MODULE STATUS

Developers: Bas Heijmans & Yunfeng Liu

Scripts status: In development

Prerequisite scripts: scripts 00, 01, 02, 03

Data upload method: Automated upload to SurfSara.

Background

A primary role for epigenetic mechanisms, and in particular DNA methylation, is the inactivation of one copy of the X chromosome in females to maintain dosage equivalence between females who carry two copies of the X chromosome, and males who carry a single copy. The identification of autosomal genetic variants affecting chromosome X methylation in females can shed light on the genes and processes involved in X inactivation. Indeed, an analysis of 1867 female and 1398 male samples profiled using the 450k array identified three female-specific loci associated with DNA methylation in regions variably escaping X-chromosome inactivation (Luijk et al. Nat Commun 2018).

Strategy

To create a saturated catalog of genetic effects on DNA methylation of the sex chromosomes, we will extend our analysis to an approximately ten-fold increased sample size and the EPIC array interrogating twice the number of CpGs in GoDMC phase 2. Also, we will include chromosome Y and include both trans- and cis-effects.

Process

Use HASE software to perform meQTL analysis of chrX probes against all SNPs for females only Use HASE software to perform meQTL analysis of chrX and Y probes against all SNPs for males only