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Effects of DNA copy number on short tandem repeat stutter ratios
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Khan, Saadia A.. Effects of DNA copy number on short tandem repeat stutter ratios. Retrieved from https://doi.org/doi:10.7282/t3-4jkm-vz40

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TitleEffects of DNA copy number on short tandem repeat stutter ratios
NameKhan, Saadia A. (author); Grgicak, Catherine (chair); Salas-de la Cruz, David (member); Kumi, George (member); Grgicak, Catherine M (member); Rutgers University; Graduate School - Camden
Date Created2021
Other Date2021-10 (degree)
SubjectBiochemistry, Chemistry
Extent1 online resource (ix, 40 pages)
DescriptionDetermining the weight of evidence against a suspect is best served by high fidelity signal representations of forensically relevant genomic regions of interest: Short tandem repeats (STR). During PCR, STR is a synthesized fragment one repeat unit shorter than wildtype. When electrophoresed and detected, the relative peak heights at the stutter and allele positions can be used as a proxy for the relative level of stutter to allele product generated during PCR, informing forensic DNA interpretation. Since many forensic samples contain only a few copies of DNA, this study explores if relative stutter abundances are of the same distributions when originating from high- and low- copy numbers. Data analysis began by categorizing the signals as noise, stutter, and allele. Only stutter and allelic peaks were retained for further analysis. Samples were amplified at 0.25 ng and 0.0313 ng; data from 5 STR loci were interrogated, resulting in analysis across 620 data points. The data was first explored through visual representation via boxplot.

Before proceeding to statistical analysis, a comprehensive literature review demonstrated that the stutter models solely relying on per-locus descriptions of stutter ratios (SRs) may be improved by considering the sequence of the STRs themselves. As such, all statistical evaluations were conducted on a per-allele basis. Next, a t-test (p-value threshold: 0.005) was employed to explore if average SRs between high- and low-copy numbers are similar. The results show significantly different mean values between the two templates. This has far-reaching forensic implications since it suggests that classical binary approaches to genotype inference for low-template samples ought not utilize boundaries developed from high-template ones.

Subsequently, we tested the SRs between low- and high- template samples by evaluating the similarity of the distributions themselves. To complete this test, a Kolmogorov-Smirnov test was performed. Mostly, the distributions were distinct, wherein low template samples demonstrated a higher proportion of stutter peaks exceeding expectation. These results are similar to the t-test results, therein suggesting a more refined approach to genotype inference is required for complex forensic signal containing both high- and low- template levels within a single mixture.
NoteM.S.
NoteIncludes bibliographical references
Genretheses
Persistent URLhttps://doi.org/doi:10.7282/t3-4jkm-vz40
LanguageEnglish
CollectionCamden Graduate School Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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