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GeneChip® Microarrays: Student Manual

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The student manual includes 5 independent activities that stress different aspects of microarray technology and the application of genetics to society. This section also contains a DNA-basics refresher.

Activity 1: Reading of Recent News Paper Articles on GeneChip® Microarrays and Group Discussion

GeneChip Microarray - Educator Resources - GeneChip

In this introductory activity you will be split up into small groups. Each student will read a recent article about the use of microarrays from different newspapers around the United States and then report out to the group about the article. Students not reporting out will write down a few key points they learned about each article. Discussion time within the group will be given as each student gives their opinion on what they learned from the article and others give their thoughts as well. Afterwards a short introduction to DNA microarrays will be given by the teacher.



Goals of Activity

  • To introduce the concept of a GeneChip® microarray and examine some of its applications.
  • To illustrate the wide variety of microarray applications.
  • To get you used to sharing and communicating your ideas within a small group.
  • To connect to you prior knowledge of DNA science and technology.

Procedure

  1. Instructor will break class into small groups and assign a particular article to read about how gene chips have already been used.
  2. Read your article, taking brief notes to yourself to help you when you present to your group & take down at least 5 main points about your article (on the provided student handout).
  3. When everyone is finished in your group, choose one student to begin.
  4. Going around the group, each student should give a brief synopsis of the article, how the microarray was used in the research or to work out some problem, and any comments or opinions they have on the topic of the article (ex: Do you see this as a useful technology? In what ways does the technology interest you? Does this technology worry you?).
  5. Each presentation should take about 3 to 4 minutes.
  6. During each presentation, the other students in the group must write down at least 5 main points about the article that they learned from the presenter.
  7. On your own, answer the questions at the end of the handout.

Articles for Activity

Introduction
Download (pdf, 81 KB)

Student Handout — Article Key Points
Download (pdf, 81 KB)

Article 1 — "Power tools for the gene age: New test can help doctors in prescribing medications"
Download (pdf, 58 KB)- San Francisco Chronicle - SFGATE 2/7/05

Article 2 — "Scientists Learn in Greater Detail How HIV Kills Immune Cells"
Download (pdf, 58 KB) - Scientific America - 6/13/01

Article 3 — "New Obesity Study Checks Genetic Link"
Download (pdf, 71 KB) - San Jose Mercury News - 6/8/04

Article 4 — "Iowa State University researcher returns from Brazil with genetic material to study Asian soybean rust"
Download (pdf, 49 KB) - SeedQuest.com - 7/8/05

Article 5 — "Ohio State Creates First Equine Gene Chip"
Download (pdf, 81 KB) - OSU "onCampus" - 1/8/04

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Activity 2: Overview of GeneChip® Microarray Structure and Function

Overview of genechip microarray structure and function

In this second lesson, you will be reading the following pages, studying the diagrams, and answering questions about the material. The reading will help you to understand the structure of GeneChip® microarrays and how they can be used to study the genetics of an organism. It will focus on the types of microarrays known as the "Gene Expression" microarray, but will also explain the other two types of arrays - the SNP Genotyping array and the Resequencing array. The reading will also focus on how these microarrays can be used in drug development and fighting diseases. During all this, you will review the basics of DNA structure and function as well as other genetic concepts.


It is essential for the rest of the module that you have a strong understanding of the structure of a GeneChip microarray, how they function, and how they are used in an experiment. The basics of microarray functions are not that difficult to understand, but as you move deeper into the different types of chips it will get much more difficult. A strong understanding now will help you as you move through the unit.

Goals of Activity

  • To understand the basic structure and chemistry of a GeneChip microarray.
  • To understand the 3 main types of microarrays (Gene Expression, Genotyping, and Resequencing) and their basic applications.
  • To understand how to read results of the three types of chips.
  • To understand how microarrays fit into an entire procedure for studying and analyzing the function of genes or studying DNA.


