Mariska Slofstra

Developing an application for researchers to compare genotypes and phenotypes of patients with chromosome 6 aberrations

Clients: Barbara Frentz and Conny van Ravenswaaij, C6 project

My internship is for 5 months (September 2015 - February 2016) and I will do my Bachelor project in the 5 months after that (probably working on the same project). I am working in the GCC’s development team and my coordinator is Mark de Haan.

The C6 data consist of two parts: phenotype data, gathered via questionnaires filled in by parents of children with chromosome 6 aberrations, and genotype data, which is array data filled in by a researcher. The data can be approached from different perspectives in my application: via individual patients, patients with certain phenotypes, patients with certain genes affected, or patients with a certain genetic region affected. Research can be done faster and more accurately using this application.

The whole application is written in JavaScript, which has pros and cons. The biggest pro was that I did not have to learn how to work with MOLGENIS (an online database program used to store the questionnaire and array data); this usually takes some time). The biggest con was that JavaScript works asynchronously when using ‘get requests’. These requests were needed in order to extract the data stored in MOLGENIS. Asynchronous JavaScript can make programming very complex.

My program will contribute to the research on chromosome 6. This type of research is very time-consuming, because in identifying links between phenotypes (the clinical features) and genotypes (the exact genetic changes on the chromosome), some links may be found by chance. To avoid missing useful leads, as much information as possible should be collected and approached from many different perspectives.                                                                                        

Gathering phenotype and genotype data is the first step. Building a program to study all the data is the second step, but there are many intermediate steps to achieving our main goal, an interactive genotype-phenotype webpage.

• GCC Genomics Coordination Centre, see http://www.systemsgenetics.nl/group/swertz/
• Chromosome 6 project, see http://chromosome6.webhosting.rug.nl/
• MOLGENIS was developed by the GCC and is commonly used in the UMCG, see http://www.molgenis.org/wiki/WikiStart