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- Creators: Barrett, The Honors College
Description
Genomic structural variation (SV) is defined as gross alterations in the genome broadly classified as insertions/duplications, deletions inversions and translocations. DNA sequencing ushered structural variant discovery beyond laboratory detection techniques to high resolution informatics approaches. Bioinformatics tools for computational discovery of SVs however are still missing variants in the complex cancer genome. This study aimed to define genomic context leading to tool failure and design novel algorithm addressing this context. Methods: The study tested the widely held but unproven hypothesis that tools fail to detect variants which lie in repeat regions. Publicly available 1000-Genomes dataset with experimentally validated variants was tested with SVDetect-tool for presence of true positives (TP) SVs versus false negative (FN) SVs, expecting that FNs would be overrepresented in repeat regions. Further, the novel algorithm designed to informatically capture the biological etiology of translocations (non-allelic homologous recombination and 3&ndashD; placement of chromosomes in cells –context) was tested using simulated dataset. Translocations were created in known translocation hotspots and the novel&ndashalgorithm; tool compared with SVDetect and BreakDancer. Results: 53% of false negative (FN) deletions were within repeat structure compared to 81% true positive (TP) deletions. Similarly, 33% FN insertions versus 42% TP, 26% FN duplication versus 57% TP and 54% FN novel sequences versus 62% TP were within repeats. Repeat structure was not driving the tool's inability to detect variants and could not be used as context. The novel algorithm with a redefined context, when tested against SVDetect and BreakDancer was able to detect 10/10 simulated translocations with 30X coverage dataset and 100% allele frequency, while SVDetect captured 4/10 and BreakDancer detected 6/10. For 15X coverage dataset with 100% allele frequency, novel algorithm was able to detect all ten translocations albeit with fewer reads supporting the same. BreakDancer detected 4/10 and SVDetect detected 2/10 Conclusion: This study showed that presence of repetitive elements in general within a structural variant did not influence the tool's ability to capture it. This context-based algorithm proved better than current tools even with half the genome coverage than accepted protocol and provides an important first step for novel translocation discovery in cancer genome.
ContributorsShetty, Sheetal (Author) / Dinu, Valentin (Thesis advisor) / Bussey, Kimberly (Committee member) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Arizona State University (Publisher)
Created2014
Description
The processes of a human somatic cell are very complex with various genetic mechanisms governing its fate. Such cells undergo various genetic mutations, which translate to the genetic aberrations that we see in cancer. There are more than 100 types of cancer, each having many more subtypes with aberrations being unique to each. In the past two decades, the widespread application of high-throughput genomic technologies, such as micro-arrays and next-generation sequencing, has led to the revelation of many such aberrations. Known types and subtypes can be readily identified using gene-expression profiling and more importantly, high-throughput genomic datasets have helped identify novel sub-types with distinct signatures. Recent studies showing usage of gene-expression profiling in clinical decision making in breast cancer patients underscore the utility of high-throughput datasets. Beyond prognosis, understanding the underlying cellular processes is essential for effective cancer treatment. Various high-throughput techniques are now available to look at a particular aspect of a genetic mechanism in cancer tissue. To look at these mechanisms individually is akin to looking at a broken watch; taking apart each of its parts, looking at them individually and finally making a list of all the faulty ones. Integrative approaches are needed to transform one-dimensional cancer signatures into multi-dimensional interaction and regulatory networks, consequently bettering our understanding of cellular processes in cancer. Here, I attempt to (i) address ways to effectively identify high quality variants when multiple assays on the same sample samples are available through two novel tools, snpSniffer and NGSPE; (ii) glean new biological insight into multiple myeloma through two novel integrative analysis approaches making use of disparate high-throughput datasets. While these methods focus on multiple myeloma datasets, the informatics approaches are applicable to all cancer datasets and will thus help advance cancer genomics.
