The Making of a COVID-19 Lab: A Business Exploration

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Description

Early on in the pandemic, ASU leadership recognized an opportunity to involve the Biodesign Institute in an effort to keep local communities safe. Equipped with capital investments (and expertise) in diagnostic testing, university president Michael Crow tasked Dr. Joshua LaBaer

Early on in the pandemic, ASU leadership recognized an opportunity to involve the Biodesign Institute in an effort to keep local communities safe. Equipped with capital investments (and expertise) in diagnostic testing, university president Michael Crow tasked Dr. Joshua LaBaer - the executive director of Biodesign - to begin mapping out the lab’s logistic capabilities and operational plan. While initially testing through nasopharyngeal swabs, the Arizona Biodesign Clinical Testing Laboratory (ABCTL) eventually developed a saliva-based COVID-19 test that demonstrated higher efficacy and resource-efficiency. By maintaining rapid turnaround times for test results, the ABCTL has helped both the university population and local community operate safely. Lauded as a highly innovative testing site, the lab proved to be an essential asset as ASU, and the world, look to return to normalcy. The purpose of this thesis is to analyze the ABCTL’s inception and development using multi-faceted approaches from the business realm. There will be five topics discussed which are: • Volume I- Stakeholder Theory and Analysis Regarding the COVID-19 Bio-design Institute at Arizona State University (Claire Agee), • Volume II- The Lab as a Business Within a University Environment (Samuel Cosgrove) • Volume III- A Managerial Economic Perspective (Michael Qian) • Volume IV- An Analysis of its Upstream Supply Chain ( Kyle Mattson) • Volume V- An Operations Management Perspective (Corinne English) After these volumes, there will be a discussion about the growth and sustainability of the laboratory looking into the future. Although the ABCTL is young,the ever-changing market dynamics leave the organization with critical decisions going forward.

Date Created
2021-05
Agent

The Making of a COVID Testing Laboratory: The Academic Response to the COVID-19 Pandemic Through qPCR, Saliva Testing, and Lab Workflow

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In mid-March of 2020, Arizona State University transformed one of its research labs into ASU Biodesign Clinical Testing Laboratory (ABCTL) to meet the testing needs of the surrounding community during the COVID-19 pandemic. The lab uses RT-qPCR, or reverse transcription

In mid-March of 2020, Arizona State University transformed one of its research labs into ASU Biodesign Clinical Testing Laboratory (ABCTL) to meet the testing needs of the surrounding community during the COVID-19 pandemic. The lab uses RT-qPCR, or reverse transcription polymerase chain reaction, to match the components of a biosample to a portion of the SARS-CoV-2 genome. The ABCTL uses the TaqPath™ COVID-19 Combo Kit, which has undergone many different types of efficacy and efficiency tests and can successfully denote saliva samples as positive even when an individual is infected with various emerging strains of the SARS-CoV-2. Samples are collected by volunteers at testing sites with stringent biosafety precautions and processed in the lab using specific guidelines. As the pandemic eventually becomes less demanding, the ABCTL plans to utilize the Devil’s Drop-off program at various school districts around Arizona to increase testing availability, transfer to the SalivaDirect method, and provide other forms of pathogen testing to distinguish COVID-19 from other types of infections in the ASU community.

Date Created
2021-05
Agent

The Making of a COVID Testing Laboratory: The FDA Emergency Use Authorization Pathway’s Impact on the ABCTL

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In the United States, clinical testing is monitored by the federal and state governments, held to standards to ensure the safety and efficacy of these tests, as well as maintaining privacy for patients receiving a test. In order for the

In the United States, clinical testing is monitored by the federal and state governments, held to standards to ensure the safety and efficacy of these tests, as well as maintaining privacy for patients receiving a test. In order for the ABCTL to lawfully operate in the state of Arizona, it had to meet various legal criteria. These major legal considerations, in no particular order, are: Clinical Laboratory Improvement Amendments compliance; FDA Emergency Use Authorization (EUA); Health Insurance Portability and Accountability Act compliance; state licensure; patient, state, and federal result reporting; and liability. <br/>In this paper, the EUA pathway will be examined and contextualized in relation to the ABCTL. This will include an examination of the FDA regulations and policies that affect the laboratory during its operations, as well as a look at the different authorization pathways for diagnostic tests present during the COVID-19 pandemic.

