Genomics Education Partnership

Laura Reed, The University of Alabama

lreed1@ua.edu

Wilson Leung
wleung@WUSTL.EDU
Washington University in St. Louis
Location: Missouri St. Louis

Abstract

The goal of the Genomics Education Partnership is to provide opportunities for undergraduate students to participate in genomics research. GEP is a collaboration between a growing number of primarily undergraduate institutions, the Biology Dept and Genome Center of Washington University in St. Louis, and the Biology Dept at the University of Alabama. Participating undergraduates learn to take raw sequence data to high quality finished sequence, and to annotate genes and other features, leading to analysis of a question in genomics and research publication. GEP organizes research projects and provides training/collaboration workshops for PUI faculty and teaching assistants.

Student Goals

  1. Describe and conduct comparative genomics analysis
  2. Correctly build a eukaryotic gene model
  3. Participate productively in the science research process

Research Goals

  1. How did the dot chromosome of Drosophila evolve, and how does its evolution impact the function of the resident genes?
  2. In the context of a pathway, how have the genes and the regulation of those genes evolved across species (e.g. Drosophila, parasitic wasps)?

Context

The CURE is designed as a collaborative laboratory investigation of a problem in genomics, involving wet-lab generation of a large data set (finishing a genomic sequence) and computer analysis of the data (including annotation of genes, assessment of repeats, exploration of evolutionary questions, etc.). The content may be taught as independent research, part of a core bioinformatics class or as a stand-alone course. The number of students involved and the duration of the course can therefore vary depending on method of instruction.

Target Audience: Introductory, Major, Upper Division
CURE Duration: A few class periods, A full term, Half a term, Multiple terms

CURE Design

The central theme of the CURE is showing students how genomic data and comparative evolutionary analyses can be leveraged to better understand the structure and function of the genome. The students are presented with background information both on the science of the project and on how the data they are analyzing was generated. They a taken through the step-by-step process for analyzing the data with example projects before being assigned their independent projects.

Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Constructing explanations (for science) and designing solutions (for engineering), Developing and using models, Planning and carrying out investigations, Using mathematics and computational thinking
Nature of Research:Basic Research, Informatics/Computational Research

Tasks that Align Student and Research Goals

Research Goals →
Student Goals ↓
Research Goal 1: How did the dot chromosome of Drosophila evolve, and how does its evolution impact the function of the resident genes?
Research Goal 2: In the context of a pathway, how have the genes and the regulation of those genes evolved across species (e.g. Drosophila, parasitic wasps)?

Student Goal 1: Describe and conduct comparative genomics analysis

Students will use genomic data from multiple sources including from related species of Drosophila to develop a hypothesis for the gene model in their assigned species.

Students will use genomic data from multiple sources including from related species of Drosophila to develop a hypothesis for the gene model in their assigned species.


Student Goal 2: Correctly build a eukaryotic gene model

Students will use tools to help test the robustness of their gene model in Drosophila.

Students will use tools to help test the robustness of their gene model in Drosophila.


Student Goal 3: Participate productively in the science research process

Students prepare a report to defend their gene model given the available evidence. This report along with their model are used in the compilation and reconciliation of the full data set for scientific analysis.

In the context of a pathway, how have the students prepare a report to defend their gene model given the available evidence. This report along with their model are used in the compilation and reconciliation of the full data set for scientific analysis.


Instructional Materials

All curriculum materials are freely available on the GEP website.

ABLE Published Paper (Acrobat (PDF) 2.7MB Nov10 18)
Comparative Genomics in Drosophila (Acrobat (PDF) 900kB Nov10 18)
Appendixes C, D and E (Acrobat (PDF) 1.4MB Nov10 18)

Instructional Staffing

The CURE is introduced to students though faculty that have been trained, either in-person or through virtual faculty mentoring networks, in the tools, curriculum, and underlying science of the project. In some implementations, teaching assistance also facilitate the learning process. Some of those TAs have also received formal training from GEP project leaders. GEP trained faculty/instructors lead students through the curriculum and are then responsible for claiming and assigning specific student research projects to their students. When the students have completed their project, the instructor submits the project back to the GEP project management system where it will be combined with other student projects to produce the dataset for eventual publication.

Laura Reed, The University of Alabama

The goal of the Genomics Education Partnership is to provide opportunities for undergraduate students to participate in genomics research for little to no cost.

Advice for Implementation

There is a wide diversity of implementation strategies used within the GEP. Institution types range from community colleges, PUIs, and research institutions. The student levels range from introductory to upper division. It is in the power of the instructor to determine the specific nature and best strategy for implementing within the context of their course and student population. We have found that students at all institution types receive the same significant benefit from their participation in GEP. The one factor that scales with the degree of benefit is the amount of class time devoted to the GEP activities. The more time devoted the better the outcomes. All that is needed to implement (once the instructor has been trained) is an internet connection. All the needed tools are web-based.

Iteration

Students are provided with a tool called a "gene model checker" that can test whether they have met the minimum requirements for a biologically valid gene model in the project. This tool can help them identify and correct likely errors. Some implementations allow multiple submissions of preliminary then final reports to allow for faculty feedback on the quality and accuracy of the results giving the student an opportunity to iterate in their process.

Using CURE Data

Each student project is completed at least twice independently. Then, a third student with extensive experience and training in the concepts underlying the gene models reconciles the findings of the independent models to produce a final model. All students who complete a full project are eligible for authorship on the resulting publication. GEP science publications have included literally hundreds of undergraduate student co-authors.

Resources

Slawson EE, Shaffer CD, Malone CD, Leung W, et al., Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains, 2006. Genome Biology, 7:R15.
Lopatto D, Alvarez C, Barnard D, Chandrasekaran C, et al., Education Forum: Genomics Education Partnership, 2008, Science 322, 684-5.
Shaffer CD, Alvarez C, Bailey C, Barnard D, et al., The Genomics Education Partnership: Successful integration of research into laboratory classes at a diverse group of undergraduate institutions, 2010, CBE Life Sci Educ 9 (1): 55-69.
Leung W, Shaffer CD, Cordonnier T, Wong J, et al., Evolution of a distinct genomic domain in Drosophila: Comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis, 2010. Genetics, 185: 1519-1534.
Elgin, SCR et al. 2016, Trends Genet. Dec 6. pii: S0168-9525(16)30151-2. The GEP: Crowd-Sourcing Big Data Analysis with Undergraduates. Full Text (DOI: 10.1016/j.tig.2016.11.004)