Microarray SNP Genotyping Analysis

This course covers SNP Genotyping microarray data analysis using Affymetrix and Dchip software, as well as Matlab and R scripts Introduction: Genomewide SNP genotypes can be determined through microarray experiments so we can identify variants that cause disease. This course teaches researchers to perform analysis on Affymetrix data and transform a chip image to genotypes for each SNP and even the copy number. Various tools will be covered such as GCOS, GTYPE, BRLMM, CNAT, Excel, MATLAB and dChip. Why learn SNP genotyping analysis: Most scientists are not able to analyze microarray data themselves and are not able to get desired results using traditional tools like Microsoft Excel or even advanced software provided by commercial vendors. The free solutions come either with a steep learning curve or as black-box interfaces that provide limited functionality, with little or no technical support. In the midst of all this is the fundamental lack of understanding among scientists on how the technology works and what the fundamental parts of the analysis are. This course demystifies the analysis. Logistics: The course is divided into 8 sessions with pre-recorded videos, handouts, reference cards, examples, data, scripts and quizzes. Enrollees can contact the instructor with questions and get help on the projects. The main topics are listed below. Homework assignments will involve running commands learned in the live lectures. Requirements:No experience is required, although prior experience with a programming language will be helpful. Math skills will also be useful. Price: $2400 for Commercial/Government enrollees and $1200 for Academic researchers and students. Instructor: Shailender Nagpal Syllabus: - - Introduction to GCOS for working with Affymetrix genotyping chips - - Algorithms, tools for generating genotypes - GTYPE, BRLMM - - Sample mismatch report, gender calls, pedigree check, creating virtual sets - - dChip software: various analysis - - Matlab software: various analysis - - Creating PLINK ped and map files for linkage analysis