Research Intern: Empirical Study of Scope of Synthetic Biology and SNP Detection in Michigan

We are an entirely student run research and engineering design team in the biological sciences. We develop and execute our own research projects in the area of synthetic biology. Students have the opportunity to gain hands on experience in conducting scientific research, running a laboratory, engineering novel biological systems, fundraising, public outreach, leadership, and working as part of a multidisciplinary team.

Any students with an interest in synthetic biology and/or biological engineering are welcome to join! Absolutely no previous experience is required. Our team comprises of undergraduate students from various majors, including (but not limited to) Molecular, Cellular, and Developmental Biology, Biomedical Engineering, Chemical Engineering, Mathematics, Biophysics, Neuroscience, Microbiology, Philosophy, and Materials Science & Engineering. We also have graduate students and faculty advisors from multiple colleges and departments on campus.

Project Description

Healthcare inequality, driven by the high price of care and a lack of accessibility to the medical system, is a serious issue in the United States. As advancements in personalized medicine bring advanced scientific techniques to the clinic, it is extraordinarily important to leverage these strategies to improve the health outcomes of historically underserved populations.

In response to this need, our team is developing an inexpensive, generalizable genetic variant detection platform for use in point-of-care settings. Our system is based on work published within the last year which combines Loop-Mediated Isothermal Amplification (LAMP) with machine learning-generated fluorescent probes to detect single nucleotide polymorphisms (SNPs). We are working to adapt their work to on-site, personalized, genomic SNP detection. In addition, we are working to support our test with a low-cost fluorescence reader and easy to use kit components for ready implementation of the assay.

Clinical SNP detection is typically done through genetic testing, which can take 2-8 weeks [1] and, if not covered by insurance, can cost the patient up to $2000 out of pocket [2]. This leads to many patients forgoing testing in situations where it could be critical. In contrast, our LAMP-based platform will provide results in under 1.5 hours for less than $3 per patient sample, all while using simple, affordable equipment such as a heating block and a basic fluorescence reader. We anticipate that healthcare providers will be able to purchase our complete platform, including all reagents and labware, for less than $1000. The speed and affordability of this system will ensure its accessibility to all patient populations and healthcare settings, especially those which are under-resourced or experience difficulty following up with patients after an initial appointment.

Clinical SNP detection is typically done through genetic testing, which can take 2-8 weeks [1] and, if not covered by insurance, can cost the patient up to $2000 out of pocket [2]. This leads to many patients forgoing testing in situations where it could be critical. In contrast, our LAMP-based platform will provide results in under 1.5 hours for less than $3 per patient sample, all while using simple, affordable equipment such as a heating block and a basic fluorescence reader. We anticipate that healthcare providers will be able to purchase our complete platform, including all reagents and labware, for less than $1000. The speed and affordability of this system will ensure its accessibility to all patient populations and healthcare settings, especially those which are under-resourced or experience difficulty following up with patients after an initial appointment.

As an initial proof of concept, we have chosen to develop a test which detects rs773902, an SNP that affects a protein in human platelets associated with increased pathological blood clotting and resistance to standard antithrombotic drugs such as aspirin and clopidogrel [3]. Conversely, the efficacy of other antithrombotic medications, such as heparin and ticagrelor, is unaffected by this SNP, indicating they could be more effective medications for patients with this polymorphism. Our SNP detection platform will enable physicians to quickly and inexpensively determine whether their patient has this SNP, then make a more informed decision when prescribing antithrombotic therapy and choice of antithrombotic medication. More generally, our system will empower physicians of any resource level to easily diagnose genetic conditions and acquire critical genetic information to inform patient care.

• Design a primary and secondary research plan for your region (Michigan) to collect relevant data.
• Execute research by contacting relevant stakeholders (cardiologists, healthcare professionals, community health workers, etc.).
• What is public awareness of stroke symptoms in Michigan communities like?
• What is the availability/organization of emergency medical services for stroke care in Michigan?
• How standard is genetic testing in the prevention of stroke?
• What are barriers associated with it in Michigan/ how many health centers are equipped to do so?
• Where are they located?
• How educated are communities in Michigan on identifying stroke symptoms/overall stroke care?
• What are some cultural barriers to stroke treatment in your region?
• What about genetic testing to inform healthcare decisions?
• What are the associations between platelet activity/aggregation and cardiovascular disease?
• What are the benefits/drawbacks of using platelet activity to measure the risk of stroke?
• How many health centers in Michigan are certified to treat stroke?
• What is the organization of stroke centers in low-resource communities?
• What are the minimum services needed to treat stroke?
• What about identifying risk of stroke?
• After treatment, what is the rehabilitation process for stroke patients like?
• What are the current policies designed to enable access to stroke care?
• What is standard hyperstability testing in the United States? (focus on genetic standpoint, factor V Leiden, activated protein C resistance, prothrombin gene mutation, etc).
• Research polygenic risk scores for thrombosis, how were they developed? Who did they have in mind?
• Note: this internship does NOT involve any human subject research.
• Ensure timely research execution, comprehensive research documentation, and development of weekly and finally reports.

Expected Outcome:

• Well-documented process and procedure that any of our research interns can use to build on using standard open-source tools like Google Docs, Google Sheets.
• Demonstrate this process working on the current research project.
• A comprehensive MS Word and PowerPoint report detailing the insights and conclusions from your research.
• A set of recommendations for the organization to engage with the regional public health officials.
• Apply Basic Statistical tools to analyze the data.
• You will receive a Certificate of Completion from the organization.

Duration: 4-6 weeks (expected 10-15 hrs per week during summer). This internship has a potential to extend through the year. Non summer hrs of commitment is 4-5 hrs per week.

Required Skills: MS Excel, MS Word, PowerPoint, attention to detail, reasoning aptitude, ability to engage stakeholders. Research design skills.

Desired Skills: survey taking skills, market research, data analytics, technical writing, interest in Biology and research highly recommended

Other Benefits: Certification on completion of course