Microsatellite Data

Microsatellites are defined in tandem repeat loci with repeat motifs 2 to 6 base pairs in length. They can be further classified by the length of the repeated motif. For example, a locus with repeat sequence CA is a dinucleotide, while one composed of CTC repeats is a trinucleotide. Microsatellite loci are densely and widely distributed in the human genome. Estimates of 300,000 tri- and tetranucleotide repeats in the genome translate to an average frequency of one locus every 10 kilobases. Dinucleotide repeats of the form CA are estimated to occur once every 30 kb. Microsatellites are found in large numbers on all chromosomes.

The Genome Database (GDB) contains the largest set of microsatellite loci data available. However, errors within the data make it necessary to screen the data before using it in analysis. Thus, the following data have been "cleaned" in a variety of ways.

Loci where complete information was not available were discarded.
If the sum of the relative frequencies for a locus was less than one, the error was corrected with the following process:

multiply the relative frequency of each allele by the number of chromosomes in the sample
take the ceiling of this value
divide this number by the number of chromosomes in the sample
round to two decimal places

The resulting value was taken as the relative frequency value for the given allele.

If the sum of the frequency values was not close to one, cut-off values became important. The values 0.90 and 1.10 were arbitrarily set as the inclusive lower and upper bounds for retaining data.
Sometimes, the recorded number of chromosomes in the sample appeared to be the number of individuals in the sample. In this case, the number was simply multiplied by 2.
In cases where the number of chromosomes sampled for a locus was not reported, the locus was retained. The number of chromosomes sampled is required for unbiased estimates of various parameters. If the value was missing, we settled for biased estimates.
Loci with missing frequency or allele size values were eliminated.

A table (postscript or pdf) with the number of loci from each chromosome, by repeat type, that contain sufficient data to be included in the set of usable data.

Here's some data. Chromosomes 15-22 were compiled by Heidi Spratt during the period May '97 to August '97. Chromosomes 1-14 were compiled by Leslea Davison (these will be added in the future).

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