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Published in final edited form as: Scholarsh Pract Undergrad Res. 2023 Spring;6(3):17–28. doi: 10.18833/spur/6/3/1

The Genomics Education Partnership: First findings on genomics research in community colleges

Paula Croonquist 1,*, Virginia Falkenberg 2, Natalie Minkovsky 3, Alexa Sawa 4, Matthew Skerritt 5, Maire Kate Sustacek 6, Raffaella Diotti 7, Anthony D Aragon 8, Tamara Mans 9, Goldie L Sherr 7, Catherine Ward 10, Monica Hall-Woods 11, Anya L Goodman 12, Laura K Reed 13, David Lopatto 14
PMCID: PMC10508916  NIHMSID: NIHMS1876557  PMID: 37731515

Abstract

The Genomics Education Partnership (GEP), a consortium of diverse colleges/universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with internet access, may be particularly accessible for 2-year institutions with limited research capacity and significant budget constraints. To understand how GEP supports student research at CCs, we analyzed student knowledge and self-reported outcomes. We found that CC student gains are comparable to non-CC student gains, with improvements in attitudes toward science and thriving in science. Our early findings suggest that the GEP model of centralized support with flexible CURE implementation benefits CC students and may help mitigate barriers to implementing research at CCs.

Keywords: Bioinformatics, CUREs, Genomics, Community Colleges, undergraduate education

INTRODUCTION

Undergraduate research is one of eleven high impact practices shown to increase deep learning among students of all backgrounds (Kuh, 2008). When undergraduate research opportunities are embedded in the curriculum through Course-based Undergraduate Research Experiences (CUREs), participation once limited to a select number of students becomes accessible to all. A well-structured CURE engages students actively in authentic and novel hypothesis-driven work, using collaboration and iteration (Auchincloss et al. 2014). CUREs have been shown to be inclusive and equitable teaching and learning practices that result in increased critical thinking skills, higher grades, greater persistence, and greater interest in STEM fields (Lopatto et al, 2008; Rodenbusch et al. 2016; Corwin et al. 2015; Staub et al. 2016). This is especially significant for students of diverse backgrounds who continue to be underrepresented in many STEM disciplines; CUREs can close the achievement gap for many (Awong-Taylor et al. 2016; Hensel, 2021; de Brey et al. 2019).

Associate’s degree-granting institutions enroll 34% of all US undergraduates, including 36% of Black or African American, 41% of Hispanic or Latino, 34% Asian, 37% Native Hawaiian or other Pacific Islander, and 40% of Native American or Alaskan native students (National Center for Education Statistics, 2021). Thus, community colleges (CCs) can be pivotal in efforts to increase diversity, inclusion, equity, and retention in STEM education. CUREs can and should be a critical tool for CCs’ efforts in this area, but there are barriers to implementation. James Hewlett, director of the Community College Undergraduate Initiative (CCURI), identified the major barrier to offering undergraduate research opportunities at CCs as the lack of an undergraduate research culture. This lack is manifested by limited financial resources, an incompatible faculty model (e.g., high teaching loads), limited student and faculty preparation, isolation from networks, marginalization from the science research enterprise and lack of administrative support (Hewlett, 2018). In addition to these institutional challenges, non-traditional, underrepresented, and first-generation students attending CCs are likely to have additional responsibilities beyond their studies. For example, 62% of full-time students at CCs are also employed during the academic year (Radwin et al. 2018). These challenges, for both the CC culture and student time, need to be addressed to fulfill the promise of CUREs for achieving inclusion and equity in STEM education. Fortunately, programs like the Genomics Education Partnership (GEP) can help overcome some of these challenges.

