Exome sequencing of Finnish isolates enhances rare-variant association power.

Exome-sequencing studies have generally been underpowered to identify deleterious alleles with a large effect on complex traits as such alleles are mostly rare. Because the population of northern and eastern Finland has expanded considerably and in isolation following a series of bottlenecks, individuals of these populations have numerous deleterious alleles at a relatively high frequency. Here, using exome sequencing of nearly 20,000 individuals from these regions, we investigate the role of rare coding variants in clinically relevant quantitative cardiometabolic traits. Exome-wide association studies for 64 quantitative traits identified 26 newly associated deleterious alleles. Of these 26 alleles, 19 are either unique to or more than 20 times more frequent in Finnish individuals than in other Europeans and show geographical clustering comparable to Mendelian disease mutations that are characteristic of the Finnish population. We estimate that sequencing studies of populations without this unique history would require hundreds of thousands to millions of participants to achieve comparable association power.

Author Correction: Exome sequencing of Finnish isolates enhances rare-variant association power.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Power loss due to testing association between covariate-adjusted traits and genetic variants.

Multiple linear regression is commonly used to test for association between genetic variants and continuous traits and estimate genetic effect sizes. Confounding variables are controlled for by including them as additional covariates. An alternative technique that is increasingly used is to regress out covariates from the raw trait and then perform regression analysis with only the genetic variants included as predictors. In the case of single-variant analysis, this adjusted trait regression (ATR) technique is known to be less powerful than the traditional technique when the genetic variant is correlated with the covariates We extend previous results for single-variant tests by deriving exact relationships between the single-variant score, Wald, likelihood-ratio, and F test statistics and their ATR analogs. We also derive the asymptotic power of ATR analogs of the multiple-variant score and burden tests. We show that the maximum power loss of the ATR analog of the multiple-variant score test is completely characterized by the canonical correlations between the set of genetic variants and the set of covariates. Further, we show that for both single- and multiple-variant tests, the power loss for ATR analogs increases with increasing stringency of Type 1 error control ( α ) and increasing correlation (or canonical correlations) between the genetic variant (or multiple variants) and covariates. We recommend using ATR only when maximum canonical correlation between variants and covariates is low, as is typically true.

Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.

Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20-30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5' and 3' untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF<1%. Additionally, two potentially deleterious variants that demonstrated significant associations (rs138726309, a missense variant in G6PC2, and rs28933094, a missense variant in LIPC) were considerably more common in these Finnish samples than in European reference populations, supporting our prior hypothesis that deleterious variants could attain high frequencies in this isolated population, likely due to the effects of population bottlenecks. Our results highlight the value of large, well-phenotyped samples for rare-variant association analysis, and the challenge of evaluating the phenotypic impact of such variants.

Bayesian Strategies in Rare Diseases.

Bayesian strategies for planning and analyzing clinical trials have become a viable choice, especially in rare diseases where drug development faces many challenges and stakeholders are interested in innovations that may help overcome them. Disease natural history and clinical outcomes occurrence and variability are often poorly understood. Standard trial designs are not optimized to obtain adequate safety and efficacy data from small numbers of patients. Bayesian methods are well-suited for adaptive trials, with an accelerated learning curve. Using Bayesian statistics can be advantageous in that design choices and their consequences are considered carefully, continuously monitored, and updated where necessary, which ultimately provides a natural and principled way of seamlessly combining prior clinical information with data, within a solid decision theoretical framework. In this article, we introduce the Bayesian option in the rare disease context to support clinical decision-makers in selecting the best choice for their drug development project. Many researchers in drug development show reluctance to using Bayesian statistics, and the top-two reported barriers are insufficient knowledge of Bayesian approaches and a lack of clarity or guidance from regulators. Here we introduce concepts of borrowing, extrapolation, adaptation, and modeling and illustrate them with examples that have been discussed or developed with regulatory bodies to show how Bayesian strategies can be applied to drug development in rare diseases.

Twins in Guinea-Bissau have a 'thin-fat' body composition compared to singletons.

The 'thrifty phenotype' hypothesis proposed that fetal undernutrition increases risk of diabetes in later life. Undernourished low birthweight Indian babies are paradoxically more adipose compared to well-nourished European babies, and are at higher risk of diabetes in later life. Twin pregnancies are an example of in utero growth restrictive environment due to shared maternal nutrition. There are few studies of body composition in twins. We performed secondary analysis of anthropometric body composition of twins and singletons in Guinea-Bissau, an economically deprived African country.Anthropometric data were available on 7-34 year-old twins (n = 209, 97 males) and singletons (n = 182, 86 males) in the Guinea-Bissau Twin Registry at the Bandim Health Project. Twins had lower birthweight (2420 vs 3100 g, p < 0.001); and at follow-up, lower height (HAZ mean Z-score difference, -0.21, p = 0.055), weight (WAZ -0.73, p = 0.024) and BMI (BAZ -0.22, p = 0.079) compared to singletons but higher adiposity (skinfolds: +0.33 SD, p = 0.001). Twins also had higher fasting (+0.38 SD, p < 0.001) and 2-hour OGTT glucose concentrations (+0.29 SD, p < 0.05). Linear mixed-effect model accounting for intrapair correlations and interactions confirmed that twins were thinner but fatter across the age range. Data on maternal morbidity and prematurity were not available in this cohort.African populations are known to have a muscular (less adipose) body composition. Demonstration of a thin-fat phenotype in twins in a low socio-economic African country supports the thesis that it could be a manifestation of early life undernutrition and not exclusive to Indians. This phenotype could increase risk of diabetes and related conditions.

Multigenerational Undernutrition Increases Susceptibility to Obesity and Diabetes that Is Not Reversed after Dietary Recuperation.

People in developing countries have faced multigenerational undernutrition and are currently undergoing major lifestyle changes, contributing to an epidemic of metabolic diseases, though the underlying mechanisms remain unclear. Using a Wistar rat model of undernutrition over 50 generations, we show that Undernourished rats exhibit low birth-weight, high visceral adiposity (DXA/MRI), and insulin resistance (hyperinsulinemic-euglycemic clamps), compared to age-/gender-matched control rats. Undernourished rats also have higher circulating insulin, homocysteine, endotoxin and leptin levels, lower adiponectin, vitamin B12 and folate levels, and an 8-fold increased susceptibility to Streptozotocin-induced diabetes compared to control rats. Importantly, these metabolic abnormalities are not reversed after two generations of unrestricted access to commercial chow (nutrient recuperation). Altered epigenetic signatures in insulin-2 gene promoter region of Undernourished rats are not reversed by nutrient recuperation, and may contribute to the persistent detrimental metabolic profiles in similar multigenerational undernourished human populations.