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theses

Biological evidence acquired from crime scenes often contains mixtures of partial genomes from an unknown number of cells from any number of unknown contributors. Therefore, assessing the probability that a person contributed to an evidentiary item becomes a complicated combinatorial challenge, which is made more difficult in the presence of extraneous signal originating from random allele drop-in events or stutter artifacts. Not only does forensic DNA signal consist of extraneous signal, but it may exhibit significant levels of allele non-detection, often referred to as allele drop-out. Given these two sources of drop-out and the desire to stabilize inference results between laboratories, it is of interest to develop laboratory protocols aimed at reducing 1) drop-out due to sampling effects; and 2) drop-out due to detection effects.
In Phase I of the project we determined, through a DNA simulator named ValiDNA, that the optimal analytical conditions consisted of 29 PCR cycles and a 25 second injection. Once optimal analytical conditions were determined, a variety of collection/extraction pipelines were evaluated. In particular, cutting versus swabbing techniques were tested, as were silica and direct-to-PCR extraction methods. Notably, coupling a cotton swab collection with a silica-based extraction forces DNA volume partitions be processed through to PCR, while the FLOQSwab® and PicoPure® method is a ‘direct-to-PCR’ method that does not fractionate the extract. Experimentation demonstrated that there was not a significant difference between the four pre-PCR processes tested.
In conclusion, this work demonstrates that stabilizing the DNA signal acquired through PCR-based techniques is possible through the implementation of a simulation-based approach, using the laboratories’ own data to parameterize an in-silico DNA laboratory. Notably, if all laboratories choose parameters that render consistent detection of a single-copy of DNA, the evidentiary signal between laboratories will contain the same information contents, substantially improving evidential inference at a national scale. Additionally, using optimal analytical pipelines clearly demonstrates that direct PCR methods are not necessarily beneficial when attempting low-copy number interpretation; rather, multiple replicate amplifications of DNA rendered from a swab-silica pre-PCR pipeline is preferred.

ETD_10003

M.S.

Includes bibliographical references

doi:10.7282/t3-2eh1-rh05

ETD graduate

The author owns the copyright to this work.