Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis

We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and γ-glutamyl transferase. Using data from 12 cohorts, including 18,265 cases with cirrhosis, 1,782,047 controls, up to 1 million individuals with liver function tests and a validation cohort of 21,689 cases and 617,729 controls, we identify and validate 14 risk associations for cirrhosis. Many variants are located near genes involved in hepatic lipid metabolism. One of these, PNPLA3 p.Ile148Met, interacts with alcohol intake, obesity and diabetes on the risk of cirrhosis and hepatocellular carcinoma (HCC). We develop a polygenic risk score that associates with the progression from cirrhosis to HCC. By focusing on prioritized genes from common variant analyses, we find that rare coding variants in GPAM associate with lower ALT, supporting GPAM as a potential target for therapeutic inhibition. In conclusion, this study provides insights into the genetic underpinnings of cirrhosis.

Genome-wide meta-analysis identifies 93 risk loci and enables risk prediction equivalent to monogenic forms of venous thromboembolism

We report a genome-wide association study of venous thromboembolism (VTE) incorporating 81,190 cases and 1,419,671 controls sampled from six cohorts. We identify 93 risk loci, of which 62 are previously unreported. Many of the identified risk loci are at genes encoding proteins with functions converging on the coagulation cascade or platelet function. A VTE polygenic risk score (PRS) enabled effective identification of both high- and low-risk individuals. Individuals within the top 0.1% of PRS distribution had a VTE risk similar to homozygous or compound heterozygous carriers of the variants G20210A (c.*97 G > A) in F2 and p.R534Q in F5. We also document that F2 and F5 mutation carriers in the bottom 10% of the PRS distribution had a risk similar to that of the general population. We further show that PRS improved individual risk prediction beyond that of genetic and clinical risk factors. We investigated the extent to which venous and arterial thrombosis share clinical risk factors using Mendelian randomization, finding that some risk factors for arterial thrombosis were directionally concordant with VTE risk (for example, body mass index and smoking) whereas others were discordant (for example, systolic blood pressure and triglyceride levels).

Loss-of-function variants in founder population highlight atrial myopathy as susceptibility to atrial fibrillation

Background

Atrial fibrillation (AF) is the most common cardiac arrhythmia, and it's associated with genes responsible for cardiac conduction, cardiogenesis, and cardiac structure. The Finnish population has evolved in relative isolation and undergone several bottlenecks, resulting in enrichment of deleterious variants. This facilitates identification of possible causal genes through protein-truncating variants that likely would not have been identified in other populations.

Purpose

To identify novel genetic associations with large effect on AF risk.

Methods

We accessed publicly available summary statistics on AF (ICD-10 code I48) from the FinnGen project R6, containing 28,670 AF cases and 135,821 controls. Then, we annotated all variants in the summary statistics and extracted variants that were predicted with a high effect impact (n=7,113). To account for multiple testing, a false discovery rate cutoff <10% was applied. The UK Biobank was assessed for comparison of allele frequencies. Afterwards, we investigated protein and single-cell RNA expression of the genes of interest in human atrial tissue. Human atrial tissue was obtained by us from 7 individuals and used for mass spectrometry-based proteomics, while single-nucleus RNA sequencing (snRNAseq) data from human hearts was acquired by Tucker [1].

Results

In a genome-wide association study (GWAS) focusing on loss-of function (LOF) variation, we report two LOF variants in the structural genes SYNPO2L and CTNNA3 with much higher allele frequencies compared to non-Finnish Europeans (85-fold and 80-fold enrichment, respectively). The variants increase the risk of AF considerably, which is emphasized as the two variants show the highest effect sizes of all GWAS variants ever associated with AF (SYNPO2L; odds ratio [OR] = 2.79, P-value = 1.32x10–8 and CTNNA3; OR = 2.43, P-value = 9.40x10–7), exceeding that of most clinical risk factors. We accessed phenome-wide association study (PheWAS) results on both variants. There was no association with other phenotypes for the SYNPO2L variant whereas the CTNNA3 variant showed suggestive association with valvular heart disease (P-value = 2.95x10–5). SYNPO2L and CTNNA3 exhibited high protein and RNA expression levels in atrial tissue and were predominantly expressed in cardiomyocytes (Fig. 1).

Conclusion

We identified novel associations between LOF variation in the structural genes SYNPO2L and CTNNA3 and AF. Our study showed how genetic examination of a European subpopulation facilitates discovery of genetic variants and pathophysiological understanding. The results underline the importance of thoroughly investigating subpopulations as unique variants with large effect sizes can be identified.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): This work was supported by the Research Foundation at Rigshospitalet and the Hallas-Møller Emerging Investigator Novo Nordisk.

Female preferences for temporal order of call components in the túngara frog: a Bayesian analysis

We employed a Bayesian statistical approach to examine female preferences in the Neotropical frog Physalaemus pustulosus for the temporal relationship of the two parts of the conspecific advertisement call. The male advertisement call consists of a 'whine', which is necessary for species recognition, followed immediately by one or more 'chucks', which make the whine more attractive to females. We conducted 42 two-choice experiments with a total of 840 individual tests to compare the attractiveness of a whine with a chuck in a variety of positions relative to the start of the whine against a normal whine or against a normal whine/chuck. Females have a bimodal preference function for chuck position. Chucks placed in a variety of positions after the whine (including the position of a chuck in a normal call) were generally as attractive as a normal whine/chuck. Chucks placed before the whine were generally more attractive than a whine alone, and in some positions as attractive as the normal whine/chuck. Chucks overlapping the end of the whine make the call more attractive than a whine alone, but not as attractive as a normal whine/chuck, while chucks overlapping an initial portion of the whine beginning 50 ms into it are ignored; previous work (Wilczynski et al. 1995, Animal Behaviour, 49, 911-929) indicates this region to be critical for species recognition. These results suggest that female P. pustulosus have preferences for the temporal relationship of the two parts of the conspecific male advertisement call that far exceed the vocal signals produced by males, and that male calls have evolved calls to exploit one peak of this function. Copyright 1999 The Association for the Study of Animal Behaviour.