Since the decoding of the human genome project concluded in 2003, rapid technological advances in the area of human genetics including genetic testing and bio banking have accelerated. Public discussion of genetic testing and biobanking are the focus of this thesis. Genetic profiling and predictive tests aim to establish the causal conditions for disorders such as Fragile X, cystic fibrosis and Huntington's disease. Biobanking involves the storage of genetic material for genetic research and can also include genealogical research. The complex and varied relationships that Maori (indigenous peoples of New Zealand) in different social locations have with western science (and human genetics in particular) is at the heart of this thesis. The thesis explores the responses of three differently located Maori social groups to the challenges posed by genetic testing and biobanking. Focus/contact group discussion with Maori members of the Church of Jesus Christ of Latter Day Saints, a group of rongoa or traditional Maori health practitioners, and a group of Maori lawyers illustrate both diversity in the ways in which Maori respond to the issues posed by human genetics, and connections among them as they draw on Maori ontologies and epistemologies. In the analyses of these discussions which constitute the core of this thesis, Maori can be seen juggling alternative frames of reference and negotiating between knowledge systems. The thesis does not purport to provide an overview of Maori responses to genetic testing. Instead it uses discussion among three groups of research participants to illustrate the relevance of temporal and relational knowledge in local situations. A range of social science and Te Ao Maori conceptual tools are used to analyse conversations among research participants. These tools include discussion of power/knowledge and governmentality, actor network theory, sociological discussions of agency as well as concepts of whakapapa, kaitiaki, mauri, and mana motuhake. My goal is to illustrate both connection and heterogeneity in Maori responses to the challenges posed by genetic testing and bio banking.

Exome sequencing, the process of sequencing the set of all known exons simultaneously using next-generation sequencing technology, has dramatically changed the landscape of genetic research and genetic testing. The incredible volume of data produced by these experiments creates challenges in: 1) annotating the affects of observed variants, 2) filtering to remove noise, 3) identifying plausible disease-causing variants, and 4) validating experimental results. Here we will present a series of bioinformatic tools and techniques intended to address these challenges with exome sequencing and associated validation experiments. First, we will present the Automated Sequence Analysis Pipeline (ASAP), a tool for the efficient and automated management, detection and annotation of Sanger sequencing-based genetic testing and variant validation. This pipeline is extended to annotate exome-sequencing derived variants. Exome sequencing experiments produce a great number of variants that do not cause a patient's disease. One of the biggest challenges in exome sequencing experiments is sorting through these false positives to discover the true disease-causing variants. We have developed several techniques to aid in the reduction of these errors. The techniques described include: 1) the construction of a catalog of systematic errors by reprocessing thousands of publically available exomes, 2) a tool for the filtering of variants based on family structure and disease assumptions, and 3) a tool for discovering regions of autozygosity from the exomes of several affected patients in consanguineous pedigrees. Classes of variants that are undiscoverable using current analysis techniques gives rise to false negatives in exome sequencing experiments. We will present a tool, the Retrotransposon Insertion Detector for Exomes (RIDE) that uses the characteristic anomalies present in sequence alignments to detect the insertion of repetitive elements. The process of identifying a the cause of a patient's disease using exome sequencing data has been equated to finding a needle in a stack of needles. Only through the proper annotation of variants and the reduction of the error rates associated with exome sequencing experiments can this task be achieved in an efficient manner.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [145]-167).

Thesis (M.A.)--Indiana University, 2007. / Department of Philosophy, Indiana University-Purdue University Indianapolis (IUPUI). Advisor(s): Jason T. Eberl, Peter H. Schwartz, William H. Schneider. Includes vitae. Includes bibliographical references (leaves 71-81).

This thesis examines the regulation of the direct-to-consumer genetic testing industry through analysis of the industry's use of wrap contracts (clickwrap and browsewrap), A significant portion of the thesis consists of a comparative document review of the publicly available wrap contracts of DTCGT companies provided tests for health purposes. It also considers other regulatory responses to date. Due to the lack of industry specific regulation it argues that the use of wrap contracts can be viewed as a means of industry self-regulation and a form of private legislation. This means that governance is skewed heavily in favour of companies and it creates an imbalance in the respective rights and obligations of the parties - company and consumer - which is likely to result in consumer detriment. It is argued that certain types of terms commonly include in DTCGT contracts, including: unilateral variation clauses; some exclusion clauses; choice of law clauses; indemnity; and consent clauses are likely to be deemed unfair and unenforceable under UK law. It recommends that in the short-term the Competition and Markets Authority should undertake a compliance review of DTCGT contracts in order to improving contracts for consumers. In the long term, companies should also be complying with data protection law, as well as legislation on medical devices and the provisions of the Human Tissue Act and there may be a need for industry specific legislation.

