Accurate measurement of microsatellite length by disrupting its tandem repeat structure

Wang, Zihua, Moffitt, Andrea B, Andrews, Peter, Wigler, Michael, Levy, Dan (September 2022) Accurate measurement of microsatellite length by disrupting its tandem repeat structure. Nucleic Acids Research. gkac723. ISSN 0305-1048

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Abstract

Tandem repeats of simple sequence motifs, also known as microsatellites, are abundant in the genome. Because their repeat structure makes replication error-prone, variant microsatellite lengths are often generated during germline and other somatic expansions. As such, microsatellite length variations can serve as markers for cancer. However, accurate error-free measurement of microsatellite lengths is difficult with current methods precisely because of this high error rate during amplification. We have solved this problem by using partial mutagenesis to disrupt enough of the repeat structure of initial templates so that their sequence lengths replicate faithfully. In this work, we use bisulfite mutagenesis to convert a C to a U, later read as T. Compared to untreated templates, we achieve three orders of magnitude reduction in the error rate per round of replication. By requiring agreement from two independent first copies of an initial template, we reach error rates below one in a million. We apply this method to a thousand microsatellite loci from the human genome, revealing microsatellite length distributions not observable without mutagenesis.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations > mutagenesis bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations
CSHL Authors:	Wang, Zihua Moffitt, Andrea B Andrews, Peter Wigler, Michael H. Levy, Dan
Communities:	CSHL labs > Levy lab CSHL labs > Wigler lab CSHL Cancer Center Program CSHL Cancer Center Program > Cancer Genetics and Genomics Program
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	12 September 2022
Date Deposited:	20 Sep 2022 21:36
Last Modified:	09 Feb 2024 20:51
PMCID:	PMC9723644
URI:	https://repository.cshl.edu/id/eprint/40721

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