Grant Number:	5R03CA192197-02 Interpret this number
Primary Investigator:	Wang, Jian
Organization:	University Of Tx Md Anderson Can Ctr
Project Title:	Method to Analyze X-Chromosomal Genetic Data
Fiscal Year:	2016

¿ DESCRIPTION (provided by applicant): Genome-wide association studies (GWAS) have been successful in identifying genetic markers associated with complex diseases. GWAS usually focus on autosomal markers and exclude X-chromosome markers. However, many complex diseases show sex biases in disease frequency, suggesting potential associations between sex chromosomes and these diseases. Particularly, X-chromosome genes are involved in many cancers, including both sex-organ-specific (e.g., ovarian and prostate) and non-sex-organ-specific (e.g., renal cell carcinoma) cancers. Therefore, ignoring X-chromosome markers in association studies might lead to the loss of potential signals for complex diseases. Nonetheless, the development of statistical tests for X- chromosome analysis based on a mixed-sex sample has received surprisingly little attention, perhaps due to the complexity of the X-chromosome inactivation (XCI) process. XCI on female X-chromosome loci states that in females during early embryonic development, 1 of the 2 copies of the X-chromosome present in each cell is randomly inactivated to achieve dosage compensation of X-linked genes in males and females. The XCI process is in general random; however, skewed, or non-random, XCI is also a biological plausibility. Skewed XCI has been defined using an arbitrary threshold of inactivation of 1 of the alleles in > 75% of cells. Another complexity in analyzing X-chromosome data is the escape from XCI outside the pseudo-autosomal regions of the X-chromosome, which results in both alleles remaining active (i.e., no dosage compensation). Statistical approaches designed for autosomal chromosomes have been used for X-chromosome analysis. However, because they ignore XCI, these approaches are not based on biologically plausible models and, therefore, are likely to lose power to detect X-chromosome-associate genetic variants. In this grant, we propose to develop a novel statistical approach for analyzing X-chromosomal genetic data that will account for different XCI processes, including random XCI, skewed XCI, and escape from XCI (Aim 1). Since individual markers only explain a small fraction of the expected heritability and the experimental evidence has shown that multiple markers/genes tend to function together on complex diseases, we will also develop gene-based and, even further, pathway-based approaches for analyzing X-chromosome data (Aim 1). We will analyze the head and neck cancer X-chromosome genetic data using the proposed and existing approaches, based on the existing data from an ongoing GWAS at The University of Texas MD Anderson Cancer Center (R01 CA131324, PI: Sanjay Shete, co-investigator of this grant) (Aim 2).