Microsatellite variation and evolution

Credit: Wilfried Guiblet

We have investigated microsatellite evolution in the framework of a life-cycle hypothesis, according to which microsatellites are born and expand into adulthood, until their degradation and death (Kelkar et al. 2011). Studies of microsatellite mutagenesis have significant utility, as microsatellites are implicated in numerous diseases and are popular markers in population genetics and forensics. To commence this project, we had to determine the minimal number of repeats constituting a microsatellite (Kelkar et al. 2010). Next, using sequenced primate genomes, we dissected the intricacies of the mutational processes leading to microsatellite birth and death (Kelkar et al. 2011). We also evaluated the contribution of transposable elements to microsatellite births and deaths, and described the mechanisms of births for many disease-causing microsatellites (Kelkar et al. 2011). We investigated how interruptions affect microsatellite mutability (Ananda et al. 2014) and developed a computational pipeline, STR-FM, to genotype microsatellites from next-generation sequencing data (Fungtammasan, Ananda, et al. 2015). (Figure: Kelkar et al. 2011). Collaborators: Kristin Eckert, Paul Medvedev, Francesca Chiaromonte.

Members

Research Technician

Ph.D. student

Publications

. Family reunion via error correction: an efficient analysis of duplex sequencing data. BMC BIOINFORMATICS, 2020.

Code Mitochondrial Microsatellite DOI

. IWTomics: testing high-resolution sequence-based `Omics' data at multiple locations and scales. BIOINFORMATICS, 2018.

Microsatellite Regional variation DOI

. Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats. MOL BIOL EVOL, 2016.

Microsatellite DOI

. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. GENOME RES, 2015.

Microsatellite DOI

. Mature Microsatellites: Mechanisms Underlying Dinucleotide Microsatellite Mutational Biases in Human Cells. G3-GENES GENOM GENET, 2013.

Microsatellite DOI

. Distinct Mutational Behaviors Differentiate Short Tandem Repeats from Microsatellites in the Human Genome. GENOME BIOL EVOL, 2013.

Microsatellite DOI

. The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes. GENOME RES, 2013.

Microsatellite DOI

. The genome-wide determinants of human and chimpanzee microsatellite evolution. GENOME RES, 2008.

Microsatellite DOI

. Tetranucleotide microsatellite markers for the Brown-headed Cowbird Molothrus ater. J AVIAN BIOL, 2003.

Microsatellite DOI

. Representational difference analysis to distinguish cryptic species. MOL ECOL, 1999.

Microsatellite DOI