Background The robustness and reproducibility of next generation sequencing technologies make them an excellent platform for gene expression profiling experiments. Despite the fact that the choice of tissue for RNA extraction and sequencing greatly depends on the clinical or research question, whole blood has become an increasingly popular choice. Especially in Huntington's Disease where the pathology originates in a difficult to obtain samples tissue (brain) blood can show promising results.
Aims We have compared 100 HD carriers with 50 age and sex matched controls and looked for transcriptomic biomarkers that can distinguish between the disease stage.
Methods We have used the serial analysis of gene expression protocol with an NlaII restriction enzyme, adapted to yield products, for next generation sequencing analysis. By comparing the abundance of sequencing tags between patients and controls we can identify the differences between patients and controls. We have used the statistical platform R and two programs for differential expression analysis edgeR and Voom. For preliminary wet lab validation of our results we have performed immunostaining of the proteins of interest in brain lysates.
Results We idenftify a set of 8 mRNA biomarkers that is differentially expressed between the late symptomatics and the control cases. Some of these biomarkers can be independently validated with another two programs for statistical analysis of gene expression data but also with wet lab techniques such as immunostaining from brain lysates between HD and control cases. Finally we are working and are interested in methods of identifying further relationships with this transcripts of interest and other transcripts but also working on validating these results in serum and on independent patient cohorts.
- next generation sequencing