NWABR

Introductory - Using Bioinformatics: Genetic Testing

This is the first of a two-part series in NWABR's bioinformatics curriculum, funded by a grant called Bio-ITEST. ITEST grants are for Innovative Technology Experiences for Students and Teachers, from the National Science Foundation (NSF). This three-year grant provides funding for education outreach programs that help secondary school teachers and their students learn about how information technology is used in biological research.

Major collaborators include Digital World Biology, EdLab Group, and Shoreline Community College. The program also draws on NWABR’s strong relationships with school districts, community groups, bioethicists and NWABR member research institutions.

Click here to access the full curriculum.

The curriculum unit explores how bioinformatics is applied to genetic testing. Specifically, the bioinformatics tools of BLAST and Cn3D are used to investigate the genetic and molecular consequences of a mutation to the Breast Cancer Susceptibility 1 (BRCA1) gene.

Students are also introduced to principles-based bioethics in order to support their thoughtful consideration of the many social and ethical implications of genetic testing.

Throughout the unit, students are presented with a number of career options in which the tools of bioinformatics are used.

Download the full Overview Unit Plan including correlation to National Science Standards and the Next Generation Science Standards.

Lesson One -- Bioinformatics and Genetic Testing
PowerPoint for Lesson One

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 which 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.

Lesson Two -- Navigating the NCBI
PowerPoint for Lesson Two

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.

Lesson Three -- Exploring Genetic Testing: A Case Study
PowerPoint for Lesson Three

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.

Lesson Four -- Understanding Genetic Tests to Detect BRCA1 Mutations
PowerPoint for Lesson Four

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 the BRCA1 mutation, students then 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.

Lesson Five -- Learning to Use Cn3D: A Bioinformatics Tool
PowerPoint for Lesson Five

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 pipe cleaner 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.

Lesson Six -- Evaluating Genetic Tests: A Socratic Seminar Discussion
PowerPoint for Lesson Six

In this lesson, students apply the ethical skills and scientific knowledge they have acquired over the previous lessons to determine (1) whether or not BRCA1 testing meets the standards of a useful genetic test, or (2) whether or not direct-to-consumer genetic testing should include genetic counseling of clients. 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.

Lesson Seven -- An Introduction to Bioinformatics Careers
PowerPoint for Lesson Seven

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.

Lesson Eight -- Genetic Testing Unit Assessment: ALAD and SOD1
PowerPoint for Lesson Eight

As an assessment to the unit, students revisit some of the bioinformatics tools that 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).

Appendix

Resource Materials

PowerPoints to accompany each "Using Bioinformatics: Genetic Testing" lesson are found under the "Lessons" tab, below each lesson title.

See our Student Career Center for career profiles, planning resources, and more.

Lesson 4
BRCA1 sequences (file containing Lawler family BRCA1 DNA and protein sequences)

Lesson 5
BRCA1 Animation
Developed by Beth Anderson (Arkitek Studios) and Jill DelSordi

BRCA1 VAST alignment
BRCA_BRCT_vastsrvalignment.val

Extension files:
HappyBirthday
HBImprov
HC1 - HC2 - HC3 - HC4

Lesson 8
Porphyria and ALS amino acid sequences (download word file containing sequences)

The Personal Genome Project
The Personal Genome Project is a public genomics research study that aims to improve our understanding of genetic and environmental contributions to human traits. They are enrolling members of the public who are willing to share their genome sequence and other personal information such as health and medical data with the scientific community and the general public for purposes that promote human welfare through the advancement of scientific and medical discovery. The mission of the Personal Genome Project is to encourage the development of personal genomics technology and practices that: are effective, informative, and responsible; yield identifiable and improvable benefits at manageable levels of risk; and are broadly available for the good of the general public. To achieve this mission they are building a framework for prototyping and evaluating personal genomics technology and practices at increasing scales. Each year additional people are recruited to participate.

A Series of articles written by Emily Singer for MIT's Technology Review detailing the rationale behind the Personal Genome Project, and how the project has grown tremendously during just the past few years.

The Personal Genome Project: What would happen if genetic and medical records were freely available to anyone who wanted them? January 20, 2006

Genomes on Display: Ten volunteers may reveal their genetic and medical data. October 20, 2008

Interpreting the Genome: New technologies will soon make it possible to sequence thousands of human genomes. Now comes the hard part: understanding all the data. January/February 2009

The Personal Genome Project Has a Growth Spurt: Thirteen thousand people will divulge their genetic and medical histories online. May 18, 2009

Harvard Mapping My DNA Turns Scary
Bloomberg's John Lauerman describes his experiences when he received the results of his genome analysis, as part of the Personal Genome Project (PGP). In addition to uncovering a rate genetic variant associated with blood disorders and an increased risk of Alzheimer’s Disease, Lauerman struggles with what to do with the information, the uncertainties associated with this type of data, and how it might impact his family.

