Genomics education in practice: Evaluation of a mobile lab design

Authors

  • Marc H.W. Van Mil,

    Corresponding author
    1. Cancer Genomics Centre, University Medical Centre Utrecht
    2. Centre for Society & Genomics, University Medical Centre Utrecht
    3. Freudenthal Institute for Science and Mathematics Education, Utrecht University, The Netherlands
    • Cancer Genomics Centre, University Medical Centre Utrecht
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    • Tel:+31 30 2535444

  • Dirk Jan Boerwinkel,

    1. Cancer Genomics Centre, University Medical Centre Utrecht
    2. Centre for Society & Genomics, University Medical Centre Utrecht
    3. Freudenthal Institute for Science and Mathematics Education, Utrecht University, The Netherlands
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  • Jacobine E. Buizer-Voskamp,

    1. Freudenthal Institute for Science and Mathematics Education, Utrecht University, The Netherlands
    Current affiliation:
    1. Rudolf Magnus Institute of Neurosciences & Department of Medical Genetics, University Medical Centre Utrecht
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  • Annelies Speksnijder,

    1. Cancer Genomics Centre, University Medical Centre Utrecht
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  • Arend Jan Waarlo

    1. Centre for Society & Genomics, University Medical Centre Utrecht
    2. Freudenthal Institute for Science and Mathematics Education, Utrecht University, The Netherlands
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Abstract

Dutch genomics research centers have developed the ‘DNA labs on the road’ to bridge the gap between modern genomics research practice and secondary-school curriculum in the Netherlands. These mobile DNA labs offer upper-secondary students the opportunity to experience genomics research through experiments with laboratory equipment that is not available in schools and place genomics research in a relevant societal context. The design of the DNA lab ‘read the language of the tumor’ is evaluated, by clarifying the goals and choices in the design, and the effects of the DNA lab are presented. Based on the analysis of the design of the DNA lab and supported by the results of the evaluating studies, we consider this module to be a good example of relevant and up-to-date genomics education.

Rapid advances in molecular biology increase the gap between research practice and school science. Implications of genomics research are rapidly finding their way to everyday practice. Major breakthroughs range from medicine to forensics, biofuels, vaccine research, and mitigation of pollution [1]. These scientific advances each bring their own choices and dilemmas. To empower future citizens to deal with these personal and societal decisions science education based on relevant and up-to-date science is needed.

Many advances in molecular life sciences are not yet represented in science curricula [2, 3]. However, simply adding new content without rethinking the curriculum is not a viable strategy. In several countries, new curricula concerning molecular life sciences have been proposed or introduced [2, 4–6]. Advances in genomics research have caused fundamental changes in the scientific view on the inner working of the living cell, while secondary-school students still have problems grasping the basic concepts of DNA and proteins [7–9].

Since 2006, an extracurricular development in the Netherlands aims to bridge the gap between school science and molecular biology research practice. The Dutch Genomics Centres of Excellence and the Centre for Society & Genomics, which are part of the Netherlands Genomics Initiative (NGI), developed the ‘DNA labs on the road’. These mobile DNA labs offer students the opportunity to experience genomics research through experiments with laboratory equipment that is not available in schools. Five different ‘DNA labs on the road’ were developed in collaboration with Dutch universities. The 4-hour educational modules for secondary-school students (ages 16–18) include an introductory lesson, a 2-hour practical taught at school by university students and a final lesson. Teacher and student manuals have been developed for each lab and are made available in advance of the introductory lesson. The labs are offered free of charge to all secondary schools in the Netherlands since January 2006. Costs for equipment, transport and training the students are covered by the genomics research centers, which are funded in part by the Netherlands Genomics Initiative (NGI: www.genomics.nl). Teachers can obtain additional information and register for the labs on the DNA lab website (www.DNAlabs.eu). The practical work of the lab takes 2 hours. Taking travel time into account, the university students can teach the lab to a maximum of two different classes within the same school in 1 day.