ContributorsYellapantula, Venkata (Author) / Dinu, Valentin (Thesis advisor) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Keats, Jonathan (Committee member) / Arizona State University (Publisher)
Created2014
Description
Geology and its tangential studies, collectively known and referred to in this thesis as geosciences, have been paramount to the transformation and advancement of society, fundamentally changing the way we view, interact and live with the surrounding natural and built environment. It is important to recognize the value and importance of this interdisciplinary scientific field while reconciling its ties to imperial and colonizing extractive systems which have led to harmful and invasive endeavors. This intersection among geosciences, (environmental) justice studies, and decolonization is intended to promote inclusive pedagogical models through just and equitable methodologies and frameworks as to prevent further injustices and promote recognition and healing of old wounds. By utilizing decolonial frameworks and highlighting the voices of peoples from colonized and exploited landscapes, this annotated syllabus tackles the issues previously described while proposing solutions involving place-based education and the recentering of land within geoscience pedagogical models. (abstract)
ContributorsReed, Cameron E (Author) / Richter, Jennifer (Thesis director) / Semken, Steven (Committee member) / School of Earth and Space Exploration (Contributor, Contributor) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
The ASU COVID-19 testing lab process was developed to operate as the primary testing site for all ASU staff, students, and specified external individuals. Tests are collected at various collection sites, including a walk-in site at the SDFC and various drive-up sites on campus; analysis is conducted on ASU campus and results are distributed virtually to all patients via the Health Services patient portal. The following is a literature review on past implementations of various process improvement techniques and how they can be applied to the ABCTL testing process to achieve laboratory goals. (abstract)
ContributorsKrell, Abby Elizabeth (Co-author) / Bruner, Ashley (Co-author) / Ramesh, Frankincense (Co-author) / Lewis, Gabriel (Co-author) / Barwey, Ishna (Co-author) / Myers, Jack (Co-author) / Hymer, William (Co-author) / Reagan, Sage (Co-author) / Compton, Carolyn (Thesis director) / McCarville, Daniel R. (Committee member) / Industrial, Systems & Operations Engineering Prgm (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
No two cancers are alike. Cancer is a dynamic and heterogeneous disease, such heterogeneity arise among patients with the same cancer type, among cancer cells within the same individual’s tumor and even among cells within the same sub-clone over time. The recent application of next-generation sequencing and precision medicine techniques is the driving force to uncover the complexity of cancer and the best clinical practice. The core concept of precision medicine is to move away from crowd-based, best-for-most treatment and take individual variability into account when optimizing the prevention and treatment strategies. Next-generation sequencing is the method to sift through the entire 3 billion letters of each patient’s DNA genetic code in a massively parallel fashion.
The deluge of next-generation sequencing data nowadays has shifted the bottleneck of cancer research from multiple “-omics” data collection to integrative analysis and data interpretation. In this dissertation, I attempt to address two distinct, but dependent, challenges. The first is to design specific computational algorithms and tools that can process and extract useful information from the raw data in an efficient, robust, and reproducible manner. The second challenge is to develop high-level computational methods and data frameworks for integrating and interpreting these data. Specifically, Chapter 2 presents a tool called Snipea (SNv Integration, Prioritization, Ensemble, and Annotation) to further identify, prioritize and annotate somatic SNVs (Single Nucleotide Variant) called from multiple variant callers. Chapter 3 describes a novel alignment-based algorithm to accurately and losslessly classify sequencing reads from xenograft models. Chapter 4 describes a direct and biologically motivated framework and associated methods for identification of putative aberrations causing survival difference in GBM patients by integrating whole-genome sequencing, exome sequencing, RNA-Sequencing, methylation array and clinical data. Lastly, chapter 5 explores longitudinal and intratumor heterogeneity studies to reveal the temporal and spatial context of tumor evolution. The long-term goal is to help patients with cancer, particularly those who are in front of us today. Genome-based analysis of the patient tumor can identify genomic alterations unique to each patient’s tumor that are candidate therapeutic targets to decrease therapy resistance and improve clinical outcome.
