Workshop in Biostatistics

M112 Alway Building, Medical Center

(next to the Dean's courtyard)

DATE: May 18, 2017
TIME: 1:30 - 2:50 pm
TITLE: Analyzing and interpreting short tandem repeat variation in humans
SPEAKER:
Melissa Gymrek
Assistant Professor, Department of Medicine
Department of Computer Science and Engineering
University of California, San Diego

 

Abstract:

Recent studies have made substantial progress in identifying genetic variants associated with disease and molecular phenotypes in humans. However, these studies have primarily focused on single nucleotide polymorphisms (SNPs), ignoring more complex variants that have been shown to play important functional roles. Here, I focus on short tandem repeats (STRs), one of the most polymorphic and abundant classes of genetic variation. I will first provide an overview of recent advances in sequencing technology and bioinformatics algorithms allowing the first characterization of hundreds of thousands of STRs on a population-wide scale. Next, I will describe how we are using deep catalogs of STR variation to interrogate the role of STRs in complex traits in humans. Finally, I will present a method leveraging per-locus mutation properties from our population-wide catalog to measure genetic constraint at individual STRs. These results provide a framework in which to interpret the significance of individual STR mutations in human disease. Altogether, our results highlight the putative phenotypic contribution of complex variants and the opportunity for a wealth of genetic discoveries to be gained by expanding analyses to less understood regions of the genome.

 

Suggested readings:

Melissa Gymrek. (2017) A genomic view of short tandem repeats. Curr Opin Genet Dev. 44:9-16 (A review article that I hope will provide relevant background).

Melissa Gymrek, Thomas Willems, David Reich, Yaniv Erlich. (2016) A framework to interpret short tandem repeat variation in humans. biorXiv. (http://biorxiv.org/content/early/2016/12/09/092734.1)