GOALS OF THE ‘DNA LABS ON THE ROAD’

The DNA labs are an important instrument for the genomics research centers in their communication with the general public. Furthermore, the DNA labs aim at improving and implementing genomics education in Dutch upper-secondary education. The specific experiments performed in the DNA labs differ, but in each case the students perform hands-on laboratory activities, such as DNA isolation, analyzing DNA using Polymerase Chain Reaction (PCR) and bioinformatics tools, in their own classroom. The ‘DNA labs on the road’ thus offer genomics techniques in the classroom. More importantly, the DNA labs provide students a context, in which new insights in genomics are used to solve everyday problems. The DNA labs deal with different contexts: producing biofuels, plant breeding, forensics, and use of bioinformatics in crime scene investigations and improving the understanding and treatment of diseases such as Alzheimer's and cancer. These topics all rely on genomics research and they reflect the research activities of the genomics centers in the Netherlands. The DNA labs show that genomics research plays an important role in society and they encourage reflection on the personal and societal implications of genomics research. These different aspects are summarized in the goals of the DNA labs formulated at the start of the project.

The DNA labs aim at:

  • Enhancing up-to-date genomics knowledge

  • Improving the image and attitude towards genomics topics

  • Increasing the notion of societal implications of genomics research (place genomics in a societal context)

  • Invoking enthusiasm and interest in genomics research

These goals have been the starting point for designing the DNA labs. In each of the DNA labs, these general goals were further specified and translated into an instructional design. Several studies were performed to test whether the formulated goals had been reached.

In this article, we focus on just one of the DNA labs named ‘read the language of the tumor’. This module on cancer research was developed by the Cancer Genomics Centre (CGC) in collaboration with the Freudenthal Institute for Science and Mathematics Education (FIsme) of Utrecht University.

The questions addressed in this article are:

  • 1)How are the general goals of the DNA labs translated into an instructional design?
  • 2)To what extent have the educational goals been reached by this design?

MATERIALS AND METHODS

We analyzed the instructional design, the classroom practice, the results in student and teacher appreciation and learning outcomes, and the contribution both to the goals of the NGI and the innovation of biology education.

We made use of study of the scientific literature, analysis of the educational materials of the module and of the student-assistant training course, interviews with people involved in the project, classroom observations, focus group interviews, questionnaires, and analysis of results of the assignments in the module.

Parallel to this study, an evaluation of five of the DNA labs was performed regarding their quality, their learning outcomes and their effect on the attitude of the students toward genomics applications. This evaluation was based on questionnaires returned by 1824 students of which 436 performed the DNA lab ‘read the language of the tumor’ [10].

Finally, a study on the effect of the DNA lab ‘read the language of the tumor’ on the attitude of the students towards biotechnology was published by Klop et al. (2009) [11]. This study was based on questionnaires filled out by 365 students who did not participate in any of the studies mentioned above. The results of these three studies are combined to come to an overview of the impact of the module.

RESULTS

The Translation of the General Goals of the DNA Labs into an Instructional Design

The general learning goal formulated for the DNA lab ‘read the language of the tumor’ is:

  • After performing the DNA lab, students are able to explain what modern DNA research related to cancer entails and how this research is used.

    To reach this goal three more specific learning goals have been determined:

  • After performing the DNA lab, students know that cancer is ‘a disease of the genes’ and they are able to explain how one can minimize the risk of getting cancer.

  • After performing the DNA lab, students are able to perform practical steps in DNA analysis (DNA isolation, PCR, and gel electrophoresis) and they can explain the purpose of each step.

  • After performing the DNA lab, students are able to explain that DNA-research is important to improve diagnosis and treatment of cancer.

These more specific goals offer design criteria for the DNA lab. Other design criteria are derived from the context-concept approach, which is broadly accepted in science education innovation in the Netherlands [12]. This approach implies that students learn new concepts and practices in the societal or professional context, in which these concepts are used. The advantage of such an approach is that students rapidly understand the value of this knowledge and can relate it to their personal experiences and/or what they observe in the media. Furthermore, they are thus taught concepts in a meaningful setting, which improves retention. A possible disadvantage is that students may find it difficult to apply the concepts learned in one context to another.

To translate these goals into an instructional design, choices were made regarding context, techniques, genes to be investigated and format of the lessons.

Context

The DNA lab ‘read the language of the tumor’ uses the context of a diagnostic DNA test on tumor tissue to determine the best treatment for a fictitious cancer patient. This patient is diagnosed with breast cancer and the physician asks for an analysis of the mutations in the DNA of the tumor. The students are asked to carry out this task and advise the physician on the optimal treatment for this particular patient.

