Selecting informative skin microbiome single nucleotide polymorphisms (SNPs) for human identification




Budowle, Bruce
Sherier, Allison
Woerner, August E.


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The human microbiome is considered the second human genome, contributing to a large portion of the genetic content of the human body. The microbiome of the skin adds additional genetic information that can be used to supplement traditional forensic DNA evidence derived from human sources. Based on past research, a massively parallel sequencing (MPS) panel called hidSkinPlex was designed as a targeted clade-specific multiplex which contains 282 bacterial and 4 phage markers. The hidSkinPlex was developed under the hypothesis that genes from stable, universal microbial species can differentiate skin microbiomes of individuals and be applied towards forensic human identification (HID) purposes. Further testing of hidSkinPlex has produced extensive sequence data from the microbiomes of 51 unrelated individuals from 3 forensically relevant body-sites in triplicate. The focus of this research study is to improve upon classification accuracies by using genetic distance to identify individuals instead of taxonomic differences like past research. Selecting SNPs that differentiate individuals based on their microbial populations will allow for a novel approach to HID using the skin microbiome, similar to past approaches for selecting SNPs that differentiate individuals based on their human bioancestry. Wright's fixation index (FST) was used as a novel genetic approach to select SNPs of interest in conjunction with supervised machine learning techniques. This work supports the hypothesis that the skin microbiome may be a viable source for HID and potentially improve analysis of samples currently yielding low level human DNA, such as touch samples