations in the SCN1A-gene. However, the females in this cohort had no mutation in this SCN1A-gene. Depienne et al. recently showed that these females could have mutations in the PCDH19-gene1. I tried to confirm the results of Depienne et al.
During my internship I have been learning not only new skills, but also new things about myself! Now I realize that I don’t want to work in a research laboratory setting for a longer period of time. However, because of all the great people in the group I had an enjoyable time. I can look back on a very successful 6 months."
1. Depienne,C. et al. Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females. PLoS. Genet. 5, e1000381 (2009).
Yvette Alblas
PCDH19 mutations in SCN1A-negative females with Dravet(-like) syndrome
Internship in research group, DMG, UMC Utrecht
July 2009 – January 2010
"I'm Marianne van Leeuwen, a 24-year-old student of the Neuroscience and Cognition MSc course at Utrecht University. For my major research project I selected the Complex Genetics Group, Dept. of Medical Genetics, UMC Utrecht, where I have spent ten months setting up a large sequencing project.
In a recent study, Stefansson et al.1 showed a significant association between a heterozygous deletion of 15q11.2 and schizophrenia. However, none of the 54 single nucleotide polymorphisms (SNPs) in this area were significantly associated with schizophrenia. Therefore, the aim of my project was to identify rare variants in the 15q11.2 area, encompassing 2 large and 2 small genes, that might explain this association. The project consisted of working with databases, such as Ensembl and UCSC Browser, designing primers, performing PCRs and sequencing reactions, and analyzing the data. In a later stage, the sequencing was automated in the Cuppen2 lab at the Hubrecht Institute, giving me the chance to see another lab, work with different settings, use robots for pipetting, and learn to use various bioinformatic tools.
As you can see, the project enabled me to experience how it feels to work in a research lab. Since the project had to start from scratch, it also gave me the chance to see how you set up a big project, how much time it takes, the importance of clear and straight communication, and so on. But of course I was not doing this alone, Eric Strengman was there for practical assistance and Prof. Roel Ophoff for the more theoretical questions and guidance.
After ten months I can say that the Complex Genetics Group has the best of both worlds: the staff work really hard and obtain interesting results, but at the same time it is a very social group, having lunch together, buying presents for Sinterklaas, playing on the Wii, and much more. So if you’re interested in this field, I would definitely recommend that you make an appointment with one of the researchers working in the Complex Genetics Group to see if they have something you are interested in doing."
1 Stefansson H. et al. Large recurrent microdeletions associated with schizophrenia. Nature 2008 455:232-6. Comment in: Nature 2008 455:178-9. 2 Prof. Edwin Cuppen was appointed head of the research group on 1st April 2009.
Marianne van Leeuwen
Internship at Complex Genetics Group, UMC Utrecht
Sequencing rare variants in 15q11.2 for schizophrenia
Sept 2008 - July 2009
"From August 2008 to January 2009, I did a 6-month internship at the Complex Genetics Group, Dept. of Medical Genetics, UMC Utrecht. My internship was in the third year of my bio-informatics vocational course at the HAN University. I worked for Clara Elbers, a PhD student working on the genetics of Type 2 diabetes. I helped on her project to experimentally test the thrifty genes hypothesis. I wrote serveral programs in Java for the analysis of GWAS data. Using these programs we tried to located new SNPs involved in Type 2 diabetes, by analysing SNPs in different populations.
I very much enjoyed this period; the colleagues in the Group were very nice and I would have liked to stay longer but I have to follow classes again."
Renske Kuiper
3rd year HBO Bio-informatics student at Hogeschool van Arnhem en Nijmegen (HAN) in Nijmegen
August 2008 – January 2009 (6 months)
"Hi, I’m Bernd Geurts, 24 years old and currently a student on the Selective Utrecht Medical Master (SUMMA) and Biomedical Sciences programme in Utrecht. As a research project I did an internship at the Complex Genetics Group, Dept. of Medical Genetics, UMC Utrecht.
During my internship I studied DNA methylation patterns, a very hot topic in psychiatry, in relation to schizophrenia. DNA methylation is an epigenetic process which can inhibit the transcription of proteins. Cytosines next to guanines can be methylated (CpG sites). Treatment of DNA with bisulphite converts every cytosine to an uracil except methylated cytosines. Methylation-specific PCR and sequencing is performed to assess the methylation status of promoter regions. The Complex Genetics research laboratory was equipped with all the supplies and machines I needed. Eric Strengman, who knows almost everything about this laboratory, did a great job in teaching me new lab skills.
