Browsing by Subject "DNA Phenotyping"

Now showing 1 - 3 of 3
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    Elucidating the mechanisms or interactions involved in differing hair color follicles
    (2016) Muralidharan, Charanya; Walsh, Susan
    Forensic DNA phenotyping is an up and coming area in forensic DNA analyses that enables the prediction of physical appearance of an individual from DNA left at a crime scene. At present, there has been substantial work performed in understanding what genes/markers are required to produce a reliable prediction of categorical eye and hair color from the DNA of an individual of interest. These pigmentation markers (variants from HERC2, OCA2, TYR, SLC24A4, SLC45A2, IRF4 to name a few) are at the core of several prediction systems for eye and hair color such as IrisPlex, HIrisPlex, and the Snipper 2.5 suite. The contribution of these markers towards prediction in most cases however, only factors in an independent effect and do not take into account potential interactions or epistasis in the production of the final phenotypic color. Epistasis is a phenomenon that occurs when a gene’s effect relies on the presence of ‘modifier genes’, and can display different effects (enhance/repress a particular color) in genotype combinations rather than individually. In an effort to detect such epistatic interactions and their influence on hair color prediction models, for this current study, 872 individuals were genotyped at 61 associative and predictive pigmentation markers from several diverse population subsets. Individuals were phenotypically evaluated for eye and hair color by three separate independent assessments. Several analyses were performed using statistical approaches such as multifactor dimensionality reduction (MDR) for example, in an effort to detect if there are any SNP- SNP epistatic interactions present that could potentially enhance eye and hair color prediction model performances. The ultimate goal of this study was to assess what SNP-SNP combinations amongst these known pigmentation genes should be included as an additional variable in future prediction models and how much they can potentially enhance overall pigmentation prediction model performance. The second part of the project involved the analyses of several differentially expressed candidate genes between different hair color follicles of the same individual using quantitative Real Time PCR. We looked at 26 different genes identified through a concurrent non-human primate study being performed in the laboratory. The purpose of this study was to gain more insight on the level of differentially expressed mRNA between different hair color follicles within the same human individual. Data generated from this part of the project will act as a pilot study or ‘proof of principle’ on the mRNA expression of several pigmentation associated genes on individual beard hair of varying phenotypic colors. This analysis gives a first glimpse at expression levels that remain constant or differentiate between hairs of the same individual, therefore limiting the contribution of individual variation.
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    Enhancing Our Genetic Knowledge of Human Iris Pigmentation and Facial Morphology
    (2019-12) Eller, Ryan; Walsh, Susan; Berbari, Nicolas; Lapish, Christopher; Picard, Christine; Roper, Randall
    The biological underpinnings that control iris pigmentation and facial morphology are two areas of research that over the last decade are becoming more thoroughly investigated due to the increased affordability of genotyping and advances in technology allowing for more advanced analysis techniques. Despite the ease of access to the data and the tools required to perform iris pigmentation and facial morphological studies, there are still numerous challenges researchers must overcome when exploring the genetics of these complex phenotypes. Some of these challenges include difficulty in working with the bioinformatic programs designed to analyze genetic associations, the inability to define a phenotype that captures the true nature of these traits, and analysis techniques that fail to model complex gene-gene interactions and their effect on a phenotype or phenotypes of interest. In this body of work, I attempted to address these challenges by designing a bioinformatic pipeline, Odyssey, that bridges the communication gaps between various data preparation programs and the programs that analyze genomic data. With this program, genome-wide association studies (GWAS) could be conducted in a quicker, more efficient, and easier manner. I also redefined iris color as a quantitative measurement of pre-defined color classes. In this way it is possible to define and quantify the unique and intricate mixtures of color, which allows for the identification of known and novel variants that affect individual iris color. I also improved upon current prediction models by developing a neural network model capable of predicting a quantitative output to four pre-defined classes; blue/grey, light brown (hazel), perceived green, and dark brown. I examined the effects of defining a simple facial morphology phenotype that more accurately captures the lower face and jaw shape. I then analyzed this phenotype via a GWAS and found several novel variants that may be associated with a square and diamond shaped face. Lastly, I demonstrated that structural equation modeling can be used in combination with traditional GWAS to examine interactions amongst associated variants, which unearths potential biological relationships that impact the multifaceted phenotype of facial morphology.
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    Forensic DNA phenotyping and massive parallel sequencing
    (2017-12-04) Breslin, Krystal; Walsh, Susan
    In the forensic science community, there is an immense need for tools to help assist investigations where conventional DNA profiling methods have been non-informative. Forensic DNA Phenotyping (FDP) aims to bridge that gap and aid investigations by providing physical appearance information when other investigative methods have been exhausted. To create a “biological eye witness”, it becomes necessary to constantly improve these methods in order to develop a complete and accurate image of the individual who left the sample. To add to our previous prediction systems IrisPlex and HIrisPlex, we have developed the HIrisPlex-S system for the all-in-one combined prediction of eye, hair, and skin color from DNA. The skin color prediction model uses 36 variants that were recently proposed for the accurate prediction of categorical skin color on a global scale, and the system is completed by the developmental validation of a 17-plex capillary electrophoresis (CE) genotyping assay that is run in conjunction with the HIrisPlex assay to generate these genotypes. The predicted skin color output includes Very Pale, Pale, Intermediate, Dark and Dark-to-Black categories in addition to categorical eye (Blue, Intermediate, and Brown) and hair (Black, Brown, Blond, and Red) color predictions. We demonstrate that the HIrisPlex-S assay performs in full agreement with guidelines from the Scientific Working Group on DNA Analysis Methods (SWGDAM), achieving high sensitivity levels with a minimum 63pg DNA input. In addition to adding skin color to complete the pigmentation prediction system termed HIrisPlex-S, we successfully designed a Massively Parallel Sequencing (MPS) assay to complement the system and bring Next Generation Sequencing (NGS) to the forefront of forensic DNA analyses methods. Using Illumina’s MiSeq system enables the generation of HIrisPlex-S’s 41 variants using sequencing data that has the capacity to xiii better deconvolute mixtures and perform with even more sensitivity and accuracy. This transition opens the door for a plethora of new ways in which this physical appearance assay can grow as sequencing technology is not limited by variant number; therefore, in essence many more traits have the potential to be included in this one assay design. For now, the HIrisPlex-S design of 41 variants using MPS is being fully assessed according to SWGDAM validated guidelines; therefore, this design paves the way for Forensic DNA Phenotyping to be used in any forensic laboratory. This new and improved HIrisPlex-S system will have a profound impact on casework, missing persons cases, and anthropological cases, as it is relatively inexpensive to run, HIrisPlex-S is easy to use, developmentally validated and one of the largest systems freely available online for physical appearance prediction from DNA using the freely available online web tool found at https://hirisplex.erasmusmc.nl/. Lastly, moving forward in our aim to include additional traits for prediction from DNA, we contributed to a large-scale research collaboration to unearth variants associated with hair morphology. 1026 samples were successfully sequenced using an inhouse MPS design at 91 proposed hair morphological loci. From this reaction, we were able to contribute to the identification of significant correlations between the SNPs rs2219783, rs310642 and rs80293268 with categorical hair morphology: straight, wavy or curly.