University at Buffalo - The State University of New York
Skip to Content
Short tandem repeats in human exons: a target for disease mutations. - PubMed - NCBI
Format

Send to

Choose Destination
See comment in PubMed Commons below
BMC Genomics. 2008 Sep 12;9:410. doi: 10.1186/1471-2164-9-410.

Short tandem repeats in human exons: a target for disease mutations.

Author information

1
Bioinformatics Research Center, University of Aarhus, DK-8000 Aarhus C, Denmark. eskerod@birc.au.dk

Abstract

BACKGROUND:

In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions), are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats) are known to be hypermutable (indel-rich), but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect) tandem repeats (STRs) which fall below the radar of conventional tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes.

RESULTS:

We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%), 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats.

CONCLUSION:

Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp) and the limited length of STR regions.

PMID:
18789129
PMCID:
PMC2543027
DOI:
10.1186/1471-2164-9-410
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Support Center