Open Access Research article

Sequence determinants of human microsatellite variability

Trevor J Pemberton1*, Conner I Sandefur2, Mattias Jakobsson13 and Noah A Rosenberg12

Author Affiliations

1 Department of Human Genetics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109 USA

2 Center for Computational Medicine and Biology, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109 USA

3 Department of Evolutionary Biology, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden

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BMC Genomics 2009, 10:612  doi:10.1186/1471-2164-10-612

Published: 16 December 2009



Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database.


Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length), under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity.


These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.