Using The Cancer Genome Atlas as an Inquiry Tool in the Undergraduate Classroom

Hankey, William; Zanghi, Nicholas; Crow, Mackenzie M.; Dow, Whitney H.; Kratz, Austin; Robinson, A; Robinson, Meaghan R.; Segarra, Verónica A.

doi:10.3389/fgene.2020.573992

Cited by 7 publications

(7 citation statements)

References 15 publications

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“…All data used in this study was from the NCI TCGA database. Informed consent was obtained by the NCI investigators from every patient in the trial [60].…”

Section: Supplementary Materialsmentioning

confidence: 99%

Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes

Freischel

Teer

Luddy

et al. 2022

Cancers

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We identify critical conserved and mutated genes through a theoretical model linking a gene’s fitness contribution to its observed mutational frequency in a clinical cohort. “Passenger” gene mutations do not alter fitness and have mutational frequencies determined by gene size and the mutation rate. Driver mutations, which increase fitness (and proliferation), are observed more frequently than expected. Non-synonymous mutations in essential genes reduce fitness and are eliminated by natural selection resulting in lower prevalence than expected. We apply this “evolutionary triage” principle to TCGA data from EGFR-mutant, KRAS-mutant, and NEK (non-EGFR/KRAS) lung adenocarcinomas. We find frequent overlap of evolutionarily selected non-synonymous gene mutations among the subtypes suggesting enrichment for adaptations to common local tissue selection forces. Overlap of conserved genes in the LUAD subtypes is rare suggesting negative evolutionary selection is strongly dependent on initiating mutational events during carcinogenesis. Highly expressed genes are more likely to be conserved and significant changes in expression (>20% increased/decreased) are common in genes with evolutionarily selected mutations but not in conserved genes. EGFR-mut cancers have fewer average mutations (89) than KRAS-mut (228) and NEK (313). Subtype-specific variation in conserved and mutated genes identify critical molecular components in cell signaling, extracellular matrix remodeling, and membrane transporters. These findings demonstrate subtype-specific patterns of co-adaptations between the defining driver mutation and somatically conserved genes as well as novel insights into epigenetic versus genetic contributions to cancer evolution.

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“…All data used in this study was from the NCI TCGA database. Informed consent was obtained by the NCI investigators from every patient in the trial [60].…”

Section: Supplementary Materialsmentioning

confidence: 99%

Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes

Freischel

Teer

Luddy

et al. 2022

Cancers

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“…Students in the CaNCURE coop program (22) were able to publish manuscripts from their time in lockdown (23,24). Data analysis, modeling and simulations (25), and data mining projects (26)(27)(28)(29) were pursued with a range of applications. Students also gained more experience in reading the literature (30) and wrote review articles.…”

Section: Research Projectsmentioning

confidence: 99%

Adapting Undergraduate Research to Remote Work to Increase Engagement

et al. 2021

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Demand for undergraduate research experiences typically outstrips the available laboratory positions, which could have been exacerbated during the remote work conditions imposed by the SARS-CoV-2/COVID-19 pandemic. This report presents a collection of examples of how undergraduates have been engaged in research under pandemic work restrictions. Examples include a range of projects related to fluid dynamics, cancer biology, nanomedicine, circadian clocks, metabolic disease, catalysis, and environmental

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“…Meanwhile, previously, bioinformatics is often taught in a computer lab by a lecture format. In recent years, there were research reporting the successful implementation of course‐based undergraduate research experience (CURE) courses in metagenomics, 8–10 as well as TCGA data analysis using Excel 11 . As an interdisciplinary subject with strong application feature, bioinformatics education lends itself especially well to CURE.…”

Section: Introductionmentioning

confidence: 99%

A course‐based undergraduate research experience for bioinformatics education in undergraduate students

Gao

Guo

2023

Biochem Molecular Bio Educ

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With rapid development of sequencing technology and the continuous accumulation of biological big data, people who are capable of using bioinformatic skills to analyze omics data and work out biological problems are urgently needed in the workforce, which highlights the importance of developing bioinformatics skills early in the undergraduate curriculum. Meanwhile, course‐based undergraduate research experience (CURE) courses have been proved to be an effective teaching format that have many advantages over traditional labs and lectures. Here we introduced an implementation of CURE course of bioinformatics data analysis and visualization for undergraduate students in major of bioinformatics and evaluated the learning outcomes. We were able to address 10 out of 15 core competencies identified by Network for Integrating Bioinformatics into Life Sciences Education. Besides, results evaluated by Laboratory Course Assessment Survey demonstrated the goals of collaboration, discovery and relevance, and iteration were accomplished in our course. Meanwhile, a significant increase in scores of final examinations and a long‐term improvement on students' research ability on bioinformatics data analysis and visualization were also observed. In summary, this CURE course is useful for undergraduate students learning related knowledge and participate in authentic research in the field of bioinformatics.

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Using The Cancer Genome Atlas as an Inquiry Tool in the Undergraduate Classroom

Cited by 7 publications

References 15 publications

Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes

Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes

Adapting Undergraduate Research to Remote Work to Increase Engagement

A course‐based undergraduate research experience for bioinformatics education in undergraduate students

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