Genome wide association study is a powerful tool for biomedical researchers to find genetic markers associated with complex diseases. Via comparing genetic marker frequency differences between patient and control groups, the genetic susceptibility loci elevating the risk of developing particular disease can be identified. We have analysis pipeline from research design, data analysis, and result interpretation. We also contribute to grant and manuscript preparations. First, sample size and power can be calculated to give a guidance of the scale of study. The statistical analysis pipeline includes SNP and copy number variation calling, data quality control, population stratification analysis, single marker analysis, multiple marker (haplotype) analysis, gene and pathway based analysis, among others. We also provide association study incorporating complex pedigrees, such as combined family and unrelated case-control individuals. A series of genetic markers, genes or pathways significantly associated with the disease will be identified. In addition to identify genetic markers associated with disease, regression, clustering and classification techniques will be used to predict the disease or other related clinical variables.