Biomolecular and DNA Biometrics
Advances in sensor technologies, leveraged by lab-on-chip components, have enabled rapid human identification using molecular signatures. Rapid DNA systems with ‘sample in/answer out’ capability have moved forensic evaluation of human STR profiles from a process performed by multiple experts on a laboratory bench top to a standard procedure performed by a single police officer at a booking station.
In addition, the time it takes to complete accurate whole-genome sequencing of complex organisms has been reduced from weeks or days to hours through the development of next generation sequencing systems. These technologies could be viewed as foundational bio-molecular biometric systems that hold the potential to augment traditional automated modalities that are based on physiological and behavioral biometrics (face, fingerprint, iris, etc.).
To address the limitations of current systems, and enable the development of new bio-molecular biometrics modalities, BIIC researchers will explore interdisciplinary concepts associated with this field. Research areas ranging from sensor component design to the analysis of results will be explored, including: methods of enhancing the utility of poor-quality STR profiles obtained from degraded DNA samples and those deposited through touch, whole-genome approaches to identification linking genes within the human genome to the microbiome of hand bacteria, as well micro- and nano-scale devices capable of improving the detection and interpretation of DNA-based signatures used for human identification.
Three different projects that have been completed by the center are described below:
Bacterial DNA as a Human Biometric Identifier
The goal of this project was to develop a method of bacteria-based identification that can overcome the degradation and throughput issues associated with human STR analysis. The presence of bacteria on human skin has a negative connotation in the realm of health and hygiene. However, recent research into the variations of these bacterial colonies in individual people has led to the application of human bacteria as an identification tool.
Because bacterial colonies remain viable and multiply on surfaces, bacterial DNA is often more robust to environmental exposure than that of deposited human epithelial cells which are used to obtain human DNA. Recent studies of human skin bacterial composition based on gender, body location, time, and even washing habits, indicate little to no colonial variability for a single individual within these parameters, and high diversity among small groups (~20) of human subjects.
The specific aim of this project is to examine the population(s) of hand bacteria colonies within a group of 200 individuals. The findings of this study will provide the basis for the development of biometric identification techniques based on human bacterial signatures as shown in Fig. 1.
The bacterial signature of a human is expected to be as rich as a conventional DNA signature, likening this phase of research to the early stages of human DNA-based identification where specific differentiating STR loci were chosen from a larger grouping of loci. In order to better understand the composition of a bacterial signature, bacterial samples collected from hand swabs from 200 individuals were sequenced using an Illumina MiSeq genome sequencing instrument. Data extracted from the 16S rRNA region of the bacteria was evaluated to determine the phylogenetic distance (a measure of similarity or dissimilarity) between bacterial families occurring in the 200-person cohort, as well as colony diversity within a single subject and potential noise sources.
Metagenomic Data Analytics for Human Identification
The availability of vast quantities of human and microbial genomic data can be exploited to uncover unique ways that the human genome impacts both internal and external bacterial communities, and conversely, how these communities may impact our own genome.
Traits inherited from maternal and paternal genes impact our outward appearance or identity, and the field of epigenetics is uncovering certain regions of the human genome that indicate uniqueness beyond a readily observable physical appearance, such as personal habits and disease. Similarly, human bacterial colonies present in locations ranging from skin surfaces to the digestive tract are greatly impacted by health and environment, but may also be correlated to the host DNA as well based on epigenetic factors.
Our long term goal is to bridge this gap by combining the various human genomic data sets with those from the microbiomes. By so doing, we can mine human and microbial genomic data for potential biomarkers that enable determination of an individual’s habits, health, and identity.
The objective of this project, as shown in Fig.2, is to study the potential association between the composition of the skin microbiome and certain genetic traits that exist in the human genome in order to build a framework for exploiting these associations for the determination of identity.
WVU has data from a previous collection effort comprised of full human genomes and bacterial genomes from the same 20 individuals, along with metadata on ethnicity, hygiene habits, and health history. We also have access to public big data collections on genomic and metagenomic datasets of different types.
In this project following tasks were investigated:
- Task 1: We developed a computational framework for improved network propagation, using novel data structures. Such a framework will make it possible to connect information from the disparate datasets.
- Task 2: Guided by panels of single nucleotide polymorphisms (SNPs) that are associated with human ethnicities, diseases, etc., we investigated how these SNPs are mutated in our 20 subjects, and whether these can correctly classify the individuals in our dataset according to their metadata.
- Task 3: We performed a characterization of their respective microbiome to provide a detailed profile for each individual’s microbiome.
- Task 4: Using human genomic variations and the information from detailed microbial characterization, we performed comparative genomic analysis to determine which markers tend to vary for groups of people, (for instance, people of the same origin), and which tend to be unique for a given individual, independent of the group variations.
These analysis provided more information on the SNPs, genomic variants, and bacterial metagenomics codes that could be used in human identification, and human bio-geographical classification.
Nanotechnology-Enabled Improvements in Rapid DNA Hardware
The goal of this project is to develop new hardware components to improve the functionality of rapid DNA systems. These methods will allow the development of rapid DNA systems that can be used by untrained operators to identify both humans and pathogens or other harmful biomolecules.
Conventional DNA processing takes a long time. The longest processes are the PCR amplification steps taken to increase the amount of DNA so it is more easily measured. In addition, standard kits used to isolate non-human DNA samples from pathogens and unknown substances are not well developed. This research will enable faster, more-accurate measurement of small amounts of DNA through enhancement of the fluorescent emission level of the labeled DNA, improving detection limits and shortening PCR amplification times.
The work also enables the development of new DNA processing kits for human STRs, pathogens and other biomolecules. This research is transformative in that it applies novel target chemistry and component development to rapid DNA identification. These research components will offer new operational uses of DNA signatures in health, security, and environmental monitoring applications.