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Flanking Variation Influences Rates of Stutter in Simple Repeats

NCJ Number
Genes Volume: 11 Issue: 8 Dated: 2017
Date Published
8 pages
This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and although there are cases where the longest uninterrupted stretch (LUS) is a better predictor of stutter than the parental allele length (PAL), examples to the contrary are apparent in commonly assayed forensic markers; further, flanking variation that is 7 bp from the repeat region can impact rates of stutter.

It has been posited that the longest uninterrupted stretch (LUS) of tandem repeats, as defined by the number of exactly matching repeating motif units, is a better predictor of rates of stutter than the parental allele length (PAL). Although there are cases where this hypothesis is likely correct, such as the 9.3 allele in the TH01 locus, there can be situations where it may not apply as well; for example, the PAL may capture flanking indel variations while remaining insensitive to polymorphisms in the repeat, and these haplotypic changes may impact the stutter rate. To address this, the current study contrasted rates of stutter against the LUS and the PAL on different flanking haplotypic backgrounds. The findings suggest that non-proximal effects, such as DNA secondary structure, may be impacting the rates of stutter in common forensic short tandem repeat markers. (publisher abstract modified)

Date Published: January 1, 2017