WGS Reports for Human iPS Cell Lines

Hi Everyone!


I'm Naomi and I've joined the Genestack team as a summer intern during my PhD in Genetics at the University of Cambridge. I'm currently working on developing an application to generate an informative, easy-to-read, visual report for genomic sequences of human iPS cell lines in partnership with the Neuroscience & Pain unit at Pfizer.

The data input to this application will most likely be genomic sequence data from cell line databases such as HipSci but it would also be widely applicable to other high-throughput genomic sequencing data. Such complex datasets require powerful computational analysis but also necessitate informative data output in order to be fully comprehensible. This challenging project requires both bioinformatic proficiency and the creativity to design an aesthetically beautiful yet practical solution to visualise data.

Once complete, the reporting application will provide an informatics-based summary of the main genomic features including the number of variants, copy number variations and karyotypic abnormalities like insertions and deletions. It will also have specific information relating to the disease model of interest, including whether there are any SNPs associated with eQTLs in particular gene cohorts, or whether there are variants associated with alternative disease traits. The overall output will therefore be a comprehensive yet easily accessible summary of the genomic features that are particularly salient in control cell lines.

Developing this type of application on the Genestack platform means that not only is the setup supported by powerful computational tools but the modular approach of the Genestack workflow enables a user to have complete control of how the data is manipulated. All preprocessing steps and many of the variant calling steps are already up-and-running on the Genestack system so that the report output will be entirely complementary to pre-existing applications and can be used in combination.

The application will hopefully be ready by the end of this summer, so watch this space for more information and to give it a test drive!