Background: This mixed-methods dissertation is multi-layered and exploratory in nature. It provides methodological contributions to the fields of evaluation and research methods by demonstrating how the root cause analysis (RCA) method can be utilized to evaluate program improvement and assist in the development of research questions and hypotheses. Additionally, it adds to the literature on reproductive genetics decision-making by contributing to the knowledge of this complex process. Research Aims: This dissertation includes the following three aims: 1) to illustrate how the RCA interview method can be a useful tool to improve programs that have not been implemented with fidelity; 2) to demonstrate how the RCA interview method can be adapted for research by elucidating research questions and hypothesis development processes; and 3) to glean information pertaining to reproductive genetics decision-making knowledge, attitudes, and behaviors among genetic counselors and women who were pregnant and had reproductive genetic counseling. Methods: Mixed-methods research took place over a 13-month period in Arizona and across the U.S. between June 2015 and August 2016 among two separate groups. The qualitative research includes semi-structured, in-depth interviews with genetic counselors (n=22), and RCA interviews (n=9) with genetic counselors sampled from 12 southwestern and western states. The quantitative research comprised of piloting two survey instruments. Survey #1 for genetic counselors (n=22) and Survey #2 for women who had genetic counseling and were pregnant between January 1, 2005 and December 31, 2015 (n=104). Results: The results by manuscript are: 1) RCA is a useful evaluation tool for evaluating program improvement when programs have not been implemented with fidelity; 2) RCA is a beneficial methodological approach for researchers for focusing areas of inquiry, generating research questions, and developing research hypotheses; and 3) Women with a master's degree or higher are more likely to have reproductive genetic testing than women with a bachelor’s degree or under. Women who received reproductive genetic testing had significantly higher genetic testing knowledge scores than women who did not have genetic testing. Women who held a master's degree or higher had significantly higher genetic testing knowledge scores than women with a bachelor’s degree or under. Conclusions: RCA is a flexible and adaptive tool that works well for evaluation and research purposes. Reproductive genetic testing is a complex field that is rapidly changing, and there are significant differences in knowledge among women facing testing decisions calling for tailored interventions around genetic testing literacy. Recommendations: Evaluators and researchers alike should be aware of RCA as a useful methodological tool that they can use to help evaluate program improvement as well as facilitate the process of developing research questions and hypotheses. Genetic literacy interventions and decision-making resources must take into consideration the role education has on genetic testing decisions as well as its part in understanding the appropriateness, benefits, and limitations of specific genetic tests. This research further advocates for women to have access to certified genetic counselors to tailor the information to meet the individuals' needs in order to promote informed, autonomous genetics decision-making.

Huntington disease (HD) is a genetically transmitted fatal neurodegenerative condition that currently has no cure. The symptoms of HD are manifested as cognitive declines, neuropsychiatric disturbances, and motor dysfunction. An autosomal dominant genetic defect is responsible for the onset of HD, which means that the children of an affected parent have a 50% chance of inheriting the disease. Predictive genetic testing for HD has been available since 1993, and a positive test result means that a person will develop HD with 100% certainty. People who have the HD-gene expansion, but have not yet manifested unequivocal motor signs, are said to be in the prodromal phase of HD. A number of studies have examined concerns about the utility of genetic testing and its negative psychological consequences for gene-expanded and non-expanded individuals (e.g., traumatization, suicidal ideation). Although research has understandably focused on the potential for distress, there has been some evidence suggesting that individuals may actually experience psychological growth related to a receiving a genetic test result (e.g., improved relationships, pursuing new opportunities). The aim of the present study was to understand the relationship between genetic testing, prodromal HD symptoms, and posttraumatic growth (PTG). Participants were recruited through the multinational PREDICT-HD study (Jane Paulsen, PI) and they completed the Posttraumatic Growth Inventory (PTGI; Tedeschi & Calhoun, 1996) to assess permanent positive psychological change as a result of learning about their HD-gene status. The Symbol Digit Modalities Test (Smith, 1991), Unified Huntington's Disease Rating Scale Motor Exam (Huntington's Study Group, 1996), and the SCl-90-R Depression subscale (Derogatis, 1994) were also completed. A total of 82 gene-expanded patients and 37 non-expanded patients took part in this study. Results revealed that gene-expanded and non-expanded individuals reported experiencing PTG, particularly in their appreciation for life and ability to relate to others. Gene-expanded and non-expanded participants did not differ in the amount of growth they reported, which indicated that the outcome of genetic testing was not related to how much growth people experienced. Age and gender were associated with PTG, with younger participants and women reporting the most growth. The amount of time elapsed since genetic testing, estimated proximity to a diagnosis of HD, and the clinical characteristics of prodromal HD were not related to PTG. In conclusion, people experience positive psychological change as result of genetic testing for HD. The findings of this study have important implications for future research and for mental health professionals assisting people through the genetic counseling process.

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