GenoKey mining the data for neuroblastoma risk genotypes

April 24, 2014 − by Suzanne Elvidge − in Data analytics, Data mining, GenoKey news, GenoKey's big data analyses, Healthcare big data analysis − No Comments

Genome-wide association studies generate huge quantities of genetic data, and it’s not always easy to find the critical linkages to disease amongst the volume of information. Using GenoKey’s data mining technology, Erling Mellerup and a team of European researchers have found a cluster of 24 combinations of genotypes that are linked to a susceptibility to neuroblastoma, a rare childhood cancer. The results were published in Cancer Genetics.

In a previous study of bipolar disorder using GenoKey’s technology, combinations of three SNP genotypes taken from 803 SNPs resulted in almost two billion combinations, 60 million of which were found in patients only. Four clusters of these patient-specific combinations were significantly associated with the disorder.

In this study, the researchers took data from a previous study of neuroblastoma that had found 16 SNPs in an analysis of 370 cases and 809 controls. The aim of this analysis was to see if there were combinations of genetic changes that could be seen in patients that weren’t there in people without the disease. Research of this type could potentially lead to tools that predict risk and indicate people who should be monitored more closely for signs of disease.

The theoretical number of combinations of three SNP genotypes taken from 16 SNPs is 15,120. Of these:

  • 14,307 were found in 370 patients and 803 controls
  • 12,772 combinations were common to both patients and controls
  • 1,213 were found in controls only
  • 322 combinations were found in patients only

Of the 322 combinations found in patients only, a cluster of 24 combinations was found to be significantly associated with neuroblastoma.

Using fast data mining methods like those developed by GenoKey make it possible to look at combinations of changes as well as single changes. This allows researchers to extract more meaningful; information from amongst the ‘noise’ of large quantities of genetic data, and finds patterns of changes that could support personalised medicine in groups of patients, or even individuals.

The next step for the researchers is to replicate the findings in an independent neuroblastoma cohort, and to further test the methods used to combine genetic data in more data sets.

In a previous study of bipolar disorder using GenoKey’s technology, combinations of three SNP genotypes taken from 803 SNPs resulted in almost two billion combinations, 60 million of which were found in patients only. Four clusters of these patient-specific combinations were significantly associated with the disorder.





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