Biochemistry and Molecular Structure Resources

3D Molecules

Protein Data Bank (PDB)
Search for the protein structures and either print, view online, or download to view with an appropriate plug-in (some of which can be downloaded from the site). Features a "molecule of the month." Also, visit the extensive Educational Resources Section.

NCBI's Structure Page allows you to view structures with a simple view, Cn3D, available for download from the site. It also maintains its own structure database, MMDB, which is a subset of the PDB.

Biotechnology and Molecular Biology Curriculum

Access Excellence

About Biotech--A wealth of biotechnology information and resources, including career information and a graphics gallery.

Access Excellence/Woodrow Wilson Biotechnology Institute--A collection of biotechnology laboratory and classrom activities from Woodrow Wilson fellows.

Human Genome Project Education Resources
Wide range of educational materials related to the human genome project including publications, teaching aids, images, and downloadable powerpoint presentations describing the project and its implications.

Cold Spring Harbor DNA Learning Center
Features a variety of high-quality resources for teaching about DNA, including introductory material about human evolution, bioinformatics, and eugenics images.

Animations Library (requires Shockwave, downloadable from site)
The PCR animations are an especially valuable resource for teaching this technique.

DNA From the Beginning--An animated primer of DNA, genes, and heredity.

Your Genes, Your Health--Provides information about genetic disorders.

Genetic Science Learning Center
Offers many valuable resources for teaching and learning about biotechnology.

Iowa State Biotechnology Resources for Educators
Includes thirteen laboratory activities, curriculum units, and more. Topics include DNA extraction, fingerprinting, bacteria transformation, bioluminescence, plant micro propagation, a PCR activity, and a soybean flavor demonstration.

National Centre for Biotechnology Education (United Kingdom)
NCBE Publications--Download curriculum to teach biotechnology in the classroom, including plant biotechnology and fermentation.

ThinkQuest Genetic Experiments
Use readily available materials to simulate genetic research and develop an understanding of DNA extraction, how enzymes work, probability and heredity pools, individual genetic variations, and chromatography. These experiments can be performed at home or school and come with both text and graphic demonstrations.

Beyond Discovery: The Path from Research to Human Benefit
Real life case studies illustrate how recent medical and technological advances arose from basic laboratory research. Some of the areas covered are Hepatitis B, polymers, designer seeds, and human gene testing.

Fred Hutchinson Cancer Research Center SEP Program Science and Education Links
An extensive collection of science links is available at Dyanna's Picks. The downloadable resource list is especially valuable for Washington State educators.

NCBI
The National Center for Biotechnology Information has links to a wealth of resources for learning about biotechnology, including information on human genome resources, model organisms, and outreach/education. Begin at the "About NCBI" section for a good overview of resources. PubMed is a valuable resource for locating scientific research articles.

Washington Biotechnology and Medical Technology Online
The home page of WBBA, the Washington Biotechnology and Biomedical Association (WBBA), provides information about biosciences in Washington State, as well as Education Materials such as a lab on gel electrophoresis and DNA fingerprinting.

WhyBiotech.Com
An informational site from the Council for Biotechnology Information.

Cell Biology Resources

Biology4Kids: The Cell Biology Pages: These pages cover all major cell organelles in detail with gorgeous color graphics and helpful analogies for understanding cellular functions. Not just for "kids," this site would provide a terrific review for high school students as well.

The Biology Project provides cell biology resources in addition to addressing other aspects of biology. It also offers activities, lesson plans, and tutorials.

Cells Alive provides a wonderful microscopic images of cells. Check out the cell model tutorial and the cell gallery!

NCBI Bookshelf: Search topics directly in the online versions of the classic texts of cell biology, Molecular Biology of the Cell, and Molecular Cell Biology. This is an amazing resource!

Stem Cells

Medline: Latest news on stem cell research from the National Library of Medicine.

PBS Newshour Online: Human Stem Cell Research: After reviewing background and a research interview on this controversial topic, view a three-minute animation on how human stem cells are cultured. Embryonic stem cell issues are debated by medical ethicists.

Science Magazine: Original article on "Embryonic Stem Cell Lines Derved From Human Blastocysts" in the October 1998 issue.