The research group comprises approximately 30 people and they meet every week to update each other about their progress. This means everyone knows what each individual is working on.
The group also is a very social team, I immediately felt at home. This really contributed to the working environment. Everyone is very eager to help and tries to answer your questions. I really enjoyed doing my research projects at Complex Genetics and can recommend it as a place to do a research project to anyone who likes genetics."
Bernd Geurts
Internship at Complex Genetics Group, UMC Utrecht
DNA methylation patterns in schizophrenia
Sept. 2008 – February 2009
"I’m a Bioinformatics student and I did my internship in the Complex Genetics section of the UMC, where I worked on Clara Elbers’ project: “Unravelling the aetiology of type 2 diabetes by genome-wide pathway analyses”. My activities involved mainly programming, data analysis and making use of bioinformatics tools. There lab experiments generate a huge amount of data, which can’t been analysed by hand. Therefore I wrote small programs to extract only the relevant information that we needed from these data. I also made use of existing bioinformatics tools to perform network and pathway analyses, to get more insight into a disease, which was in our case type 2 diabetes.
I really enjoyed working here. The project was interesting, the colleagues are really nice and the atmosphere was great! Unfortunately I had to leave, because that’s the way it goes with internships, but maybe I’ll come back someday! Who knows ..."
"Ik heb 5 maanden stage gelopen op de afdeling complexe genetica van het UMC. Ik werkte mee aan het project van Clara Elbers: “Unravelling the aetiology of type 2 diabetes by genome-wide pathway analyses”. Ik doe de opleiding Bioinformatica en mijn werkzaamheden bestonden voornamelijk uit programmeren, data analyseren en gebruik maken van bioinformatica tools. Er komt ontzettend veel data uit het lab, wat niet met de hand geanalyseerd kan worden. Daarom schrijf ik kleine programmaatjes om uit deze data alleen de informatie te halen die wij nodig hebben. Daarbij maakte ik gebruik van bestaande bioinformatica tools om netwerk en pathway analyse uit te voeren, om zo meer te weten te komen van een ziekte, in dit geval type 2 diabetes. Ik heb het hier heel erg naar mijn zin gehad. Het project was leuk, de collega’s erg aardig en gezellig, en de sfeer in z’n totalitair was erg fijn! Ik vind het jammer dat ik weg ga, maar zo gaat dat nu eenmaal met stages maar ik hoop hier ooit weer terug te komen, dus wie weet!"
Kristel van Eijk
Bioinformatics internship
Sept 2007 - January 2008
P.S. Kristel is now doing a PhD under Prof. Roel Ophoff (started Sept. 2009)
"Tijdens de zomer van 2008 wilde ik graag werken binnen een universitaire setting in Utrecht. Met een open sollicitatie heb ik die gevonden in de complexe genetica groep in het UMC. Het is een groep waar een grote variatie in genetisch onderzoek plaats vind. In het natte lab zijn veel mogelijkheden voor onderzoek en de data analyses met gebeurd met computers die in de buurt van het lab zijn. Het was zeer leerzaam omdat er serieus en hard gewerkt word. Ook wordt je meteen betrokken bij andermans onderzoek wat natuurlijk erg leuk is.
Daarnaast heb ik er ook veel plezier gehad want het is een gezellige groep die altijd wel bezig is met het plannen van een leuke activiteit. Zo zijn we met een groot deel van de groep gaan BBQen en een andere keer werd er druk gebokst met wii!
Al met al heb ik het erg naar mijn zin gehad en was het een zeer waardevolle ervaring!"
"During the summer of 2008 I was looking for a summer job on a university level. I therefore submitted an open application and found a job at the Complex Genetics group in the UMC. It’s a group where a wide variety of genetic research takes place. They have a laboratory where a lot of genetic tests can be done and the analysis of the data is done using computers near the laboratory. It was a very educational experience because of the serious attitude and hard work of the group. The direct involvement with other research projects made it even more interesting.
The group was very active making it a lot of fun to work there. There was always some kind of activity being planned for those who wanted to join in: one time we went for a BBQ, while another time we played boxing on the wii!
It was a pleasant time and a great experience!"
Juliaan Meijboom
Data analysis of micro-array data by means of the R program for statistical computing
Work student: June – August 2008