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Principal Investigator  
Principal Investigator's Name: Ameck Dosseh
Institution: IMSP
Department: DATA SCIENCE
Proposed Analysis: The data used for this final exercise correspond to data from the Alzheimer’s Disease Neu- roimaging Initiative (ADNI). ADNI is a longitudinal multicenter study designed to develop clinical, imag- ing, genetic, and biochemical biomarkers for the early detection and tracking of Alzheimer’s disease (AD). Since its launch more than a decade ago, the landmark public-private partnership has made major con- tributions to AD research, enabling the sharing of data between researchers around the world (https: //adni.loni.usc.edu/about/). In this exercise we will use data from the first batch of ADNI. It contains information of around 800 individuals (200 normal controls, 400 individuals with cognitive decline, and 200 mild AD). Genotype data is available in PLINK format (virtual campus). Phenotype data (‘adni_demographics.txt’) is also available in the moodle. You need to do the following tasks: • Perform all the required steps (QC and association analyses) to find those SNP which are associ- ated with Alzheimer’s disease status (DISEASE_STATUS). Adjust the models by age, sex, years of education, apoe4 status and the two first principal components. • Create a Manhattan plot and highlight those SNP that are statistically significant after Bonferroni correction. • Create a table including the SNPs with a p-value < 10-8, its chromosome, genomic position, minor allele, minor allele frequency, the annotated gene and the OR under dominant, recessive and additive model. (HINT: use odds function in SNPassoc package). NOTE: If there are no SNPs that pass this significant level use another threshold. • Create a genetic score by combining the SNPs you think are more appropiated and assess its perfor- mance in an association model.
Additional Investigators