The GEP (thegep.org), a consortium of over 200 diverse colleges and universities established in 2006, provides a well-established framework for integrating authentic genomics research experiences into undergraduate curricula. The GEP has supported the adoption of effective pedagogical practices (e.g. active learning strategies, emphasizing CUREs) through centralized resources and distributed peer-to-peer support, coupled with an effective curriculum on eukaryotic gene structure and workflow to allow students to conduct comparative genomics studies (Shaffer et al. 2010; Lopatto et al. 2014; Shaffer et al. 2014). Results from student research projects have led to three major scientific publications on which the students are co-authors (Leung et al. 2010; Leung et al. 2015; Leung et al. 2017). Through active recruitment since 2015, the GEP presently has twenty-six CC institutions as members. Undergraduate in silico research opportunities in genomics are especially suitable to Associate’s-degree granting institutions as the research is conducted online, using publicly available resources (data and tools). These in silico research experiences are also well-suited to non-traditional, underrepresented, and first-generation students due to flexibility in location and timing for accessing the research materials.

The GEP curriculum and research projects are highly adaptable for flexible implementation. This allows CC faculty, with high teaching loads, to incorporate these experiences into existing programs without the need for creating new courses. GEP-associated faculty may choose to present first year students with a series of self-guided, active learning modules exploring eukaryotic gene structure and expression while developing familiarity with a genome browser (Laakso et al. 2017). Faculty are encouraged to involve students in the comparative annotation of a previously unstudied region of a Drosophila genome in support of ongoing GEP scientific research projects when the course schedule permits. Two current projects focus on the genomes from the genus Drosophila to promote better understanding of a) the evolution of the heterochromatic Drosophila F element and b) the evolution of genes in the Drosophila insulin signaling pathway. With both projects, students must utilize all lines of available evidence (at a minimum, homology to D. melanogaster, de novo gene predictions, RNA-Seq data) to arrive at a best-supported gene model; this often involves several rounds of iteration (Lopatto et al. 2020). A successful student will understand that there is no “right answer,” but that they can generate a gene model that they can defend based on available evidence.

Student learning gains after engaging in a GEP project (both knowledge gains as shown by a pre/post quiz and self-reported gains in science understanding and science skills) have been previously reported by Lopatto et al. 2014. However, that study did not include newly recruited CCs. Here we investigate how student outcomes compare between CC and non-community college (non-CC) students participating in GEP-supported research opportunities and/or introductory active learning curriculum. We hypothesize that CC student outcomes will be comparable to non-CC student gains based on previously published evidence demonstrating that gains are observed regardless of institution type (Shaffer et al. 2014).

MATERIALS AND METHODS

Faculty Reports

GEP faculty members submit a voluntary report in the Fall and Spring of each academic year. The questions on the report address a variety of GEP community needs and are updated every year. A subset of questions interrogates about the details of all unique implementations of the GEP materials and, the answers to select questions were utilized in this study (Supplemental Material). The reports are collected using a Qualtrics survey. During 2020–2021 academic year, 127 faculty submitted 246 reports describing implementation styles. Among these reports, 17 were from 10 faculty members teaching at community colleges. Of the 246 reports, 239 were included in the analysis. These reports indicated that GEP curriculum was implemented as independent study and/or in a course, with the course number and title provided.

To separate the upper-division and lower-division courses at the 4-year institutions, we used a two-step process. First, student academic standing reported by the faculty was used to classify the courses and the course number was used for courses that could not be classified based on enrollment alone. The reports were labeled as “lower-division” if faculty indicated only freshmen and/or sophomore enrollment (N=27). Reports were labeled as “upper-division” if they included junior and/or senior level enrollment, but no freshmen and sophomore-level students (N=131). For reports that indicated mixed enrollment (both lower- and upper-class standing enrollment, N=63), course-number was analyzed for each report. If the course number was at a 200- or 100-level, the mixed enrollment course was assigned to the “lower division” category. As a result, of the 222 reports from 4-year colleges, 51 (23%) were classified as lower division and 171 (77%) received the “upper-division” classification. To distinguish between required and elective courses, several response options for the question were combined (Supplemental Material).

