Events / Comparative genomics enhances capabilities of high throughput CRISPR screens in diverse laboratory microbe populations (CANCELED)

Comparative genomics enhances capabilities of high throughput CRISPR screens in diverse laboratory microbe populations (CANCELED)

March 6, 2020
12:00 pm - 1:00 pm

This event was canceled.

Invited Speaker: Dr. Ian Fiddes

Senior Manager of Content and Curation at Inscripta, Inc.

Abstract

The availability of a high-quality reference assembly and inexpensive, high throughput genome sequencing has revolutionized our view of biology. Despite our ability to observe vast amounts of genetic diversity we still lag in our ability to predict phenotype from sequence alone. This holds true across multiple applications, from protein engineering to clinical sequencing. The development of CRISPR systems to facilitate the editing of genomes has created excitement around the idea of engineering biology, but current implementations do not scale, are not accessible and perform poorly for many applications. We have developed an automated, benchtop instrument that can generate up to 10,000 variants, in either E. coli or S. cerevisiae, in a single run. These libraries consist of multiple variant types, including SNVs, MNVS and block substitutions in both coding and non-coding regions.

The quality and similarity of a reference assembly that is used to design a high throughput CRISPR experiment is essential to the ability to evaluate the results after editing. SNVs present in the cells being edited relative to the reference confuse edit detection software. Sequence divergence can lead to ineffective guide designs. In addition, high quality annotations are required to drive guide design. We have implemented a comparative genomics approach for annotating assemblies of laboratory E. coli and yeast strains that enables strain-specific CRISPR guide design. We also leverage IsoSeq sequencing of yeast strains to improve the yeast annotation, adding UTR information that greatly improves quantification of single-cell RNA-seq data.

Biography

Ian T. Fiddes is a computational scientist at Inscripta. His team works on genomic content and curation, developing tools, APIs and databases that enable design of high quality high throughput CRISPR screen libraries. Ian was a PhD candidate in the Biomolecular Engineering and Bioinformatics program here at UCSC from 2013 to 2017, and worked as a computational scientist at 10x Genomics before joining Inscripta. His research interests include comparative genomics, genome annotation, single cell RNA and DNA sequencing, and structural variation.

To accommodate a disability, please contact Ben Coffey at the UC Santa Cruz Genomics Institute (becoffey@ucsc.edu, 831-459-1477).