The deluge of next-generation sequencing data nowadays has shifted the bottleneck of cancer research from multiple “-omics” data collection to integrative analysis and data interpretation. In this dissertation, I attempt to address two distinct, but dependent, challenges. The first is to design specific computational algorithms and tools that can process and extract useful information from the raw data in an efficient, robust, and reproducible manner. The second challenge is to develop high-level computational methods and data frameworks for integrating and interpreting these data. Specifically, Chapter 2 presents a tool called Snipea (SNv Integration, Prioritization, Ensemble, and Annotation) to further identify, prioritize and annotate somatic SNVs (Single Nucleotide Variant) called from multiple variant callers. Chapter 3 describes a novel alignment-based algorithm to accurately and losslessly classify sequencing reads from xenograft models. Chapter 4 describes a direct and biologically motivated framework and associated methods for identification of putative aberrations causing survival difference in GBM patients by integrating whole-genome sequencing, exome sequencing, RNA-Sequencing, methylation array and clinical data. Lastly, chapter 5 explores longitudinal and intratumor heterogeneity studies to reveal the temporal and spatial context of tumor evolution. The long-term goal is to help patients with cancer, particularly those who are in front of us today. Genome-based analysis of the patient tumor can identify genomic alterations unique to each patient’s tumor that are candidate therapeutic targets to decrease therapy resistance and improve clinical outcome.
ContributorsPeng, Sen (Author) / Dinu, Valentin (Thesis advisor) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Arizona State University (Publisher)
Created2015
Description
For as long as humans have been working, they have been looking for ways to get that work done better, faster, and more efficient. Over the course of human history, mankind has created innumerable spectacular inventions, all with the goal of making the economy and daily life more efficient. Today, innovations and technological advancements are happening at a pace like never seen before, and technology like automation and artificial intelligence are poised to once again fundamentally alter the way people live and work in society. Whether society is prepared or not, robots are coming to replace human labor, and they are coming fast. In many areas artificial intelligence has disrupted entire industries of the economy. As people continue to make advancements in artificial intelligence, more industries will be disturbed, more jobs will be lost, and entirely new industries and professions will be created in their wake. The future of the economy and society will be determined by how humans adapt to the rapid innovations that are taking place every single day. In this paper I will examine the extent to which automation will take the place of human labor in the future, project the potential effect of automation to future unemployment, and what individuals and society will need to do to adapt to keep pace with rapidly advancing technology. I will also look at the history of automation in the economy. For centuries humans have been advancing technology to make their everyday work more productive and efficient, and for centuries this has forced humans to adapt to the modern technology through things like training and education. The thesis will additionally examine the ways in which the U.S. education system will have to adapt to meet the demands of the advancing economy, and how job retraining programs must be modernized to prepare workers for the changing economy.
ContributorsCunningham, Reed P. (Author) / DeSerpa, Allan (Thesis director) / Haglin, Brett (Committee member) / School of International Letters and Cultures (Contributor) / Department of Finance (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Businesses stand to face many uncertainties from the moment they start up to every moment in between. A business can try to recognize them and plan ahead, react to them as they occur, or be rocked by a black swan they never saw coming. How a business deals with unforeseen events can increase its potential for success or failure. With this in mind, there is no better bridge between the here and now and the future than planning for change in order to move a company toward preparing for change, adapting to change and achieving optimal results. Interested in taking a step toward the digital age, Alpha Homes Management, Inc. (Alpha Homes) sought our help to explore ideas and options to take their company to a new level. This Barrett Creative Project was centered on designing a system for Alpha Homes that will replace their outdated paper-based system with a more digital one. This aligns with the project also featured as a capstone project as required by the information technology degree expectations. In supplement to the capstone, and for the Barrett Creative Project, the final product was presented to the owners of Alpha Homes Management, Inc. to be utilized by the business. The end goal is to provide a platform which provides a paperless environment for documentation and bring the company a step closer to having a robust internet presence. Now that the web-based application product has been created and presented, the testing phase can now begin to evaluate its efficacy.
ContributorsBrice-Nash, Tristan (Co-author) / Alfawzan, Mohammad (Co-author) / Doheny, Damien (Thesis director) / Rodriguez, Carlos (Committee member) / Information Technology (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
An ethical dilemma is not a matter of “right” versus “wrong,” but rather it is a situation of conflicting values. A common ethical dilemma is that of honesty versus loyalty—is it better to tell the truth, or remain loyal to the company? In the Japanese culture, truth is circumstantial and can vary with different situations. In a way, the Japanese idea of honesty reflects how highly they value loyalty. This overlap of values results in the lack of an ethical dilemma for the Japanese, which creates a new risk for fraud. Without this struggle, a Japanese employee does not have strong justification against committing fraud if it aligns with his values of honesty and loyalty.
