SPUR 2021: DEVELOPING STRATEGIES AND TOOLS TO MINE CLINICAL VARIANT ASSERTIONS

Faculty Name:
Karen Eilbeck

Department:
Biomedical Informatics

Faculty College:
Medicine

Email:


Project Description:

**This project is a part of the Summer Program for Undergraduate Research (SPUR), which provides undergraduate students with an intensive 10-week research experience under the mentorship of a University of Utah faculty member. SPUR 2021 begins on May 26 and ends on August 5. If you are interested in this project, please review all program information on the SPUR site. If you wish to apply to this project, you must apply using the SPUR 2021 application.**

As sequencing technologies have advanced; sequencing data has shown the extent of polymorphism in the human population. Understanding which of these DNA changes impact an individual’s clinical phenotype (cause disease), and which are silent is necessary for the interpretation of genetic tests.  ClinVar is an international, submission-driven archive of variant-condition-interpretations hosted by the National Center for Biotechnology Information (NCBI). ClinVar is increasingly becoming the central repository of interpreted genomic variants; as of July 2018, 997 submitters had contributed 427,882 unique variants and 11099 conditions to ClinVar. Sharing variants and associated supporting evidence in the ClinVar database enables the transparent review of data by users and supports clinical variant interpretation. Submissions to ClinVar represent the first time that clinical labs and other submitters have shared and compared their variant interpretations, and this reveals both conformity and discrepancy in variant interpretation. In some cases the disagreement in interpretation is clinically significant – pathogenic versus benign. This growing and evolving database relies on submitters to resolve discrepancies and update findings when knowledge changes. It also provides the starting point for expert curation of variants and genes. My group developed ClinVar Miner; a tool that enables deep exploration of the ClinVar dataset. The goal of ClinVar Miner is to enable management of the upstream and downstream processes related to submitting to and using the data. ClinVar Miner as a counterpoint to facilitate use of ClinVar data.



Opportunity Type:

This is a paid research position


Student Role:

The student will be involved in a project that builds tools to better analyze and understand the clinical assertions made about genetic variants. The student will develop strategies to help a user interact with the system and get the desired output. Users include genetic counsellors, medical directors and bioinformatics analysts.


Student Benefits:

This project is flexible depending on the skillset of the student. The student will explore a use-case, and develop a strategy to begin to implement a solution. Outcomes could be detailed workflow descriptions, data integration, database schema updates, python scripts, visualizations and statistical analysis.


Project Duration:

35-40 hours per week on research and program-related activities, begins May 26, 2021, and ends August 5, 2021


Minimum Requirements:

Admission to the program is competitive. Applicants must meet all of the following criteria: 1) be a matriculated, degree-seeking undergraduate student in the Fall 2021 semester (beginning or continuing college career in Fall 2021 and not graduating before December 2021; concurrent enrollment while in high school does not meet this eligibility requirement). Applicants do not need to be a University of Utah student. 2) eligible to work in the United States: If you are a University of Utah Dreamer (with or without DACA), you are eligible to participate. If you are a Dreamer from a different institution: If you have DACA, you are eligible to participate. If you do not have DACA, you are able to participate and gain research experience, but might not be able to be compensated. For more information, please contact Megan Shannahan at megan.shannahan@utah.edu or 801-581-2478. If you are an international student or scholar, you must either a) be a degree-seeking undergraduate student at an American institution of higher education and verify with your institution’s international center that your visa allows you to participate in this program, OR b) possess documentation that establishes your eligibility to work in the United States (if you hold US citizenship, it is likely you have these documents). 3) able to commit to approximately 35-40 hours per week of employment at the University of Utah for the entire duration of the program (May 26-August 5, 2021). 4) at least 18 years old by May 24, 2021 (required if you wish to use on-campus housing; preferred if you will not be using on-campus housing). Please note that no previous college coursework or previous research experience is required.