Regional variation in mutation rates

Credit: Marta Tomaszkiewicz

Mutation rates vary at a fine scale - even within individual chromosomes. We are using statistical modeling to study such regional variation in mutation rates. Our analysis of insertions vs. deletions revealed that they are formed, at least in part, by different molecular mechanisms and that, in addition to replication, recombination plays an important role in indel formation (Kvikstad et al. 2007). Employing wavelet transformation techniques, we demonstrated the importance of genomic scale for regional variation in mutation rates (Kvikstad et al. 2009). Using specialized statistical approaches, we have investigated the structure of rate co-variation for four mutation types (point mutations, insertions, deletions, and microsatellite mutations) and simultaneously exploring the associations with multiple genomic features (Ananda et al. 2011). Moreover, we were able to segment the genome into regions with high and low rates of different mutations (Kurupummulage Don, Ananda, et al. 2013). Collaborator: Francesca Chiaromonte.

Members

Ph.D. student

Publications

. Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate. GENOME RES, 2018.

Regional variation DOI Press Release

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

Microsatellite Regional variation DOI

. Genomic Landscape of Human, Bat, and Ex Vivo DNA Transposon Integrations. MOL BIOL EVOL, 2014.

Regional variation DOI

. Segmenting the human genome based on states of neutral genetic divergence. P NATL ACAD SCI USA, 2013.

Regional variation DOI

. Rescuing Alu: Recovery of New Inserts Shows LINE-1 Preserves Alu Activity through A-Tail Expansion. PLOS GENET, 2012.

Regional variation DOI

. Molecular Clocks. eLS, 2008.

Regional variation DOI

. Human-macaque comparisons illuminate variation in neutral substitution rates. GENOME BIOL, 2008.

Regional variation DOI

. A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms. PLOS COMPUT BIOL, 2007.

Regional variation DOI

. Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network. BMC BIOINFORMATICS, 2006.

Regional variation DOI

. Initial sequence of the chimpanzee genome and comparison with the human genome. NATURE, 2005.

Regional variation DOI

. Oscillating Evolution of a Mammalian Locus with Overlapping Reading Frames: An XLαs/ALEX Relay. PLOS GENET, 2005.

Regional variation DOI

. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. NATURE, 2004.

Regional variation Sex chromosome DOI

. Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. NATURE, 2002.

Regional variation DOI

. Male-driven evolution. CURR OPIN GENET DEV, 2002.

Regional variation Sex chromosome DOI