Student Demographics

This report includes data collected in the Academic Year 2020–2021. The CC student data utilized for this report included 96 cases, which is 39% of the student enrollment reported by CC instructors. 70% of the respondents identified as female, 30% as male. Students were invited to report their race/ethnicity by selecting all the categories that applied to them. Of those who chose to identify themselves by one category, the responses were White (35%), Black (4.5%), Hispanic (9%), and Asian (4%), while the remainder chose more than one category or chose not to answer (6.5%). Student participants also indicated if they were first generation (28%) and if they were eligible for a Pell grant (45%).

Measures

Student Data

Students were asked to complete a voluntary pre-course quiz and survey before using GEP materials, and a post-course quiz and survey after (Supplemental Material). After informed consent was obtained for participation in general, students could opt out of any or all questions. All research protocols involving human subjects were reviewed and approved by the Internal Review Board at the University of Alabama (protocols 18-10-1678 and 19-06-2428). All GEP institutions contributing student data to this study have an established IRB Authorization Agreement (IAA) with the University of Alabama. Confidentiality was maintained throughout by using encryption to eliminate identification of individual students. These unidentified responses were aggregated at Washington University in St. Louis and made available for analysis. The sections of the student surveys used for this study are described below. It should be noted that the four assessment instruments (pre-course survey, post-course survey, pre-course annotation quiz, and post-course annotation quiz) were accessed independently such that students could readily opt out of some the assessment tools. The consequence of these student choices was a differing sample for each measure. Two of the measures, the self-reported benefits, and the thriving items, were post-survey only.

RESULTS

Curriculum and Implementation

The GEP community has developed an extensive collection of curricular resources freely available to all faculty via the GEP website and CourseSource (Laakso et al. 2017, Weisstein, et al. 2019). GEP members choose and tailor curriculum that best fits the needs of their students and programs. Some modules focusing on the introduction of basic concepts (genes, exons, splicing, genetic code) and tools (UCSC Genome Browser) are widely used by the GEP members; 70% of all faculty reports in 2020–2021 indicate use of these modules. The GEP curriculum spans multiple levels of inquiry, as described by Buck et al. 2008: from confirmation inquiry (e.g., walk-throughs that provide answers, conclusions, and illustrate reasoning for arriving at each conclusion), to structured and guided inquiry, where conclusions are not known to students. Faculty often provide additional guided inquiry or practice activities before offering research projects to students.

To understand how GEP members implement CUREs in their courses, we compared the answers to pertinent questions on the faculty report among community college implementations, and non-CC lower-division and upper-division implementations (Figure 1). Community college implementations were similar to those in the lower-division courses at the 4-year institutions (Figure 1.A). The largest category for CC was implementation as a module of the course (59%); similarly, 53% of lower division implementations were a module in a course. These were typically in introductory genetics or molecular and cell biology courses. In the upper-division implementations, independent study (30%) or the entire course (29%) were the most common implementation types. The examples of courses where the entire course relied on GEP include research and genomics. When comparing the role of the courses or experiences in the degree programs, CC and lower-division implementations were primarily in the required courses (71% and 63% of reports), while upper division implementation in required courses comprised only 29% of reports (Figure 1.B). Most reports for the upper division courses indicated implementation in elective courses (62%, examples: Biology Research, Genomics courses). To estimate how many courses engaged students in research, we asked whether implementation involved claiming research projects. About half of CC and lower-division implementations involved claiming projects, while majority of upper division implementations did so (Figure 1.C). The text comments expanding on details of implementation revealed that using “claimed projects” under-estimated whether students in the courses engaged in doing research. Some faculty reported engaging students in gene annotation without claiming projects, some used annotation as a starting point to generate research proposals (open inquiry), and some planned to submit research projects’ reports in the future but did not complete submission at the time of the faculty report.

FIGURE 1.

FIGURE 1.

FIGURE 1.

FIGURE 1.

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A-C. The implementation styles for community college students are very similar to those for LD non-community college students. Reported implementations for Community College students, (CC, N=17), Lower Division courses from other institutions, (LD, N=51), and Upper Division courses from other institutions (UD, N=171). A. Shows the implementation style. B. Displays the type of course where the GEP curriculum was used. C. Shows the percentage of research projects claimed compared to active learning modules. Total percentages may deviate from 100% due to rounding.

