Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease

Abstract

Common variants in RET and NRG1 have been associated with Hirschsprung disease (HSCR), a congenital disorder characterised by incomplete innervation of distal gut, in East Asian (EA) populations. However, the allelic effects so far identified do not fully explain its heritability, suggesting the presence of epistasis, where effect of one genetic variant differs depending on other (modifier) variants. Few instances of epistasis have been documented in complex diseases due to modelling complexity and data challenges. We proposed four epistasis models to comprehensively capture epistasis for HSCR between and within RET and NRG1 loci using whole genome sequencing (WGS) data in EA samples. 65 variants within the Topologically Associating Domain (TAD) of RET demonstrated significant epistasis with the lead enhancer variant (RET+3; rs2435357). These epistatic variants formed two linkage disequilibrium (LD) clusters represented by rs2506026 and rs2506028 that differed in minor allele frequency and the best-supported epistatic model. Intriguingly, rs2506028 is in high LD with one cis-regulatory variant (rs2506030) highlighted previously, suggesting that detected epistasis might be mediated through synergistic effects on transcription regulation of RET. Our findings demonstrated the advantages of WGS data for detecting epistasis, and support the presence of interactive effects of regulatory variants in RET for HSCR.

Figure 1

The LD pattern and − log10 (p-value) for 65 significant epistatic variants identified in RET. The 65 significant epistatic variants are those identified as significant (p < 0.05/727) based on at least in one epistasis model (phasing/phase-independent, cis, trans and C&T). The − log(p-value) are the log of the most significant p-values obtained for those 65 epistatic variants across epistasis models. The variants are ordered based on the physical location.

Figure 2

LD measures among three SNPS (rs2506030 (RET-7), rs7069590 (RET-5.5), rs2435357 (RET+3)) and the three representative epistatic variants (rs2506026, rs2506025, rs2506028). The conditional p-value refers to the p-value for the analysis conditioning on the lead variants; the additive p-value refers to the p-value obtained from the phasing-independent model.

Figure 3

The epistatic effects in log odds between the two representative epistatic variants with the lead variant (rs2435357) in RET. On the left panel, CT (Cis) refers to the scenario where the risk allele (T) in rs2506026 and the risk allele (T) in rs2435357 are inherited from the same parent; CT (Trans) refers to the scenario where the risk allele (T) in rs2506026 and the risk allele (T) in rs2435357 are inherited from the different parents; Similarly, on the right panel AG (Cis) refers to the scenario where the risk allele (A) in rs2506028 and the risk allele (T) in rs2435357 are inherited from the same parent; AG (Trans) refers to the scenario where the risk allele (A) in rs2506028 and the risk allele (T) in rs2435357 are inherited from the different parents.