Bio-ITEST Genetic Testing

Individual lessons and curriculum support materials are described in the table below and can be downloaded there


**NEW** Find all the Bio-ITEST genetic testing structures in one place. Check out our new Bio-ITEST collection.


**NEW** Find all the BRCA1 structures in one place in our new BRCA1 structure collection!


 


To cite the Bio-ITEST Genetic Testing materials, or to download the entire curriculum:


Chowning, J., Kovarik, D., Grisworld, J., Porter, S., Spitze, J., Farris, C., and K. Petersen.  Using Bioinformatics: Genetic Testing.  Published Online April 2012. figshare. http://dx.doi.org/10.6084/m9.figshare.936566


**Note:  An updated version of Lesson 5 that uses Molecule World can be downloaded below.  


The development of these materials was funded in part by an ITEST grant from the National Science Foundation DRL-0833779. 


Click here to view the two-part BRCA1 animation described in the Genetic Testing curriculum.


Any opinions, findings, conclusions, or recommendations expressed on this website are those of the authors and do not necessarily represent the official views, opinions, or policy of the National Science Foundation.

Title Description

Overview of Genetic Testing Unit

The Bio-ITEST genetic testing curriculum is designed for high school students in grades 9-12.  In a series of eight lessons, students are introduced to the idea of genetic testing and the implications for managing information about their personal health.  Through this curriculum, students:

  • Learn how to navigate databases at the NCBI
  • Explore the story of a family debating whether or not to get genetic testing for mutations related to breast cancer
  • Compare and align DNA sequences to identify family members' samples that contain mutations in BRCA1
  • Work with molecular structures to understand how a common mutation changes the structure of the BRCA1 protein
  • Utilize a process for evaluating genetic risks
  • Learn about bioinformatics careers
  • Work through activities to assess understanding

Download Genetic Testing Overview (pdf)

Lesson One: Bioinformatics and Genetic Testing

A short topical play introduces students to the fields of bioinformatics, genetic testing, direct-to-consumer genetic testing, and ethical considerations. Students discuss some of the broad implications and ethical questions raised from gaining information through genetic testing. Students then consider a number of genetic tests and their potential usefulness and value and, as a class, explore the website of 23andMe, a company that offers direct-to-consumer genetic tests. The lesson wraps up as it began—by engaging students in a story. Through a short video, students are introduced to a family impacted by breast cancer. In Lesson One, students also learn how bioengineers might use bioinformatics tools in their career.

Download Genetic Testing Lesson 1 (pdf)

Download Genetic Testing Lesson 1 PowerPoint (ppt)

Lesson Two: Navigating the NCBI

Students navigate parts of the National Center for Biotechnology Information (NCBI) website and work independently to explore databases, focusing on the BRCA1 gene and the bioinformatics tool Map Viewer. Through an analogy that compares two collections of databases (iTunes® and the NCBI), students connect with their own prior knowledge to better understand database structure and function. In Lesson Two, students learn how veterinarians might use bioinformatics tools in their career.

Download Genetic Testing Lesson 2 (pdf)

Download Genetic Testing Lesson 2 PowerPoint (ppt)

Lesson Three: Exploring Genetic Testing: A Case Study

In this lesson, students engage in a case study about a family with a history of breast cancer. Students consider ethical issues surrounding genetic testing as they decide whether or not family members should get tested for BRCA1 or BRCA2 mutations. Students then evaluate the case through the principles-based bioethics concepts of: Respect for Persons, Maximize Benefits/Minimize Harms, and Justice. Students apply the principles to help them reason through their decision as they participate in a Structured Academic Controversy. In Lesson Three, students learn how genetic counselors might use bioinformatics tools in their career.