Based on the analysis of faculty reports about specific implementations of GEP curriculum, community colleges and lower division courses at 4-year institutions show similar patterns distinct from implementations in the upper-division courses.

Quality of student work: genomic annotation

As of Spring 2021, 159 annotation projects, 134 pertinent to the evolution of the Drosophila F element and 25 related to the evolution of the Drosophila insulin signaling pathway, had been completed by CC students and submitted by GEP faculty affiliated with these institutions to the research project leaders. For quality control, all GEP projects are completed at least twice independently by GEP students (usually from different institutions), and those project submissions are reconciled by experienced GEP students working during the summer with the research project leaders. 70 F element and 7 insulin pathway projects gene models have been reconciled respectively.

Annotation Quiz

Students had the option of completing a 20-item quiz on the gene annotation projects. Participating community college students from six institutions completed both the pre-course quiz N=43 and post-course quiz N=33 with a difference (post-quiz minus pre-quiz) of N=21. Students showed a significant increase in scores from pre-course (mean = 3.1) to post-course (mean = 5.5; t(14) = 2.79, p < .05) as shown in Figure 2. Of important note, both CC and non-CC students showed a significant increase in quiz scores from the pre- to post-quiz (p<0.001), and those gains were very similar between the CC and non-CC students (p>0.7).

FIGURE 2.

FIGURE 2.

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Community college and non-community college students show comparable learning gains using the GEP curriculum. (light grey bars) and students at non-community colleges (dark grey bars) are shown. For community college students, Pre-quiz N=43, Post-quiz N=33, and Difference (post-quiz minus pre-quiz) N=21; for students from other institutions Pre-quiz N=1294, Post-quiz N=588, and Difference (post-quiz minus pre-quiz N=262). The error bars show 95% confidence intervals around the means. The results for the community college students are very similar to those for non-community college students: post-quiz scores are higher than pre-quiz scores for both groups (** is p<0.001) and the difference in scores (post-quiz minus pre-quiz) is similar for both groups (p > 0.7).

SURE benefits

Students evaluated a series of statements regarding potential learning benefits from their genomics experience as part of the post-course survey. These items were previously included in a survey of undergraduate research experiences (SURE) (Lopatto, 2004, Lopatto, 2007). The students evaluated the items on a scale of 1 (little or no gain) to 5 (large gain). A comparison of post survey self-reported benefits between CC students and other students for the academic year 2020–2021 is shown in Figure 3. The mean evaluations by CC students, shown as light gray circles, are similar to the non-CC students, shown as dark gray triangles. Like other genomics students, the CC students rated “Understanding science” (mean = 4.02) and “Understanding that scientific assertions require supporting evidence” (mean = 4.0) highly. “Skill in how to give an effective oral presentation” (mean = 2.70) and “Confidence in my potential to be a teacher of science” (mean = 2.86) had the lowest ratings. A mixed design ANOVA with 20 related items and two groups (CC students versus comparison students from 4-year institutions) resulted in no main effect for groups (F = 0.9, df = 1,829, p >0.05). We conclude that self-reported learning benefits for CC students are positive and not different from ratings by comparison students.

FIGURE 3.

FIGURE 3.

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GEP students self-report gains for twenty learning benefits. Students at community colleges show comparable gains to GEP students at non-community colleges. N = 96 for community college students (grey circles) and N = 758 for students from other institutions (black triangles) (complete data sets). Mean responses are shown; error bars given for the community college means represent 95% confidence intervals. For most items, the means are very similar for the two groups of students (F = 0.9, p = .347, df = 1, 829).

