Sequence the Genome once, use any time: Web Based System for Real Time, in silico Genotyping and Visualization of High Throughput Sequence Data

Agricultural researchers studying livestock have successfully used high throughput genotyping technologies to identify genotype/phenotype associations in their research populations.  However, it has been demonstrated that in order to identify the functional alleles, it is necessary to comprehensively catalog and genotype the variants found in the locus surrounding the statistically significant allele.  Historically, this has been an arduous process requiring PCR resequencing of gene regions from large populations that are both expensive, and time intensive to perform and acquire respectively.  Massively parallel sequencing has been used by livestock researchers, and has resulted in a wealth of freely available, high quality sequence data.  This data is a powerful resource, and, if managed appropriately, it may be accessed for selective genotyping and inspection of specific loci in seconds per animal.

We have developed an architecture and a web based interface that supports real time genotyping of arbitrary gene loci using all next generation sequence data available to our system.  We present here, the software system that makes it possible to genotype populations of 100s of animals in hours at specific whole genes or variant sites, capturing not only genotype data, but the sequence data used to make the call such that it can be investigated further by other researchers who wish to interrogate the findings.