Industrial-Scale Variant Analysis Enabling the 99 Lives Cat Genome Project

Next generation sequencing has ushered in the era of massive data sets that require specialized bioinformatics expertise, enhanced computing resources, and ample time to extract knowledge from raw data. Here we describe a complete DNA sequencing “analysis kit” on the Maverix Analytic Platform, with robust scalability to handle massive projects. A biologist-friendly web-based interface requires only a few steps to configure and launch variant detection using industry-standard tools including GATK and FreeBayes. Key results are summarized in reports, while individual annotated variants can be explored interactively via sorting and filtering on annotated qualities. For those who wish to visualize the full genomic context of variants, a link is provided to a secure, private version of the UCSC Genome Browser for advanced exploration. We demonstrate this powerful integrated system with early successes from the 99 Lives Cat Whole Genome Sequencing Initiative, led by Professor Leslie Lyons at the University of Missouri. By studying variants in cats of different breeds and physical characteristics, consortium researchers have started to identify mutations correlated with genetic causes of feline illnesses, enabling development of new diagnostics and leads for future therapies. Numerous findings will also have implications to human diseases, such as Leber’s Congential Amaurosis, a rare inherited eye disease. The complete analyses will be made freely available to the public as a “Community of Discovery” to maximize their value and encourage deeper exploration.