Download Genetic Testing Lesson 3 (pdf)

Download Genetic Testing Lesson 3 PowerPoint (ppt)

Lesson Four: Understanding Genetic Tests to Detect BRCA1 Mutations

Students begin this lesson by working through a pedigree chart and Punnett squares for the Lawler family, attempting to track the BRCA1 mutation across generations. Based on the decisions as to who should be tested for mutations in the BRCA1 gene, students use the bioinformatics tool known as BLAST (Basic Local Alignment Search Tool) to compare individual DNA and protein sequences to reference sequences that are known to be free of BRCA1 mutations associated with cancer. At the end of the lesson, students compile class information from the Lawler family in order to revise their pedigree charts and Punnett squares. In Lesson Four, students learn how laboratory technicians might use bioinformatics tools in their career.

Download Genetic Testing Lesson 4 (pdf)

Download Genetic Testing Lesson 4 PowerPoint (ppt)

AttachmentSize
Microsoft Office document icon Genetic-Testing-Lawler-Family-Sequences-Lesson4.doc49.5 KB

Lesson Five: Learning to Use Molecular Models

****UPDATED April 2015****  This activity has been updated to use Molecule World, a user-friendly molecular modeling app for the iPad.  

Some of the advantages of using Molecule World for this activity are:

  • Better representations of atom sizes
  • Ability to select and change views by touch
  • Easier to use than Cn3D
  • ​Structures can be loaded in Molecule World ahead of time
  • Easier to compare normal vs mutant structures
  • Molecule World has color keys

Up to this point in the curriculum, students have seen the BRCA1 protein represented in a linear, sequence form. In this lesson, students are introduced to the  importance of a protein’s three-dimensional structure. Students engage in a short activity first in which they use a chenille pipe cleaner stem to make a "protein" with a simple function, to illustrate the relationship between a protein’s structure and function. Students then learn to navigate between linear protein sequences and three-dimensional structures by using Molecule World. Students begin by viewing and manipulating DNA—a familiar molecule to students. When students are familiar with the program, students visualize parts of the BRCA1 protein to show how a specific mutation in the BRCA1 gene ultimately changes or destroys the protein’s function. In Lesson Five, students learn how 3D animators might use bioinformatics tools in their career.

We have a short (<2 minute) video to show how this works in Investigating breast cancer with Molecule World in the Bio-ITEST curriculum

Materials:  

1.  Get Molecule World from the iTunes app store.

2.  Download Genetic Testing Lesson 5 Slides updated March 2015 Powerpoint (ppt)

3.  Download Genetic Testing Lesson 5 Using Molecular Models Teacher guide, updated April 2015 (pdf)

4.  Download Genetic Testing Lesson 5 Using Molecular Models Student Instructions (pdf)

5.  Download Genetic Testing Lesson 5 Using Molecular Models Student Worksheet (pdf)

 

AttachmentSize
Binary Data 1NAJ_DNA.cn329.57 KB
Binary Data 1Y98_BRCT_Domain.cn3104.91 KB
Binary Data 1JNX.cn3101.94 KB
Binary Data 1N5O.cn395.5 KB
Audio icon Primary_Structure_Song.mp3154.7 KB
Audio icon Secondary_Structure_Song.mp3180.5 KB
Audio icon Tertiary_Structure_Song.mp3184.49 KB
Audio icon Quarternary_Structure_Song.mp3154.7 KB
Audio icon Happy_Birthday.mp3277.64 KB
Audio icon Happy_Birthday_ Improv.mp3247.35 KB

Lesson Five: Learning to Use Cn3D: A Bioinformatics Tool

Up to this point, students have seen the BRCA1 protein represented in a linear, sequential form. In this lesson, students are introduced to the high importance of a protein’s three-dimensional structure. Students first engage in a short activity in which they use a chenille stem to perform a simple function, as an analogy for the relationship between a protein’s structure and function. Students then learn to navigate between linear protein sequences and three-dimensional structures by using the bioinformatics tool Cn3D. Students begin by viewing and manipulating DNA—a familiar molecule to students—using Cn3D. When students are familiar with the program, students visualize parts of the BRCA1 protein to show how a specific mutation in the BRCA1 gene ultimately changes or destroys the protein’s function. In Lesson Five, students learn how 3D animators might use bioinformatics tools in their career.

