The focus of this RCN-UBE project was to support and expand participation in the Genome Consortium for Active Teaching using Next-Generation Sequencing (GCAT-SEEK). Genomics and bioinformatics are dynamic fields well-suited for capturing the imagination of undergraduates in both research laboratories and classrooms. However, high costs, demanding technical skills, and high rates of change inhibit integration of next-generation sequencing approaches into the undergraduate curriculum. GCAT-SEEK aimed to generate and use massively parallel sequencing data associated with the research interests of network faculty members as the catalyst for producing innovative and broadly disseminated educational modules that offer authentic research experiences to students.  The goals of this project were to increase network participation, produce and disseminate educational modules that are assessed for student learning gains, foster a sense of community among network faculty and students, and support network communications. Hands-on faculty/student workshops centered on participant research projects were the key implementation strategy.  Workshops were co-sponsored by a grant from Howard Hughes Medical Institute to Juniata College. 

Eight summer workshops were organized and run over a six-year period.  Three genomics workshops were performed at Minority Serving Institutions including Morgan State University, California State University at Los Angeles, and Hampton University.  Approximately 200 different faculty and students completed at least one summer workshop.  The workshop included wet-lab sessions for preparing samples for sequencing, training for genomics data analysis including high performance computing, training for assessing student learning, sessions devoted to educational planning, and a session on how to teach the ethical, legal, and societal implications of genomics to biology students.  Research projects included RNAseq, prokaryotic genomics, eukaryotic genomics, and microbial community sequencing approaches.

Over the six year period the network grew from 100 to 300 faculty distributed around the country.  Faculty reported use of network protocols, data, or computational resources to help teach approximately 5000 students genomic data analysis, 600 of which were mentored in an independent research setting.  Over 60,000 jobs were submitted to the Juniata HHMI high performance computing cluster by network faculty and students since 2013.  To date, the network has supported 38 educational or disciplinary manuscripts, 29 of which included student authors, with over 60 different student authors in total.   Educational modules were developed by workshop participants and are available on the network webpage (https://gcat-seek.weebly.com/).

Faculty reported increases in confidence and skills at analyzing bioinformatics data as a result of the workshops.  A cohort of students at Juniata College were given a genomics core concepts multiple-choice test developed by the network during their first year (pretest), at the end of the sophomore year (midtest) and at the end of the senior year (posttest). Student scores improved significantly from pre- to mid- to posttest, indicating that exposure to genomics course content that was integrated into Juniata's core curriculum by GCAT-SEEK faculty improved understanding of the material.  Students in the program are learning valuable skills in bioinformatics, computer science, data analysis, and genomics.  Graduates have already gone on to work for governmental labs like the NIH, many are in graduate programs where their skills will increase, and some have formed their own genomics companies.

A Genomics Education Alliance (GEA) has formed from leaders of similar national genomics networks, including several GCAT-SEEK facilitators.  The GEA is working to survey faculty teaching genomics for preferences and needs with respect to tools, curricula, and professional development strategies that enable genomics research with undergraduates.  Survey results will help inform productive and sustainable next-steps for GCAT-SEEK and other similar networks.

Last Modified: 05/01/2019
Modified by: Vincent P Buonaccorsi