Thriving

Recent research on student culture has included discussions of “thriving,” a concept of student attitude or morale that suggests the student is happy and positively motivated to succeed. The thriving literature suggests that thriving includes at least five factors, including “engaged learning,” “academic determination,” “positive perspective,” “social connectedness,” and “diverse citizenship” (Schreiner, 2013). We constructed eleven items based on common thriving questions but focused on the genomics experience for the post-course survey. Figure 4 depicts student ratings of the eleven items constructed to reflect “thriving.” The mean ratings by CC students are shown in light gray, while the mean ratings for comparison non-CC students are shown in dark gray. The overall pattern of responses is similar for each group. The means for the most highly rated item, “I am optimistic about being successful in my future science courses,” were identical for the two groups (mean = 4.11). The lowest rated item for both groups was “I enjoyed doing the genomics work and made it a priority for my time and effort,” but the mean of the comparison group (mean = 3.6) fell just above the upper boundary of a 95% confidence interval for the CC mean. Other ratings for the non-CC group fell within the boundaries of the 95% confidence intervals around the CC means (Figure 4). A mixed design ANOVA with the eleven items treated as repeated measures for two groups (CC students versus comparison non-CC students) resulted in no main effect for groups (F = 1.03, df = 1, 1023, p > 0.05). We conclude that thriving ratings for CC students are not different from ratings by comparison students, and all are very positive. In addition, the data reveal some preliminary but suggestive evidence that CC students engaged in CURE activities (e.g., submitting a gene annotation project) report nominally higher scores on the thriving items than CC students who were limited to using the introductory guided inquiry modules (actively learning to use a genome browser), but not submitting research projects; Figure 5. Although the cause of these differences is subject to many interpretations, the result is consistent with the view that research engagement is related to enhanced thriving. CC students appreciated the realistic nature of the genomics projects, the opportunity for group work, and the relation to future careers (Supplemental Table 1.A–D).

FIGURE 4.

FIGURE 4.

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Community college and non-community college students show comparable ratings for thriving. Mean scores for eleven items related to thriving from reports by students at community colleges (light grey bars) and by students at non-community colleges (dark grey bars). N = 96 for community college students and N = 936 for non-community college students (complete data sets). The error bars show 95% confidence intervals. The results for the community college students are very similar to those for non-community college students (F = 1.03, p = .3, df = 1, 1023).

FIGURE 5.

FIGURE 5.

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Community college student participation in the research project may produce additional benefits in thriving compared to using only the introductory training as guided inquiry modules. Mean scores for eleven items related to thriving from reports by community college students who participated in the research project (white bars, N=22) and by those community college students who did not participate in the research (light grey bars, N=74). The error bars show 95% confidence intervals around the means. Students participating in the research report nominally higher scores; while the differences are not large, the direction of the shift is consistently positive.

DISCUSSION

This report includes preliminary but promising data on the effects of implementation of the GEP CURE at CCs. We hypothesized that CC student outcomes would be comparable to non-CC gains. Our rationale was based on previously published evidence demonstrating that outcome gains, while sensitive to time investment on task, instructional time and iteration, have been observed regardless of institution type (Shaffer et al. 2014). When evaluating knowledge gains, we found that CC students improved significantly on the knowledge post-quiz. Although the baseline score means for the pre-quiz are higher for non-CC students, the gain in learning due to experiencing the GEP curriculum is not different between the groups (Figure 2). One limitation of these data is the small sample size (due to low response rate on the post-quiz) for the CC group; thus, this observation, although promising, should be interpreted with caution. Additionally, we assessed CC student outcomes based on self-reported gains and on self-reports of the student experience while coping with the uncertainty of an open-ended and authentic genomics research project, utilizing a post-survey with both the SURE survey items and eleven items constructed to reflect student thriving while engaged on that work. Our analysis demonstrates that CC students’ self-reported gains are not significantly different from those reported by non-CC students involved in the GEP projects (Figure 3). Furthermore, CC students’ ratings on “thriving” items were similar to their non-CC counterparts (Figure 4).