Date Created
2021-05
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The Making of a COVID Testing Laboratory: Deconstructing the Saliva Sample Collection Process and Preanalytical Standardization

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This thesis project is the result of close collaboration with the Arizona State University Biodesign Clinical Testing Laboratory (ABCTL) to document the characteristics of saliva as a test sample, preanalytical considerations, and how the ABCTL utilized saliva testing to develo

This thesis project is the result of close collaboration with the Arizona State University Biodesign Clinical Testing Laboratory (ABCTL) to document the characteristics of saliva as a test sample, preanalytical considerations, and how the ABCTL utilized saliva testing to develop swift COVID-19 diagnostic tests for the Arizona community. As of April 2021, there have been over 130 million recorded cases of COVID-19 globally, with the United States taking the lead with approximately 31.5 million cases. Developing highly accurate and timely diagnostics has been an important need of our country that the ABCTL has had tremendous success in delivering. Near the start of the pandemic, the ABCTL utilized saliva as a testing sample rather than nasopharyngeal (NP) swabs that were limited in supply, required highly trained medical personnel, and were generally uncomfortable for participants. Results from literature across the globe showed how saliva performed just as well as the NP swabs (the golden standard) while being an easier test to collect and analyze. Going forward, the ABCTL will continue to develop high quality diagnostic tools and adapt to the ever-evolving needs our communities face regarding the COVID-19 pandemic.

Date Created
2021-05
Agent

The Making of a COVID Testing Laboratory SalivaDirect: The Gold Standard of an Epidemic

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Description

In the middle of the COVID-19 epidemic, flaws in the SARS-CoV-2 diagnostic
test were identified by the impending supply shortages of nasopharyngeal swabs and nucleic acid isolation and purification kits. The ASU Biodesign Clinical Testing Lab (ABCTL), which converted from a

In the middle of the COVID-19 epidemic, flaws in the SARS-CoV-2 diagnostic
test were identified by the impending supply shortages of nasopharyngeal swabs and nucleic acid isolation and purification kits. The ASU Biodesign Clinical Testing Lab (ABCTL), which converted from a research lab to SARS-CoV-2 testing lab, was not an exception to these shortages, but the consequences were greater due to its significant testing load in the state of Arizona. In response to the shortages, researchers at The Department of Epidemiology of Microbial Diseases, at the Yale School of Public Health created SalivaDirect method, which is an epidemic effective test, that accounts for limitations of materials, accessibility to specialized lab equipment, time per test, and cost per test. SalivaDirect simplified the diagnostic process by collecting samples via saliva and skipping the nucleic acid extraction and purification, and did it in a way that resulted in a highly sensitive limit of detection of 6-12 SARS-CoV-2 copies/μL with a minimal decrease in positive test agreement.

Date Created
2021-05
Agent

The Making of a COVID Testing Laboratory: A Response to COVID-19 through qPCR, Robotics, and Safety Measures

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The ASU Biodesign Clinical Testing Laboratory began in March 2020 after the severe acute respiratory syndrome, coronavirus 2, began spreading throughout the world. ASU worked towards implementing  its own efficient way of testing for the virus, in order to assist

The ASU Biodesign Clinical Testing Laboratory began in March 2020 after the severe acute respiratory syndrome, coronavirus 2, began spreading throughout the world. ASU worked towards implementing  its own efficient way of testing for the virus, in order to assist the university but also keep the communities around it safe. By developing its own strategy for COVID-19 testing, ASU was on the forefront of research by developing new ways to test for the virus. This process began when research labs at ASU were quickly converted into clinical testing laboratories, which used saliva testing to develop swift COVID-19 diagnostic tests for the Arizona community. The lab developed more accurate and time efficient results, while also converting Nasopharyngeal tests to saliva tests. Not only did this allow for fewer amounts of resources required, but more individuals were able to get tested at faster rates. The ASU Biodesign Clinical Testing Laboratory (ABCTL) was able to accomplish this through the adaptation of previous machines and personnel to fit the testing needs of the community. In the future, the ABCTL will continue to adapt to the ever-changing needs of the community in regards to the unprecedented COVID-19 pandemic. The research collected throughout the past year following the breakout of the COVID-19 pandemic is a reflection of the impressive strategy ASU has created to keep its communities safe, while continuously working towards improving not only the testing sites and functions, but also the ways in which an institution approaches and manages an unfortunate impact on diverse communities.

Date Created
2021-05
Agent

The Making of a COVID-19 Laboratory: Exploring SARS-CoV-2 Antibody Testing

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This thesis project is part of a larger collaboration documenting the history of the ASU Biodesign Clinical Testing Laboratory (ABCTL). There are many different aspects that need to be considered when transforming to a clinical testing laboratory. This includes the

This thesis project is part of a larger collaboration documenting the history of the ASU Biodesign Clinical Testing Laboratory (ABCTL). There are many different aspects that need to be considered when transforming to a clinical testing laboratory. This includes the different types of tests performed in the laboratory. In addition to the diagnostic polymerase chain reaction (PCR) test that is performed detecting the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), antibody testing is also performed in clinical laboratories. Antibody testing is used to detect a previous infection. Antibodies are produced as part of the immune response against SARS-CoV-2. There are many different forms of antibody tests and their sensitives and specificities have been examined and reviewed in the literature. Antibody testing can be used to determine the seroprevalence of the disease which can inform policy decisions regarding public health strategies. The results from antibody testing can also be used for creating new therapeutics like vaccines. The ABCTL recognizes the shifting need of the community to begin testing for previous infections of SARS-CoV-2 and is developing new forms of antibody testing that can meet them.

