Identity-by-descent analysis of a large Tourette's syndrome pedigree from Costa Rica implicates genes involved in neuronal development and signal transduction

Abstract

Tourette Syndrome (TS) is a heritable, early-onset neuropsychiatric disorder that typically begins in early childhood. Identifying rare genetic variants that make a significant contribution to risk in affected families may provide important insights into the molecular aetiology of this complex and heterogeneous syndrome. Here we present a whole-genome sequencing (WGS) analysis from the 11-generation pedigree (>500 individuals) of a densely affected Costa Rican family which shares ancestry from six founder pairs. By conducting an identity-by-descent (IBD) analysis using WGS data from 19 individuals from the extended pedigree we have identified putative risk haplotypes that were not seen in controls, and can be linked with four of the six founder pairs. Rare coding and non-coding variants present on the haplotypes and only seen in haplotype carriers show an enrichment in pathways such as regulation of locomotion and signal transduction, suggesting common mechanisms by which the haplotype-specific variants may be contributing to TS-risk in this pedigree. In particular we have identified a rare deleterious missense variation in RAPGEF1 on a chromosome 9 haplotype and two ultra-rare deleterious intronic variants in ERBB4 and IKZF2 on the same chromosome 2 haplotype. All three genes play a role in neurodevelopment. This study, using WGS data in a pedigree-based approach, shows the importance of investigating both coding and non-coding variants to identify genes that may contribute to disease risk. Together, the genes and variants identified on the IBD haplotypes represent biologically relevant targets for investigation in other pedigree and population-based TS data.

Fig. 1. Outline of the analysis strategies implemented in this study.

A IBD analysis pipeline: WGS data were pre-filtered to produce an LD-pruned set of common variants (MAF > 5%) for IBD analysis. Haplotype phasing was performed using SHAPEIT2 + duoHMM plug-in, pairwise IBD analysis was performed using the refined-IBD algorithm. Clusters of individuals sharing haplotypes IBD (multi-IBD clusters) were identified using the efficient multiple-IBD (EMI) algorithm. B Haplotype and variant filtering strategy: IBD haplotypes identified from the IBD pipeline were filtered on length, clustered by founder pair, filtered to exclude haplotypes seen in population controls and seen in unaffected pedigree individual. The most informative subset of haplotypes was taken forward to search for deleterious variants. Using this approach, the number of haplotypes to investigate was reduced from 339 to eleven, from which five deleterious haplotype-specific variants were identified (two coding and three non-coding).

Fig. 2. Fine-mapping of the IBD haplotypes (yellow block) using the phased chromosome data (blue; above the fine-mapped haplotype) and the WGS data (green/grey; below the fine-mapped haplotype).

The arrows show the origin of the allele assigned to the fine-mapped haplotype. The backbone of the haplotype was built from the SNPs present on the IBD haplotype in the phased chromosome data. The remaining variants from the WGS data (~3.2% of the total variants on the haplotype) were mapped to the haplotype based on the genotype status of the IBD haplotype carriers (light green) versus the individuals who do not carry the IBD haplotype (grey), as demonstrated by the alleles highlighted in bold. Where a definitive haplotype allele could not be assigned due to uninformative genotypes, no allele was assigned at that position (WGS positions marked with red arrows).