Relationships between estimated autozygosity and complex traits in the UK Biobank

Abstract

28Inbreeding increases the risk of certain Mendelian disorders in humans but may 29 also reduce fitness through its effects on complex traits and diseases. Such inbreeding 30 depression is thought to occur due to increased homozygosity at causal variants that are 31 recessive with respect to fitness. Until recently it has been difficult to amass large 32 enough sample sizes to investigate the effects of inbreeding depression on complex 33 traits using genome-wide single nucleotide polymorphism (SNP) data in population-34 based samples. Further, it is difficult to infer causation in analyses that relate degree of 35 inbreeding to complex traits because confounding variables (e.g., education) may 36 influence both the likelihood for parents to outbreed and offspring trait values. The 37present study used runs of homozygosity in genome-wide SNP data in up to 400,000 38 individuals in the UK Biobank to estimate the proportion of the autosome that exists in 39 autozygous tracts-stretches of the genome which are identical due to a shared 40 common ancestor. After multiple testing corrections and controlling for possible 41 sociodemographic confounders, we found significant relationships in the predicted 42 direction between estimated autozygosity and three of the 26 traits we investigated: age 43 at first sexual intercourse, fluid intelligence, and forced expiratory volume in 1 second. 44Our findings for fluid intelligence and forced expiratory volume corroborate those of 45 several published studies while the finding for age at first sexual intercourse was novel. 46These results may suggest that these traits have been associated with Darwinian fitness 47 over evolutionary time, although there are other possible explanations for these 48 associations that cannot be eliminated. Some of the autozygosity-trait relationships were 49 attenuated after controlling for background sociodemographic characteristics, suggesting 50 that care needs to be taken in the design and interpretation of ROH studies in order to 51 glean reliable information about the genetic architecture and evolutionary history of 52 complex traits. 53 3 54 Author Summary 55Inbreeding is well known to increase the risk of rare, monogenic diseases, and there has 56 been some evidence that it also affects complex traits, such as cognition and 57 educational attainment. However, difficulties can arise when inferring causation in these 58 types of analyses because of the potential for confounding variables (e.g., 59socioeconomic status) to bias the observed relationships between distant inbreeding and 60 complex traits. In this investigation, we used single-nucleotide polymorphism data in a 61 very large (N > 400,000) sample of seemingly outbred individuals to quantify the degree 62 to which distant inbreeding is associated with 26 complex traits. We found robust 63 evidence that distant inbreeding is inversely associated with fluid intelligence and a 64 measure of lung function, and is positively associated with age at first sex, while other 65 trait associati...

Autozygosity influences cardiometabolic disease-associated traits in the AWI-Gen sub-Saharan African study

“…Clark et al 10 , analyzing a large sample size of 1.4 M found that for all the traits affected by inbreeding depressionβ F ROH jF GRM was of greater magnitude and in many casesβ F GRM jF ROH was also nonsignificant. Our results therefore confirm what Clark et al 10 and Johnson et al 14…”

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity

“…1 By examining their genomic location and prevalence in a population, we can learn about the history and adaptation of natural populations, 96,97 and we can make discoveries about the genetic basis of complex phenotypes. [32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48] Given the importance of demographic history and socio-cultural practices in the generation of ROH in individual genomes, and their relationship to complex phenotypes including many genetic diseases, it naturally follows to study the distribution of deleterious alleles and their relationship to ROH.…”

“…The prevalence of ROH in individual genomes has also been an important factor for understanding the genetic basis of complex phenotypes. [32][33][34] High levels of ROH have been associated with heart disease, 35,36 cancer, [37][38][39] blood pressure, 40,41 LDL cholesterol, 41 various mental disorders, [42][43][44][45] human height, 46,47 and increased susceptibility to infectious diseases. 48 Indeed, these results are consistent with the idea that many rare alleles of small effect may be the cause of increased risk for complex diseases, [49][50][51] especially if these mutations are recessive.…”

Unbalanced Sample Size Introduces Spurious Correlations to Genome-Wide Heterozygosity Analyses

“…Studies have emerged that investigate the role of genome-wide genetic diversity in human diseases and traits [11][12][13][14][15][16]. These studies usually adapt traditional population genetic measures, such as the H score [27], runs of homozygosity [28], and inbreeding coefficients [29] that were originally developed to measure diversity at a small number of genetic loci to analyzing tens of thousands of loci produced from high-throughput sequencing data.…”

“…However, these studies often produce contradictory results [10]. For instance, Campbell et al [11] reported significant associations of low genome-wide heterozygosity with high blood pressures, while three other studies did not observe these relationships [12][13][14]. Similarly, Bihlmeyer et al [15] and Xu et al [16] independently reported a positive impact of genomic diversity on human mortality and longevity.…”