Download Genetic Testing Lesson 5 (pdf)

Download Genetic Testing Lesson 5 PowerPoint (ppt)

AttachmentSize
Binary Data 1NAJ_DNA.cn329.57 KB
Binary Data 1Y98_BRCT_Domain.cn3104.91 KB
File BRCA_BRCT_VAST_valignment.val195.26 KB
Audio icon Primary_Structure_Song.mp3154.7 KB
Audio icon Secondary_Structure_Song.mp3180.5 KB
Audio icon Tertiary_Structure_Song.mp3184.49 KB
Audio icon Quarternary_Structure_Song.mp3154.7 KB
Audio icon Happy_Birthday.mp3277.64 KB
Audio icon Happy_Birthday_ Improv.mp3247.35 KB

Lesson Six: Evaluating Genetic Tests: A Socratic Seminar Discussion

In this lesson, students apply the ethical skills and scientific knowledge they have acquired over the previous lessons to determine (1) whether BRCA1 genetic testing meets the standards of a useful genetic test, or (2) whether direct-to-consumer genetic testing should be subject to additional regulations. Students or teachers may choose from one of two readings, after which students participate in a Socratic Seminar in order to deepen their understanding about genetic testing. Through the seminar discussion of the first reading, students become familiar with a framework for considering genetic tests in terms of their clinical validity and the availability of effective treatment. Through the seminar discussion of the second reading, students become familiar with issues and preliminary data regarding the effects of direct-to-consumer genome-wide screening. After the seminar, students are supported in coming to an individual position about genetic testing through the integration of scientific facts, stakeholder viewpoints, and ethical considerations. In Lesson Six, students learn how bioethicists might use bioinformatics tools in their career.

Download Genetic Testing Lesson 6 (pdf)

Download Genetic Testing Lesson 6 PowerPoint (ppt)

Lesson Seven: An Introduction to Bioinformatics Careers

In this lesson, students explore more deeply the information they have learned throughout the unit about people in various careers that use bioinformatics. Students choose one career they would like to learn more about. They further explore that career by reading a series of in-depth questions asked of the person highlighted in that career, as well as provided internet resources. Students then respond to a job posting for a summer internship in their chosen field, developing a resume for that position. Optional activities include peer-editing of resumes and socializing in a professional environment.

Download Genetic Testing Lesson 7 (pdf)

Download Genetic Testing Lesson 7 PowerPoint (ppt)

Lesson Eight: Genetic Testing Unit Assessment: ALAD and SOD1

As an assessment of the unit, students revisit some of the bioinformatics tools they have used in prior lessons in order to locate a mutation in a protein associated with a genetic condition. Students also evaluate current genetic tests for the condition using the criteria of clinical validity and treatment options. Two conditions and their tests are presented: porphyria and amyotrophic lateral sclerosis (ALS).

Download Genetic Testing Lesson 8 (pdf)

Download Genetic Testing Lesson 8 PowerPoint (ppt)

AttachmentSize
Microsoft Office document icon Genetic-Testing-ALAD-SOD1-Sequences-Lesson8.doc27 KB

Genetic Testing Unit Appendix

This Unit Appendix contains background information and additional reading to supplement the Genetic Testing lessons, including:

  • BRCA1 and BRCA2 Background
  • BRCA1: Is it Dominant or Recessive?
  • “GINA” The Genetic Information Nondiscrimination Act of 2008: Information for Researchers and Health Care Professionals
  • Ethics Background
  • Creating Discussion Ground Rules
  • Amino Acid Abbreviations and Chemistry Resources
  • Codons and Amino Acid Chemistry
  • Behind the Scenes with the NCBI Databases and the Entrez Search Engine
  • Understanding BLAST
  • Finding Structures in the NCBI Structure Database

Download Genetic Testing Appendix (pdf)