The Estimation the Association of Rare Variants and Disease in Random Effect Model

The GWAS (genome-wide association study) always be used to find the disease-associated variants. They have explained a small hereditary variation of disease and the results of two GWASs could be find the different candidates SNPs in different time point, that could not offer the genetics information of disease. Recently, the next generation sequencing (NGS) technology is very popular. It could detect the smaller allele frequency of variants (the penetrance is smaller than 0.01), we called the rare variants (RVs) of disease. The NGS also detected the exome sequencing and this is very distinct from GWAS. Hence, the statistical methods of GWAS could not be suitable in NGS data. RVs have the nature of high risk and smaller penetrance, any one of RVs carried the risk allele within one specific range of chromosome could increase the risk of disease, this case called the functional variants. In this study, we would focus on the relationship between RVs and disease in case-parent triad data. We have already proposed RVs random effect model to test the association on family based. Next step, we would discuss the point estimator risk magnitude and confidence interval of each variant site and the overall estimator of functional variants. The pooled estimators could calculate by Mantel-Haenszel method, meta-analysis methods or Bayesian methods.