This context was chosen because it illustrates the three different ways knowledge about specific gene mutations can be used: first to understand the genetic changes that lead to cancer, second, to properly diagnose tumors with different genetic make ups and third, to design tailored treatment strategies based on the genetic make up of a tumor. Through this context students learn that cancer is caused by multiple gene mutations, that cancer patients can be further diagnosed by gene analysis, and that knowledge about the specific genes that are mutated in a tumor and the biological effects such mutations have can provide a basis for personalized treatment.

Techniques

Within this context, steps in the diagnostic practice should include isolating DNA from tumor and normal cells, and comparing selected genes in tumor cells with those in normal cells. Techniques to illustrate this practice were chosen with the following criteria in mind:

  • Authenticity: techniques must be used in real practice

  • Comprehension: techniques must be understood by students of the age of 16–18 years

  • Complexity: techniques that can be performed by inexperienced students

  • Transportability: techniques that can easily be transported to and set up at schools

  • Time: techniques that offer results within the time constraints of the module

  • Cost: techniques that rely on equipment and materials that fit within the set budget

  • Safety: techniques that rely on equipment and materials that can be safely used in a school environment

In authentic clinical practice, gene mutation analysis on tumor tissue is performed by sequencing the region of interest and using bioinformatics tools to detect mutations. However, using such sequencing techniques in a mobile DNA lab would be too complex, too time consuming and too expensive. Therefore, the techniques selected for the mobile lab are a simple version of DNA isolation, amplification by PCR, and analysis by gel electrophoresis on agarose gel. Due to technical and legal limitations, it was decided to have students isolate DNA from calf thymus to illustrate the principles of DNA isolation and to use plasmid based fragments to obtain the PCR products that simulate the fictitious results we want the students to analyze. The PCR is performed with PCR tubes containing ready-to-go™ beads that include nucleotides and Taq polymerase. Students only have to add DNA and primers to the tubes and the small inserts used in these plasmids make it possible to use a very short PCR protocol that fits within a 2 hour module.

The three techniques performed in the classroom are illustrated in Fig. 1.

Figure 1.

The three techniques in the practical: (A) student isolating DNA from calf thymus (B) PCR tubes placed in the thermocycler (C) student using a simple micropipette to load the PCR products on the agarose gel.

Genes

Gene mutations were selected based on the following criteria:

  • The mutated genes must represent different steps inthe process from a normal cell to a tumor cell to demonstrate that cancer is caused by multiple mutations.

  • The mutated genes must have implications for the choice of therapy to demonstrate that current therapies are based on specific mutations in tumor cells.

  • The gene mutations must be diagnosable by gel electrophoresis following PCR-amplification.

  • The function of the mutated genes must be comprehendible for students in upper-secondary education.

We chose a combination of three mutations that fulfill these criteria: a p53 deletion, HER2 amplification and a CDH1 truncation. Students identify mutations in these genes by comparing PCR fragments obtained from DNA from in healthy cells and tumor cells. An example of the result of the gel electrophoresis is shown in Fig. 2.

  • A deletion of the p53 gene results in the absence of a p53 fragment in the tumor cell PCR product. Students can conclude that the absence of p53 will lead to the loss of apoptosis (programmed cell death), which is one of the characteristic features of cancer cells. Their conclusion concerning the treatment can be: the tumor cells are not able to destroy themselves, thus therapy must be aimed at removing or destroying cancer cells. Options are surgery, chemotherapy, and radiotherapy.

  • A HER2 gene amplification leads to an over-expression and thereby autoactivation of HER2 receptors at the plasma membrane. A HER2 gene amplification is illustrated by an increased quantity of HER2 PCR product from tumor cells compared to healthy cells. Students conclude that an amplification of this gene results in the presence of an excess of growth receptors causing the cell to be continually stimulated to divide. Students are told that screening for HER2 positive breast cancer is common clinical practice. They are asked to think of a treatment that will stop overstimulation ofHER2 positive cells. In our experience, almost every group of students comes up with the idea of blocking the receptor. This is exactly the mechanism by which Trastuzumab (Herceptin®) blocks growth of HER2 positive tumors. So the advice to the physician will be Trastuzumab treatment.

