There is a lack of information on how individual microsatellite loci differ with respect to their mutation properties. Such variation will have an important bearing on our understanding of the ubiquitous occurrence of simple repeat sequences in eukaryotic genomes and on deriving proper mutation models that can be incorporated into genetic distance estimates. We genotyped approximately 100 families of the bird barn swallow (Hirundo rustica) for two hypervariable (heterozygosity >95%) microsatellite markers: HrU6, an (AAAG)n tetranucleotide repeat, and HrU10, an (AAGAG)n pentanucleotide repeat. A total of 27 germline mutation events were documented, corresponding to mutation rates of 0.57% (HrU6) and 1.56% (HrU10). The mutation rate increased with allele size, at approximately 0.1% per repeat unit over the observed range of allele sizes (approximately 10-100 repeat units). Single repeat unit changes dominated, with 21/27 mutations representing the gain or loss of one repeat unit. There was no clear difference in the number of gains versus losses nor was there an effect of allele size on the magnitude or direction of mutation. Unexpectedly, the mutation rate of females (maternally transmitted mutations) was 2.5-5 times higher than that of males. Contrasting these observations with mutation data from other microsatellite loci reveals differences not only in the mutation rate, but also in the magnitude, direction and effect of sex on mutation. Thus, microsatellite mutation and evolution may be viewed as a dynamic and variable process.

A simple method of inferring the genotyping error rate of SNP arrays and similar high-throughput genotyping methods from Mendelian errors is described. Application to genotypes from small families using the Affymetrix GeneChip Human Mapping 50 k Array indicates an error rate of about 0.1%, and this rate can be reduced by increasing the quality criterion for calls, though at the cost of a reduced genotype call rate, which limits the benefit available. Simulated data are used to show that the number of SNPs on this array is sufficient for such a low error rate to have little impact on identical by descent-based inference for disease linkage in sib-pair studies.

Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.

Though extensively used in a variety of disciplines, the evolutionary pattern of microsatellite sequences is still unclear. We addressed several questions relating to microsatellite evolution by analysing historically accumulated mutation events in a large set of artiodactyl (CA) n repeats, through sequence analysis of orthologous bovine and ovine loci. The substitution rate in microsatellite £anking sequences was not di¡erent from that in intron sequences, suggesting that if intron sequences in general are selectively neutral, sequences close to microsatellites are similarly so. This observation thus does not support the idea that successful heterologous ampli¢cation of microsatellites across distantly related taxa would be due to £anking sequences generally being under some form of selection. Interestingly, the substitution rate at the ¢rst nucleotide positions £anking repeats was signi¢cantly higher than in sequences further away. Moreover, the substitution rate in repeat units in the very end of microsatellites was signi¢cantly higher than that in the middle of repeat regions. Together these observations suggest a relative instability close to the boundary between repetitive and unique sequences. We present three models that potentially could explain such a feature, all involving ine¤ciency of mismatch repair systems.

Presence of extracellular amyloid plaques is a neuropathological hallmark of Alzheimer disease. Here the authors have compared the methylation status of a CpG-island in the amyloid precursor protein gene (APP) in DNA extracted from the more plaque-vulnerable cortex regions with DNA from the more plaque-resistant cerebellum using material from six familial Alzheimer disease cases. Bisulfite sequencing of a 188 bp fragment in the APP associated CpG-island showed no methylation in any sample, suggesting that APP is not transcriptionally regulated by methylation in any of the investigated brain regions.