The lower scores on the “readiness for more demanding research” and improvement in the “skill in how to give an effective oral presentation” reported by the CC students (Figure 3) may be attributed to limited course offerings at the 2-year colleges, where individualized mentored research projects are rare and opportunities for project presentation in both informal and formal settings are limited. There is an imperative and a potential, nevertheless, for the improvement of the latter score, especially since oral presentation skills are an important general education competency for all college students. To achieve this goal, the CC faculty, and the GEP, may need to be more deliberate in creating opportunities for student project presentations as well as in teaching presentation skills to their students.

The flexibility of the GEP curriculum allows for successful adoption at various types of educational institutions (Shaffer et al. 2014). Implementation may include use of active learning modules and/or genome annotation research projects. However, there are significant differences in possible implementations between CCs and other institutions, mainly due to differences in available courses in which the curriculum can be used. At 4-year institutions research projects can be embedded in a wide variety of courses, from introductory to advanced-level specialized topics courses (e.g., Bioinformatics or Genomics), while adoption at CCs is often limited to Introductory Biology and sophomore-level Genetics, in which there can be strict prescriptions for curriculum content for accreditation purposes. A course number for “Independent Research” or other experiential learning may be more common at 4-year institutions than at CCs. Such a curriculum slot can be very useful in initiating a CURE. Interestingly, our analysis shows comparable types of implementations between CC and lower division undergraduate courses but distinct from upper division offerings (Figure 1.A–C). Our analysis suggests that different types of implementations may impact the CC student experience (Figure 5), with genome annotation research projects resulting in greater gains in “thriving” measures than use of the active learning modules alone. Evidence of improved outcomes with the addition of the research project is consistent with previous reports that student gains from GEP curriculum are dependent on student time investment and iteration (Shaffer et al. 2014; Lopatto et al. 2020).

Other bioinformatics and genomics research consortia (such as SEA-PHAGES) are working to scale-up CURE participation across institutes of higher learning (Hanauer et al. 2017). Like GEP, these programs have been shown to have benefits for participating students. Hanauer et al. (2017) also reported student gains after engagement in the SEA-PHAGES research experience regardless of institutional type. This report included eight Associate’s degree-granting institutions; most of these institutions offered biotechnology programs, which may result in more research capacity and/or research culture than most CCs. In general, participation of CCs in CURE research partnerships is limited. Understanding how centrally supported CURE organizations can attract and sustain CC participation will be critical as higher education takes aim at increasing equity, inclusion, and retention in STEM. Our early analysis suggests that the GEP model, which integrates centralized support with flexible CURE implementation provides similar benefits for CC and non-CC students.

Supplementary Material

supplemental materials
supplemental Tables

Acknowledgements

We thank Frances Thuet (Department of Biology, Washington University in St. Louis) for supervising the collection of GEP student responses to the pre- and post- surveys, as well as collecting GEP faculty reports and institutional data. Our deep gratitude goes to Dr. Sarah Elgin, Wilson Leung, and all the GEP staff and members, for their invaluable expertise, assistance, and support. This material is based upon work supported by the National Science Foundation (1915544) and the National Institute of General Medical Sciences of the National Institutes of Health (R25GM130517) to the Genomics Education Partnership (https://thegep.org/, PI-LKR). Any opinions, findings, and conclusions or recommendations expressed in this material are solely those of the author(s) and do not necessarily reflect the official views of the National Science Foundation nor the National Institutes of Health.

Footnotes

Conflict of Interest

The authors declare that they have no conflicts of interest.

Internal Review Board

All research protocols involving human subjects were reviewed and approved by the Internal Review Board at the University of Alabama (protocols 18-10-1678 and 19-06-2428).

Data Availability

All supplemental material is available at https://doi.org/10.6084/m9.figshare.21365727.v1

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

supplemental materials
NIHMS1876557-supplement-supplemental_materials.pdf (195.6KB, pdf)
supplemental Tables
NIHMS1876557-supplement-supplemental_Tables.docx (102.1KB, docx)

Data Availability Statement

All supplemental material is available at https://doi.org/10.6084/m9.figshare.21365727.v1

RESOURCES