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MotivationBiobank scale genetic associations results over thousands of traits can be difficult to visualize and navigate.ResultsWe have created LAVAA, a visualization web-application to generate genetic volcano plots for simultaneously considering the P-value, effect size, case counts, trait class and fine-mapping posterior probability at a single-nucleotide polymorphism (SNP) across a range of traits from a large set of genome-wide association study. We find that user interaction with association results in LAVAA can enrich and enhance the biological interpretation of individual loci.Availability and implementationLAVAA is available as a stand-alone web service (https://geneviz.aalto.fi/LAVAA/) and will be available in future releases of the finngen.fi website starting with release 10 in late 2023.

Although network visualizations are becoming increasingly common, designing such visualizations can be challenging due to the number of visual elements and non-linear relations that they need to display. The main design challenge faced is finding the right trade-off between providing a sufficient level of information detail while keeping the visual complexity of the visualization as low as possible. One way of overcoming this challenge is to rely on the use of mental models that are familiar to the users of network visualizations. In this paper, we propose the use of a mental interaction model similar to that of map visualizations – generally based on geographical maps – as the basis for visual design of network diagrams. We argue that such a mental model would foster a set of network interaction tasks that can be defined broadly as wayfinding. We present the process of wayfinding from a semiotic standpoint, and match its main key points to those of interaction tasks with network diagrams. As a case study forthis analysis, we also present a prototype network diagram visualization tool, called Colocalization Network Explorer, which we have developed to support the exploration of the relationships between various diseases and the portion of the human genome that is potentially involved in their onset. Additionally, we describe how the design process has benefited from the adoption of the wayfinding mental model.

Information about individual-level genetic ancestry is central to population genetics, forensics and genomic medicine. So far, studies have typically considered genetic ancestry on a broad continental level, and there is much less understanding of how more detailed genetic ancestry profiles can be generated and how accurate and reliable they are. Here, we assess these questions by developing a framework for individual-level ancestry estimation within a single European country, Finland, and we apply the framework to track changes in the fine-scale genetic structure throughout the 20th century. We estimate the genetic ancestry for 18,463 individuals from the National FINRISK Study with respect to up to 10 genetically and geographically motivated Finnish reference groups and illustrate the annual changes in the fine-scale genetic structure over the decades from 1920s to 1980s for 12 geographic regions of Finland. We detected major changes after a sudden, internal migration related to World War II from the region of ceded Karelia to the other parts of the country as well as the effect of urbanization starting from the 1950s. We also show that while the level of genetic heterogeneity in general increases towards the present day, its rate of change has considerable differences between the regions. To our knowledge, this is the first study that estimates annual changes in the fine-scale ancestry profiles within a relatively homogeneous European country and demonstrates how such information captures a detailed spatial and temporal history of a population. We provide an interactive website for the general public to examine our results., Author summary We have inherited our genomes from our parents, who, in turn, inherited their genomes from their parents, etc. Hence, a comparison between genomes of present day individuals reveals genetic population structure due to the varying levels of genetic relatedness among the individuals. We have utilized over 18,000 Finnish samples to characterize the fine-scale genetic population structure in Finland starting from a binary East-West division and ending up with 10 Finnish source populations. Furthermore, we have applied the resulting ancestry information to generate records of how the population structure has evolved each year between 1923 and 1987 in 12 geographical regions of Finland. For example, the war-related evacuation of Karelians from Southeast Finland to other parts of the country show up as a clear, sudden increase in the Evacuated ancestry elsewhere in Finland between 1939 and 1945. Additionally, different regions of Finland show very different levels of genetic mixing in 1900s, from little mixed regions like Ostrobothnia to highly mixed regions like Southwestern Finland. To distribute the results among general public, we provide an interactive website for browsing the municipality and region-level genetic ancestry profiles at https://geneviz.aalto.fi/genetic_ancestry_finland/