Integrating the impact of exome variations

BACKGROUND, OBJECTIVES: Our group developed a method to estimate the impact of missense mutations, that we call the “Action” of missense mutations. This method is better than current state-of-the-art approaches at matching experimental data on mutational loss of function, not just in our own controls but also in blind competitions assessed objectively by independent judges (CAGI 2011, and 2012-13). When we used Action on head and neck cancer patient data (TCGA) we obtained significant separation of patient survival among those with a high Action and those with a low Action in somatic TP53 mutations. However, mutations in other genes may also correlate with patient outcome, such as the mutations of IDH1 in glioblastomas (Nobusawa et al., Clin Cancer Res, 2009). Therefore, we plan to integrate mutation impact information over the human proteome and identify how severely they affect the pathways associated with each cancer type. In addition, we like to test the same principles in data from complex diseases such as Alzheimer’s Disease. To do so, we developed a network diffusion method that uses current information of protein interactions (in a physical or broader sense) in order to project the dysfunction of a protein to its near neighbors (Lisewski et.al., Physica A, 2010). Putting these together, our hypothesis is that the diffusion of Action to the human protein network can identify novel Alzheimer’s disease-associated genes and provide a better stratification of patient outcome. STUDY DESIGN, ANALYSIS PLAN: To test our hypothesis we need to access “Individual germline variant data” of patients. For each individual, we will score the germline missense mutations by Action and treat it as the potential dysfunction on the protein. Then, we will diffuse this action over the network and measure the effect on each gene and on each pathway. When we compare these data to those from healthy individuals (1000 Genomes Project), i) we can identify genes associated to each disease and ii) the pathways that affect mostly the disease, and iii) measure the severity of the mutational damage to these genes or pathways. USE RESTRICTIONS: We will follow all restrictions described.

My group is interested in developing computational tools that predict i) disease-associated genes, ii) disease-causing mutations, and iii) the impact of an individual’s mutations to the phenotype. We make these predictions by comparing the mutational patterns of the cases with those expected either by random chance or given the purifying section observed in human polymorphisms. Here, we request access to the database of the NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) Data Sharing Service (DSS), in order to obtain protein mutation data from patients and healthy individuals.