This paper looks at the Japanese values relating to honesty and loyalty to show how much these ideas overlap. The lack of a conflict of values creates a risk for fraud, which will be shown through an analysis of the scandals of two Japanese companies, Toshiba and Olympus. These scandals shine light on the complexity of the ethical dilemma for the Japanese employees; since their sense of circumstantial honesty encourages them to lie if it maintains the harmony of the group, there is little stopping them from committing the fraud that their superiors asked them to commit.
In a global economy, understanding the ways that values impact business and decisions is important for both interacting with others and anticipating potential conflicts, including those that may result in or indicate potential red flags for fraud.
This paper looks at the Japanese values relating to honesty and loyalty to show how much these ideas overlap. The lack of a conflict of values creates a risk for fraud, which will be shown through an analysis of the scandals of two Japanese companies, Toshiba and Olympus. These scandals shine light on the complexity of the ethical dilemma for the Japanese employees; since their sense of circumstantial honesty encourages them to lie if it maintains the harmony of the group, there is little stopping them from committing the fraud that their superiors asked them to commit.
In a global economy, understanding the ways that values impact business and decisions is important for both interacting with others and anticipating potential conflicts, including those that may result in or indicate potential red flags for fraud.
ContributorsTabar, Kelly Ann (Author) / Samuelson, Melissa (Thesis director) / Goldman, Alan (Committee member) / WPC Graduate Programs (Contributor) / W.P. Carey School of Business (Contributor) / School of Accountancy (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This paper will be exploring a marketing plan for a Kpop Fan artist, Jennifer Lee. Kpop is a genre of music originating from South Korea that provides a whole-package entertainment. Fan artists are producers who create produce for the consumption and purchase of other Kpop fans. The paper will consider segmentation and the products and platforms that best target them in order to maximize revenue. A survey was performed with a sample size of 314 participants to find out consumer behavior and preference as well as producer situation. Consumers come from both the United States and abroad. Customers come directly and almost exclusively from followers. Therefore, increasing the number of followers on Instagram is essential to increasing revenue. Jennifer has time, resource, and ability constraints, while the market has limited potential. The conclusion is that Jennifer should become more organized as a business. To grow her following, she should cater more towards the most popular fandoms (BTS), make art tutorials, consider collaborations, and better inform followers of her products/services available for purchase. The social media platforms key to marketing Jennifer's products are Instagram and Twitter. Other platforms to be used to increase exposure are Tumblr, Amino Apps, DeviantArt, Reddit, and YouTube. She must also declutter all of these virtual storefronts of unnecessary content to varying degrees in order to build ease of access and a trustworthy brand image. The best platforms for transaction is a personal store, RedBubble (a website that allows users to sell a variety of products with their uploaded images printed onto them), Patreon, and in-person at conventions.
ContributorsXu, Everest Christine (Author) / Eaton, Kathryn (Thesis director) / Ingram-Waters, Mary (Committee member) / Department of Marketing (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
In recent years, sex trafficking awareness and intervention have skyrocketed in the United States. The 2016 Polaris Hotline Statistics Sheet reports a drastic increase of reported sex trafficking cases over the span of four years, with only 3,409 cases of human trafficking in 2012 and 8,042 in 2016, 73% of which were specifically sex trafficking cases (Polaris Project, 2016). The incidence of sex trafficking has not increased, but rather, attention to sex trafficking and implementation of legislation has increased awareness and reporting (Farrell et al., 2012). While this rise in public awareness of sex trafficking has positively impacted victim identification, there has not been an increase in convicting sex traffickers (Polaris Project, 2016). According to the 2016 Trafficking in Persons Report, 3,000 federal investigations that involved human trafficking, the majority of which specifically involved sex trafficking, were opened in 2015. Of these federal investigations, only 10% led to case prosecutions. Analyzing the relationship of law enforcement, specifically vice units, and victims of sex trafficking is just one of the many ways to address this complex issue. This study consisted of a qualitative analysis of the makeup, training, and policing methods of vice units nationwide. It further aimed to determine the vice officer perceptions regarding the elements that make sex trafficking cases convictable.
ContributorsPradhan, Krishnaa (Author) / Maienschein, Jane (Thesis director) / Kinzig, Ann (Committee member) / Kim, Grace (Committee member) / Barrett, The Honors College (Contributor)
Created2018-05