  • Due to its role in cell junctions, truncation of the CDH1 (e-cadherin) gene may result in incorrect cell adhesion. From the differences in the size of the PCR fragments, students conclude that part of the e-cadherin protein is missing, which may lead to tumor cells not adhering correctly. Students hypothesize that this mutation increases the risk of metastasis and they advise the physician to check for secondary tumors and use chemotherapy as a treatment.

Figure 2.

Differences in PCR fragments analyzed using gel electrophoresis. H p53, HER2, and CDH1: represent the three genes in healthy cells. T p53, HER2, and CDH1: represent the three genes in tumor cells.

Format

The practical work is guided by university bachelor students that visit the school with the necessary equipment. Introductory and concluding lessons are taught by the teacher. In this way, the teacher participates actively in the lessons, thereby linking the lab to regular biology education.

The aim of the introductory lesson is to activate prior knowledge about cancer and to relate known molecular concepts such as DNA, gene, and protein to cancer. Students formulate their own questions about cancer, for example, ‘is cancer age-dependent?’ ‘What is the role of heredity in cancer?’ ‘What is the difference between benign and malignant tumors?’ During the module students try to find answers to these questions, thereby relating biological knowledge to real-world questions and problems.

The final lesson is used to look back at the results of the experiment and to stimulate the students to think of personal and societal implications of cancer genomics research.

Effects of the DNA Lab ‘Read the Language of the Tumor’

The effect of the DNA lab can be specified in the implementation of the instructional design of the entire module, the outreach volume and appreciation of the lab, the learning outcomes, and the effects on student attitude.

Implementation

Interviews with teachers indicate that not all teachers perform the introductory and final lesson. Reasons differ, from lack of time to the conviction that the students already have enough prior knowledge to carry out the practical. The exact percentage of teachers that perform these lessons is at present unknown. However, from the number of students that answered questions about these lessons in the questionnaires, it is estimated that from 325 students about 75% had an introductory lesson and about 64% were given a concluding lesson [10]. In some cases, only the results of the practical were discussed in the final lesson without further reflection on the personal and societal implications of cancer genomics research.

Outreach Volume and Appreciation

From the start of the project in September 2005 until June 2009, the five mobile labs reached 54,000 students in 342 different schools, which means that 64% of the Dutch secondary schools were visited and about 35% of all students in upper-secondary biology education experienced one or more DNA labs during their school career. The DNA lab ‘read the language of the tumor’ reached 188 different schools and 17,000 students during the same period.

From the point of view of the research institutes and universities involved, the ‘DNA labs on the road’ are a powerful outreach activity. After performing the DNA lab, 16% of the students indicate that they consider a study in the natural sciences as a result of having done the DNA lab ‘read the language of the tumor’ [10].

In general, both teachers and students are very enthusiastic about the module and consider it relevant. They appreciate university students visiting the school and the possibility to work with modern equipment. Students find the practical instructive, interesting, and fascinating and they consider the context of cancer research appealing and motivating (score 4.16 on a five-point Likert scale). These findings are confirmed in the evaluation of all five labs performed by Knippels [10]. In this study, only 10% of the 1824 students indicated that they did not like the DNA lab.

Teachers experience the DNA lab to be a good addition to the regular curriculum and most of them indicate that they want to continue using the ‘DNA lab on the road’.

Learning Outcomes

Analysis of the materials, classroom observations during the module and interviews with teachers shows that almost all the specific learning goals formulated are reached and that the module does indeed contribute to the students' knowledge of genomics. Results of the questionnaires show that after performing the DNA lab, students consider themselves capable of explaining the importance of DNA-research in hospitals in the context of cancer diagnosis (score 4.25 on a five-point Likert scale). When asked to complete the sentence ‘the main message of this DNA lab is…’ 80% of the students report ‘… how DNA and cancer research is performed’. In interviews students indicate that their biggest learning experience resulted from studying the function of the three genes. The fact that different characteristics of tumors are caused by mutations in different genes and the idea that therapies can be tailored based on analysis of these mutations are a novel insight for secondary-school students. After the module, students know that cancer is ‘a disease of the genes’ but not all students grasped the principle that multiple mutations are needed to turn a healthy cell into a tumor cell. In the questionnaire, about 30% of the students answer that one mutation in the DNA can cause cancer. The exact relation between DNA and cancer is difficult to describe for a lot of students. About 5% of the students state that: ‘by analyzing a persons DNA you can see if there is a tumor in the body.’ Also the relation ‘gene–protein-function’ appears to remain unclear to many students. Although this central dogma ought to be prior knowledge even before the introductory lesson, university students that teach the practical report that this concept is one of the most difficult elements in the module. These experiences correspond with studies in molecular biology and genetics education reporting that concepts at the molecular level, such as gene and protein, can be very difficult for students. [7, 9, 13] Relating these concepts to higher-level phenomena, such as cell division (on the cellular level) or cancer (on the organism level) appears also to be very difficult [14–17].