Procedure

  1. Read Part I and answer Questions #1-25 on the Student Handout
  2. Read Part II and answer Questions #26-37 on the Student Handout
  3. Read Part III and answer Questions #38-44 on the Student Handout


Suggestions
: Before you start, you may want to review some important terms by reviewing the Appendix A "Glossary" and the Appendix B "DNA Basics review". Ask your teacher for copies if these are not already provided for you. Look through the glossary to review some of the basic terms and to become familiar with some of the more complex terms. If you do not have a firm understanding of DNA structure, function, and gene expression (transcription and translation), you may want to review Appendix B. Also, while doing the reading, be sure to refer to the diagrams provided. They provide helpful models and visual to help with your understanding.

Articles for Activity

Reading: Structure & Function of GeneChip® Microarrays
Download (pdf, 1.2 MB)

Student Handout — Reading Questions
Download (pdf, 56 KB)

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Activity 3: Photolithography: How GeneChip® Microarrays are Manufactured

GeneChip Microarray - Educator Resources - Manufacturing

GeneChip microarrays are on the cutting edge of technology. They combine knowledge of biomolecules and computer processor manufacturing. They give scientists the ability to access and analyze complex genomic information much faster than anyone could've imagined just ten years ago! What makes them even more amazing is their size. These DNA chips are just over 1 centimeter by 1 centimeter. The manufacturing process for these chips is similar to that used in the semiconductor industry - a combination of chemistry and photolithography. Photolithography is a process of using light to control the manufacture of multiple layers of material.

In this activity, you will learn about the type of process used to manufacture a GeneChip microarray - photolithography. Then, in groups, you will use what you learned to build models of the process out of every day household items. You will present this model to the rest of the class.

Goals of Activity

  • To understand the process of photolithography.
  • To understand how GeneChip microarrays are manufactured.
  • To illustrate your understanding by building simple models using everyday office supplies and candy!

Procedure

  1. Read the following information on the process of photolithography and the manufacture of GeneChip microarrays. Check and demonstrate your knowledge by answering the question set.
  2. View the presentation of the manufacturing of GeneChips at the Affymetrix facility in Sacramento, California.
  3. In groups of 3, demonstrate the basic process of photolithographic microarray manufacturing by building a model. Use the 15 - 20 items provided to illustrate your demonstration.
  4. The model(s) should depict the process of photolithographic microarray manufacturing. You will be given 20 minutes to come up with your idea, build the model and then prepare to demonstrate your model to the class.
  5. Demonstrate your model to the class, explaining how each part illustrates the different steps in manufacturing GeneChip microarrays

Articles for Activity

Manufacturing of GeneChip® Microarrays — Reading and Model Building Activity
Download (pdf, 1.4 MB)

Student Handout — Reading Questions
Download (pdf, 32 KB)

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Activity 4: Reading and Analyzing GeneChip® Microarray Results from Real Life Scenarios

GeneChip Microarrays - Educator Resources - Real Life Lab Usage

In this activity, you will get the opportunity to use what you learned about GeneChip® microarrays from Activity #2. Students will be organized into groups of five or six and each group will be assigned a different scenario that uses one of three different types of DNA chips, Gene Expression, Resequencing, or Genotyping, in the research. Each scenario will have its' own set of results that the group must analyze, interpret, and then present to the class what they determined in a short, five minute presentation. The presentation should include relevant experimental background, the experiment itself, the results, the analysis, and possible future research.

The purpose of this activity is to challenge you to analyze and interpret data in a group setting and work out a real life research problem. All scenarios and results are simplified, but are related to real research and medical studies occurring in recent studies.

Goals of Activity

  • To apply knowledge of the function of DNA chips to the analyze results of DNA chips in simulated scenarios.
  • To work as a group to analyze and interpret data.
  • To work as a group to present the results and their implications to the class.
  • To communicate within a small group and to an entire class.

Procedure

  1. Teacher will organize students into up to 6 groups.
  2. Teacher will assign each group a different scenario with a background, results, and data to analyze.
  3. Students will spend 20 minutes reading the background to the scenario, looking at the results, interpreting the results, and discussing the implications of the results to the research and to further studies.
  4. Student groups will spend 20 minutes working on a class presentation, being sure to cover the following:
    • The background to the scenario or experiment that was conducted
    • The scenario data or experimental results
    • A breakdown and analysis of what the data / results mean
    • The background to the scenario or experiment that was conducted
    • If possible, what future research should be done as a result of this work
  5. This presentation should be well organized, clear in its interpretation, and must include some sort of visuals (overheads / poster, handouts, etc.) to help the class understand the results.
  6. Each group will get 5 to 7 minutes for their presentation (not every person is required to talk for each group, but more than one student needs to speak).
  7. Students will be graded on their work while in the groups and on the presentation using a rubric as a scoring guide.
  8. During the presentation, students not in the group presenting should fill out the summary sheet for each presentation (but their own).

