Description

Expression VNTR (eVNTR) is defined by association between repeat length of VNTR and level of expression of genes within +/-500 kb of each other. The gene expression levels were obtained from RNAseq and the repeat length for VNTRs were estimated using CNVnator on Whole Genome Sequencing.

Display Convention

The Track shows association between VNTR and gene expression. The red color indicate negative correlation, while blue color indicate a positive correlation.

Method

We utilized data from the Parkinson’s Progression Markers Initiative (PPMI) cohort (https://www.ppmi-info.org/), corresponding to 712 individuals (189 healthy controls and 523 samples with varying types of Parkinsonism) with available Illumina WGS data aligned to the reference genome. RNAseq data generated from peripheral blood were available for 676 PPMI samples, comprising read counts for 22,582 genes listed in GENCODE v19. The read counts were filtered, normalized and subject to rank-based inverse normal transformation using scripts provided by the GTEx consortium (https://github.com/broadinstitute/gtex-pipeline). These normalized expression data were adjusted for gender, the first three ancestry-related principle components derived from PCA of SNVs, and 60 additional components estimated using PEER. We performed linear regression between VNTR copy number and corrected expression level of each gene located within ±500kb using the lm function in R. We applied a False Discovery Rate correction, and reported all VNTR:gene pairs with FDR q<0.1.

References

The manuscript is currently under review. A copy of the manuscript is available here: https://www.biorxiv.org/content/10.1101/2020.12.16.423078v1