One of the goals of the DNA labs is to increase the notion of societal implications of genomics research. As mentioned before, students consider themselves capable of explaining the importance of DNA research in hospitals in the context of cancer diagnosis (score 4.25). However, an increased notion of societal implications of genomics research also implies better grounded views on ethical dilemmas and enhancement of opinion-forming skills to judge societal implication. In this respect, the study of Knippels (2006) [10] reveals that students report little enhancement of opinion-forming skills and better grounded views on ethical dilemmas. Analysis of the instructional design of the module shows that no specific classroom activities are incorporated in the module to enhance opinion-forming skills and reflection on ethical dilemmas. Improvements can be made to meet these goals.

Effects on Attitude

The module stimulates a positive attitude towards DNA-research (see also Klop, 2009) [11]. All students indicate that they are positive about DNA research. Not surprisingly, 80% of the students report improved diagnosis and treatment of diseases, mainly cancer, as a reason for this opinion.

CONCLUSION AND DISCUSSION

Our results show that most goals of the DNA lab are reached, namely: enhancing up-to-date genomics knowledge; improving the image and attitude towards genomics topics; increasing the notion of societal implications of genomics research and invoking enthusiasm and interest in genomics research.

However, some points for improvement remain. More attention should be paid to students' opinion forming on personal and societal implications of genomics research. This is in line with previous research [11]. In new versions of the DNA labs, specific lessons on opinion forming have been developed and are now being tested.

Also, the coherence between different biological concepts and biological levels of organization could be made more explicit. This has been attended to in the new versions by including a framework, in which students can categorize concepts, relations, and questions [3]. This framework includes the levels of biological organization and has the function of an ‘advanced organizer’ in the learning process [18]. The framework is in line with the current pedagogical approach in biology education in the Netherlands, i.e. the use of systems thinking, and learning concepts in the context in which they are used.

Another finding is that the importance of the introductory lesson and final lesson is being under-rated by teachers. The study of Knippels (2006) [10] shows that this is the case for all five DNA labs. Teachers indicate that they wish to have more background on current genomics research and support on the content and didactics of the module. To meet this need and to ensure the correct implementation of the introductory and final lessons, a teacher training course was developed in which these aspects are combined. This one day course is offered twice a year at Utrecht University.

The practical work in the DNA lab ‘read the language of the tumor’ is guided by third year bachelor students (age 20–22) of the biomedical sciences program at Utrecht University. Although the results show that teachers and students highly appreciate the way university students teach the lab, some improvements were made in the students' training program. Their training and participation in the DNA lab is now embedded in an optional 10 week (2 days/week) university course on science communication offered by the Cancer Genomics Centre, of which two weeks are used for training and reflection and eight for teaching the lab in schools. In this way, the DNA lab offers students a unique training and practical experience in science communication within their university curriculum.

In summary, the context of cancer research is very much appreciated by the students and teachers. Students can perform and understand the techniques and the materials and equipment are interesting and appealing to them. Most of the cognitive and affective goals are reached and improvements have been made to optimize the module. Thus, we wish to conclude that the DNA lab ‘read the language of the tumor’ is a good example of relevant and up-to-date genomics education.

Initiatives with similar goals have recently started in Europe. For instance, in France the Strasbourg University Ph.D School Life and Health Sciences launched an initiative called ‘OpenLab’ (http://www-ed-sdvs.u-strasbg.fr/openlab/). The European Molecular Biology Laboratory offers in-house training for secondary-school teachers called ‘the European Learning Laboratory for the Life Sciences’ (ELLS) (http://www.embl.de/training/sciencefor schools/). We hope that these initiatives can inspire other research institutes, didactics experts and teachers to cooperate in designing relevant and up-to-date genomics education.

Acknowledgements

This work is supported by Centre for Society & Genomics and the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (NWO).

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