Articles for Activity

Introduction — Goals & Procedure
Download (pdf, 49 KB)

Scenario A: Food Contamination Analysis
Download (pdf, 36 KB)

Scenario B: Drug Metabolism Analysis
Download (pdf, 102 KB)

Scenario C: HIV Genotyping
Download (pdf, 90 KB)

Scenario D: Gene Expression in Vitis Vinifera (Grape)
Download (pdf, 109 KB)

Scenario E: Breast Cancer Progression Research
Download (pdf, 79 KB)

Scenario F: E.coli Strain Identification Using Resequencing Arrays
Download (pdf, 93 KB)

All Scenarios
Download (pdf, 202 KB)

Student Handout — Presentation Summaries
Download (pdf, 26 KB)

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Activity 5: Ethics Focus: Application of New Technologies to Society

The use of GeneChip® microarray technology can lead to a wide range of extremely powerful and useful genetic information to all areas of our society. Whether it is in medical research and drug manufacturing, insurance, reproductive technology, or public policy, the information this technology affects everyone in one way or another. It can change the way we live our lives! An educated and informed public is a key part of making sure this genetic information is used in the most ethical manner possible and for the benefit of all.

However, as with all technology, there is the possibility of abuse in a manner that complicates, discriminates or endangers the lives of others. Who has access to the information? What about health issues? Should insurance companies have free access to the information? Employers? Once we are able to identify the function of genes, how much "tinkering" is too much? Should we be able to screen embryos for genetic defects? Could this be used to go beyond racial profiling and lead to a sort of genetic profiling? Can we predict the chances of someone getting a certain disease? What about being able to identify diseases for which we have no cure? The questions go on and on...

In this activity, you will work in groups to analyze a given ethical scenario for either pros or cons (or both). You will discuss and brainstorm ideas with your group, then report out to the class. Under the teacher's direction, a discussion and debate will occur around the topics. The object is not to "prove" anyone right or wrong, but to look at each issue from both angles and think about your own point of view about these topics. You will also act out a scenario where you are part of an advisory committee for a DNA chip company. You will have to come up with an ethical principle statement for the company.

Goals of Activity

  • Be more informed about the ethical issues surrounding the use of genetic information in society.
  • Look at the positives and negatives of the use of DNA chips.
  • Begin to formulate your own opinions about the ethical dilemmas that DNA chips and genetic testing methods bring to society.
  • Think about how the ethical principles apply to a biotechnology company.

Procedure

  1. Your teacher will organize the class into small groups.
  2. Each group will be given a different ethical scenario and asked to come up with a list of positives (pros) or negatives (cons), or both, regarding the situation.
  3. You will be given 20 minutes to discuss the situation as a group and brainstorm a pro/con list. Be sure to go around the group and get everyone's opinion / ideas.
  4. Once you have come up with as many points as possible, discuss your list further and narrow it down to 4 to 5 key issues.
  5. Choose a speaker who will report out to the class what your situation was and the list your group came up with.
  6. After time is up, the teacher will go around the room and allow each group to report out and lead a class discussion around the topic.
  7. Once each group is finished and the class has discussed each topic, you will break back into groups and pretend you are on the ethics committee for a company that manufactures DNA chips. You job is to come up with a "ethical principles" statement that explains your company's stance on the use of your technology in the areas of genetic information, genetic testing, and medical privacy.
  8. The ethical policy statement should be 1 to 2 paragraphs and clearly explain your point of view.
  9. You will be given 10 minutes to come up with the ethics policy statement.
  10. Time permitting, one person from each group will read their statements to the class. If possible, you will come up with a class statement that best addresses all the statements.

Articles for Activity

Discussion of Ethical Scenarios and Company Ethical Policy Statement
Download (pdf, 485 KB)

Student Handout — Ethical Scenario Brainstorm
Download (pdf, 57 KB)

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