Automated binning of microsatellite alleles: problems and solutions

摘要: As genotyping methods move ever closer to full automation, care must be taken ensure that there is no equivalent rise in allele-calling error rates. One clear source of lies with how raw allele lengths are converted into classes, a process referred as binning. Standard automated approaches usually assume collinearity between expected and measured fragment length. Unfortunately, such often only approximate, the consequence alleles do not conform perfect 2-, 3- or 4-base-pair periodicity. To account for these problems, we introduce method allows repeat units fractionally shorter longer than their theoretical value. Tested on large human data set, our algorithm performs well over wide range dinucleotide loci. The size problem caused by sticking whole numbers bases indicated fact effective length was within 5% assumed 68.3% time.