LAVAA: a lightweight association viewer across ailments

Eric B Fauman; Stella Keppo; Nicola Cerioli; Rupesh Vyas; Mitja Kurki; Mark Daly; Mary Pat Reeve

doi:10.1093/bioadv/vbad018

LAVAA: a lightweight association viewer across ailments

Bioinform Adv. 2023 Feb 15;3(1):vbad018. doi: 10.1093/bioadv/vbad018. eCollection 2023.

Authors

Eric B Fauman¹, Stella Keppo², Nicola Cerioli², Rupesh Vyas², Mitja Kurki^{3

4

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7}, Mark Daly^{3

4

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7}, Mary Pat Reeve³

Affiliations

¹ Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA.
² Visual Communication Design, Aalto University, Espoo 02150, Finland.
³ Finnish Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00014, Finland.
⁴ Program for Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁶ Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
⁷ Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.

Abstract

Motivation: Biobank scale genetic associations results over thousands of traits can be difficult to visualize and navigate.

Results: We 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 implementation: LAVAA 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.