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Genes 2017, 8(11), 329; doi:10.3390/genes8110329

Flanking Variation Influences Rates of Stutter in Simple Repeats

1
Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
2
Center of Excellence in Genomic Medicine (CEGMR), King Abdulaziz University, Jeddah 22252 3270, Saudi Arabia
*
Authors to whom correspondence should be addressed.
Received: 29 September 2017 / Revised: 7 November 2017 / Accepted: 7 November 2017 / Published: 17 November 2017
(This article belongs to the Special Issue Forensic Genomics)
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Abstract

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). While 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, rates of stutter were contrasted against the LUS as well as the PAL on different flanking haplotypic backgrounds. This study shows that rates of stutter can vary substantially depending on the flanking haplotype, and while there are cases where the LUS is a better predictor of stutter than the 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. These 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. View Full-Text
Keywords: stutter; flanking variation; longest uninterrupted stretch (LUS); parental allele length (PAL); short tandem repeats (STR) stutter; flanking variation; longest uninterrupted stretch (LUS); parental allele length (PAL); short tandem repeats (STR)
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Woerner, A.E.; King, J.L.; Budowle, B. Flanking Variation Influences Rates of Stutter in Simple Repeats. Genes 2017, 8, 329.

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