Date Created
2021-05
Agent

Leveraging Artificial Intelligence to Find Previously Undiscovered Patterns in Tumor Molecular Data to Aid in Diagnosis and Therapy Selection

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Description
Cancer researchers have traditionally used a handful of markers to understand the origin of tumors and to predict therapeutic response. Additionally, performing machine learning activities on disparate data sources of varying quality is fraught with inherent bias. The

Cancer researchers have traditionally used a handful of markers to understand the origin of tumors and to predict therapeutic response. Additionally, performing machine learning activities on disparate data sources of varying quality is fraught with inherent bias. The Caris Life Sciences Molecular Database (CMD) is an immense resource for discovery as it contains over 215,000 molecular profiles of tumors with consistently gathered clinical grade molecular data along with immense amounts of clinical outcomes data. This resource was leveraged to generate two artificial intelligence algorithms aiding in diagnosis and one for therapy selection.

The Molecular Disease Classifier (MDC) was trained on 34,352 cases and tested on 15,473 unambiguously diagnosed cases. The MDC predicted the correct tumor type out of thirteen possibilities in the labeled data set with sensitivity, specificity, PPV, and NPV of 90.5%, 99.2%, 90.5% and 99.2% respectively when considering up to 5 predictions for a case.

The availability of whole transcriptome data in the CMD prompted its inclusion into a new platform called MI GPSai (MI Genomic Prevalence Score). The algorithm trained on genomic data from 34,352 cases and genomic and transcriptomic data from 23,137 cases and was validated on 19,555 cases. MI GPSai can predict the correct tumor type out of 21 possibilities on 93% of cases with 94% accuracy. When considering the top two predictions for a case, the accuracy increases to 97%.

Finally, a 67 gene molecular signature predictive of efficacy of oxaliplatin-based chemotherapy in patients with metastatic colorectal cancer was developed - FOLFOXai. The signature was predictive of survival in an independent real-world evidence (RWE) dataset of 412 patients who had received FOLFOX/BV in 1st line and inversely predictive of survival in RWE data from 55 patients who had received 1st line FOLFIRI. Blinded analysis of TRIBE2 samples confirmed that FOLFOXai was predictive of OS in both oxaliplatin-containing arms (FOLFOX HR=0.629, p=0.04 and FOLFOXIRI HR=0.483, p=0.02).
Date Created
2020
Agent

Hepatitis C Prevention Measures in Pakistan

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Description
Hepatitis C virus (HCV) is endemic in Pakistan, with 5% of the population suffering from the disease. A unique aspect about HCV in Pakistan is the major role that healthcare workers play in its transmission, by reusing needles and giving

Hepatitis C virus (HCV) is endemic in Pakistan, with 5% of the population suffering from the disease. A unique aspect about HCV in Pakistan is the major role that healthcare workers play in its transmission, by reusing needles and giving therapeutic injections when they are not needed. This issue is furthered by patients’ misconceptions that invasive treatments, like injections, are more effective than oral medicines. The purpose of this project was to create a short video that addressed this inaccurate and dangerous perception, by educating Pakistanis about HCV and how to prevent infection and reinfection. In addition to disease transmission, accessibility to treatment options in Pakistan were also discussed. The video featured Pakistani physicians and some young adults. There were several limitations that delimited the project, including time, budget, the sudden death of a project participant, and the current COVID-19 epidemic as well as cultural, language, and physical barriers that come from filming a video about Pakistan as Americans. In the future, this video can serve as a framework for future efforts.
Date Created
2020-05
Agent

The Relationship Between Healthcare Provider’s Physical Activity and Predictive Patient Care Treatment Plans

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This research evaluates the need for health providers to prioritize their personal health as a means to improve their patient care. Due to the traditional healthcare system maintaining a patient-centric focus, physicians became victims to the very diseases they were

This research evaluates the need for health providers to prioritize their personal health as a means to improve their patient care. Due to the traditional healthcare system maintaining a patient-centric focus, physicians became victims to the very diseases they were treating their patents for. The sacrifice of one's own health caused physicians to be more susceptible to both institutional and perceptual barriers that limited their engagement in preventative care counseling. Their own personal lifestyle habits, such as physical activity, played an influential role when prescribing treatment plans, and thus, could serve as a compromising factor in substandard care of a patient. The research suggested that providers who sustained healthier lifestyles by practicing what they preach are more efficient at delivering quality care to their patients in comparison to providers living an unhealthy lifestyle. With a provider's responsibility and obligation to continuously provide optimal care, there is a need to promote the health of a provider to establish both reliable and standardize patient care within the healthcare system. In addition to the research, three personal testimonials are included to help demonstrate the potential effects of a physician’s personal health in their medical practice.
Date Created
2020-05
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