Molecular Quantitative Trait Locus Mapping in Human Complex Diseases

Abstract

Mapping quantitative trait loci (QTLs) for molecular traits from chromatin to metabolites (i.e., xQTLs) provides insight into the locations and effect modes of genetic variants that influence these molecular phenotypes and the propagation of functional consequences of each variant. xQTL studies indirectly interrogate the functional landscape of the molecular basis of complex diseases, including the impact of non-coding regulatory variants, the tissue specificity of regulatory elements, and their contribution to disease by integrating with genome-wide association studies (GWAS). We summarize a variety of molecular xQTL studies in human tissues and cells. In addition, using the Alzheimer's Disease Sequencing Project (ADSP) as an example, we describe the ADSP xQTL project, a collaborative effort across the ADSP Functional Genomics Consortium (ADSP-FGC). The project's ultimate goal is a reference map of Alzheimer's-related QTLs using existing datasets from multiple omics layers to help us study the consequences of genetic variants identified in the ADSP. xQTL studies enable the identification of the causal genes and pathways in GWAS loci, which will likely aid in the discovery of novel biomarkers and therapeutic targets for complex diseases. © 2022 Wiley Periodicals LLC.

Keywords: complex human diseases; molecular traits; xQTLs.

Figure 1.

Types of genetic effects on different layers of molecular traits from chromatin to metabolites

Figure 2.. Examples of genetic driver SNPs:

A) a SNP (black triangle) cis-regulates a miRNA gene and also trans-regulates its mRNA targets (anti-correlated); B) a SNP cis-regulates a transcription factor (TF) gene encoding a repressor/activator, and this SNP also trans-regulates its miRNA targets (anti-/positively-correlated).