Tim Kosfeld
Faculty Advisor: Jim Giovannoni
Year: 2021

“Pipeline development for identification of high-impact structural variants”

Project Summary:

Structural variants (SV) are recognized as a prominent source of genetic variation, with single variants manifesting significant influence over phenotypic expression, but their effects remain poorly understood due to computational limitations and a continued focus on SNPs. Addressing this need, we introduce the Variant Identification Pipeline with Expression Realization (VIPER), a robust computational pipeline capable of identifying and annotating structural variants with significant expressional impact. Using a publicly available structural variant library as reference (Alonge et al., 2020), VIPER accepts processed RNA sequence data and constructs a list of SV-gene pairs based on chromosomal position. These SV-gene pairs are then evaluated by their differential expression values, with pairs expressing significantly concatenated to form a library of high-impact SV-gene pairs. This library of causal genomic variants within tomato accessions, annotated for gene function, allowed for the identification of 105 high-impact leaf development variants, and the isolation of a single insertion with substantial effect on leaflet morphology.

My Experience:

In my time at BTI I always enjoyed a strong sense of community. I felt welcomed by every member of my lab, not only academically, even though everyone was happy to instruct me on new practices like seed germination in medium or tomato cultivation in the greenhouses, but socially. I was quickly welcomed into lab social activities like ice cream trips, hiking or festivals on the weekend, and group exercises on BTI’s lawn after a long day. Professionally, I was constantly offered new experiences or conversations with knowledgeable mentors who provided great advice on not only academic pursuits, but on how to apply to graduate studies or market myself appropriately. Outside of BTI, Ithaca manages to be welcoming to newcomers while retaining a wonderful closeness, and I quickly found social groups for rock climbing, sand volleyball and pickup basketball. I strongly recommend this REU for wonderful social and academic experiences.