MySeq: privacy-protecting browser-based personal Genome analysis for genomics education and exploration

Abstract

Background: The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing the need for specialized software tools will increase access to hands-on genomics pedagogy.

Results: MySeq is a React.js single-page web application for privacy-protecting interactive personal genome analysis. All analyses are performed entirely in the user's web browser eliminating the need to install and use specialized software tools or to upload sensitive data to an external web service. MySeq leverages Tabix-indexing to efficiently query whole genome-scale variant call format (VCF) files stored locally or available remotely via HTTP(s) without loading the entire file. MySeq currently implements variant querying and annotation, physical trait prediction, pharmacogenomic, polygenic disease risk and ancestry analyses to provide representative pedagogical examples; and can be readily extended with new analysis or visualization components.

Conclusions: MySeq supports multiple pedagogical approaches including independent exploration and interactive online tutorials. MySeq has been successfully employed in an undergraduate human genome analysis course where it reduced the barriers-to-entry for hands-on human genome analysis.

Keywords: Genomics education; Personal Genome analysis; Web application.

Fig. 1

Overview of dataflow in MySeq. The MySeq single-page web application performs personal genome analyses in the user’s web browser. (1) MySeq components query a locally stored or remotely available VCF file by genomic coordinates. (2) Internally MySeq uses the Tabix index to fetch and parse only the portion of the file containing variants in the query region. (3) MySeq further analyzes the VCF records entirely in the browser (e.g. displays the genotypes to the user, performs ancestry analysis, etc.). Optionally MySeq can utilize the publicly available MyVariant.info and MyGene.info APIs [37] to annotate variants or translate gene symbols or rsIDs to genomic coordinates for queries (e.g. query for all variants in BRCA1), but does not send any genotypes to a remote server

Fig. 2

Example of MySeq VCF loading, variant query and PGx interfaces. a The user can load data is several ways, including pre-configured publicly available genomes. b Having loaded NA12878’s genome, the user’s query of chr7:141672604 returned one overlapping variant 7:g.141672604 T > C for which NA12878 is heterozygous. The user clicked on the variant to obtain functional and other annotations from MyVariant.info [37]. (c) Via the “Analyses” dropdown in the header bar (shown fully expanded in the larger screenshot), the user can launch other analyses, e.g. extract variants associated with Warfarin dosing