Volume 14, Issue 1/2012 - Medtech

Individualised Patient Stratification Using Whole Genome Sequencing

IT @ Networking Awards 2012 - 2nd Place
Introducing Innovation in  Healthcare  

These advances in genomic medicine are  only possible due to the equal progress  in the information technology sector. The  diagnostic opportunities also bring new  challenges to medical centres regarding  privacy in general and the necessary ICT  infrastructure to secure this privacy at  the individual patient level.  


Clinical genetic testing in adults is at present  typically done for a few patients who,  as a result of family history or clinical indications,  are considered at risk of carrying  genetic variations that are linked to a  particular disease or disease predisposition.  This is going to change and in the  near future, when at relative low cost, all  variants in coding and non-coding DNA  is mapped at once. The vast amount of  knowledge that is offered by wholegenome  sequencing means that informed  consent for this procedure is more complex  than that for existing genetic testing.  

 

The ICT Solution  

In order to facilitate this genomics project  an Oracle Exadata server was installed  as the initial component for the ErasmusMC  Translational Research Center  (TRC) personal cloud architecture. The  aim of this next generation sequencing  data storage and analysis project is being  used as proof of concept to evaluate  outsourcing of IT services.  

Additionally, the bioinformatics team is  using this environment to benchmark the  performance of the Exadata technology  against an existing standard IT architecture.  The project is a success in that  the genomics solution started by the  team of professor Peter van der Spek at  ErasmusMC has attracted interest for  adoption by organisations worldwide and  now needs to be managed by an external  company. To grow this solution to an  international standard the support of Oracle  is required.  

 

Impact of the Project  

As the focus in the clinic shifts from sequential  testing of individual genes associated  with a particular disease, to mapping  all variants within an individual’s whole  genome to all known information on all  diseases and traits, the consequence is  the need for massive parallel processing  and high volume data storage.  The added value to the clinic is for higher  efficiency in diagnosis, with decreased  time to delivery and a view of the whole  genome not just the individual genes. Increased  knowledge can result in medical  or lifestyle changes that reduce risks, or  it can affect the patient’s life decisions  or strategies for coping. Risks of genetic  testing also centre on the accuracy of  the knowledge that patients (or others)  take away from the tests and how that  knowledge is used. Over time our knowledge  will rapidly expand and new ways to  re-annotate the genome data will be developed.  Historical data for both the clinician  and patient, which has an updated  diagnosis should be made available  via a secure web based application.  Genome sequencing will have its major  impact in three areas listed below:  

  • Genetic testing of inherited conditions;  
  • Cancer diagnostics; and  
  • Pharmacogenetics.  

Every individual will learn that he or she  is a heterozygous carrier of more than  one serious or lethal autosomal recessive  disease. This information might affect  a patient’s lifestyle decisions, and  have implications for existing children or  other relatives.  

Education  

This technological solution offers a platform  for training medical professionals  (physician scientists) to deal with large  volumes of sensitive patient related data  and learn to diagnose clinical relevant  variants within the genome. These actionable  items will help reducing costs by  providing the right drug to the right patient  in therapy. To make informed decisions  about whole-genome sequencing,  patients will need to have the opportunity  to ask questions and get accurate  answers from knowledgeable and trained  professionals.  

 

For more information on the IT @ Networking  awards and pictures from this  year's event, please visit:  www.itandnetworking.org


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IT @ Networking Awards 2012 - 2nd PlaceIntroducing Innovation in  Healthcare  These advances in genomic medicine are  only possible due to t

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