Dr. Filippo Geraci, Istituto di Informatica e Telematica, CNR, Pisa, Polymorphic Tandem repeats in the human genome: identification of rare aberrant variants in ALS patients

event date: 8 March 2019

The Centre of New Technologies invites to a seminar by

Filippo Geraci, PhD

 Polymorphic Tandem repeats in the human genome: identification of rare aberrant variants in ALS patients.

Date: March 8th, 2019 at 12 p.m.

Venue: Centre of New Technologies, Banacha 2C,
Lecture Hall 0142 (Ground floor)

Host: Prof. Dariusz Plewczyński

Abstract: Tandem repeats (TRs) are one of the most common structures in eukaryotic DNA and consist of approximate replicates of a (typically small) DNA motif that lie adjacent to each other. In spite of this simple definition, identifying TRs in the genome is computationally challenging because of the absence of any a-priori information about: the motif length, the number of copies, and the purity of each replicate. The task is further complicated by the lack of an agreed method to discriminate biologically/functionally relevant TRs from spurious not significant repetitions.
Several papers have shown that a relevant fraction of TRs is polymorphic, namely, the number of copies of the base consensus motif is variable in at least one allele. Although not completely understood yet, this intrinsic polymorphism (in particular an aberrant expansion), often related to meiotic instability, is known to be among the causative factors in several degenerative diseases.

In the first part of the talk we introduce some algorithmic strategies for TRs discovery and for measuring the polymorphism: we present our experience in compiling a comprehensive census of polymorphic tandem repeats. Then we focus on population studies of tandem repeats variability: we discuss our experience with a cohort of 70 ALS patients, the challenges and the opportunities.