Stem Cell Primer from the NIH provides an overview of stem cells and issues related to their growth.

TIME magazine 2001 article on stem cells provides an introduction to the topic at the layperson's level.

Virtual Cell, An Education Index Top Site. Zoom into the cell, cut sections, and learn about different organelles in this highly interactive site.

Neurobiology Resources

Digital Anatomist Interactive Atlas (Neuroanatomy): This is an advanced program provided by the University of Washington that can be taken for credit, used in a classroom, or enjoyed for individual learning purposes. Graphics and photos illuminate many components of the nervous system. Online movies are available for every subject. The overview details how to customize the program, label photos and diagrams, navigate the site, and how to use quiz mode.

Neuroscience for Kids--This home page has been created for all students and teachers who would like to learn more about the nervous system. Enjoy the activities and experiments on your way to learning more about the brain and spinal cord. This includes a scavenger hunt to help familiarize students with the site and nervous system.

Drugs and the Brain

Alcohol and Drug Abuse Institute, University of Washington
A Multidisciplinary Center at the University of Washington, whose mission is to support and facilitate research and research dissemination in the field of alcohol and drug abuse. There is information about research being conducted and local clinical trials; in addition, there is an extensive list of links related to drug and alcohol abuse, treatment, and recovery.

American Council for Drug Education
Drug Prevention Lesson Plans
Lesson plans for K-12 grade levels. Each lesson plan describes the objective of the leson, background on the topic, resources and teacher tips, and then the activities to plan for this class time. There are also downloadable PDF files containing activity worksheets.
Tips for Talking About Drugs in the Classroom
Includes appropriate messages and communication strategies for talking to students about drugs.

National Institute on Drug Abuse (NIDA)
NIDA provides easy-to-use powerpoint "Slide Teaching Packets" on several topics related to drugs and the brain, including: The Brain and the Actions of Cocaine, Opiates, and Marijuana, The Neurobiology of Drug Addiction, and the Neurobiology of Ecstasy (MDMA). NIDA and NIH also offer a free curriculum supplement called "The Brain: Understanding Neurobiology through the Study of Addiction."

Click through some of the slideshows:
--The Neurobiology of Drug Addiction
--Bringing the Power of Science to Bear on Drug Abuse and Addiction

General Online Resources

Access Excellence is a great site for health and science teachers originally developed by Genetech.

Action Bioscience provides readings and curriculum ideas for topics such as biotechnology, the human genome, and a variety of other topics in biology.

The Biology Project provides activities, lesson plans, and tutorials, especially strong on problem sets, and tutorials.

The DNA Files--Experts and public radio watchdogs explore cutting edge topics in biomedical research.

The Genetics Science Learning Center (GSLC)--The GSLC partnership between scientists and educators produces innovative and effective genetic science learning programs utilizing information from leading-edge research.

The Science Lab offers links to many science-related sites, including science education resources.

Office of Science Education at NIH is an outstanding resource for teachers and students with access to a wealth of free curriculum materials. Be sure to look at the valuable Curriculum Supplements, as well as the "Snapshots of Science and Medicine" newsletter.

The NIH has also created a Women in Science Career page, with complimentary videos, posters, and career profiles. Other areas of the NIH site, such as NIH: For the Public, may also be of interest.

Online Texts

Kimball's Biology Pages
Modified from the author's text "Biology" published in 1944 by Wm. C. Brown. Search alphabetically or by search engine. There are a lot of diagrams.

NCBI Bookshelf
The bookshelf is growing number of biology reference boks that can be searched directly. Several important biology reference texts, such as" Molecular Biology of the Cell" by Alberts et. al, and "Immunology" by Janeway et. al, are available.

Upcoming Introductory Bioinformatics: Genetic Testing Events

An Introduction to Bioinformatics Teacher Workshop

Friday, February 3, 2012 - 18:00

Seattle

United States

This workshop will be presented on February 3 starting at 4pm and February 4 starting at 9am, 2012.

Program Description
The Northwest Association for Biomedical Research (NWABR) is excited to share our new bioinformatics program, Bio-ITEST: New Frontiers in Bioinformatics and Computational Biology funded by the National Science Foundation. Our curriculum, which was developed in collaboration with scientists, ethicists, and teachers, is comprised of two different units or “Strands.” The Introductory Strand, highlighted in this workshop, utilizes bioinformatics resources to teach basic concepts in molecular biology. The Advanced Strand, currently in field testing, incorporates additional informatics resources and includes an authentic inquiry-based investigation specifically for advanced students.

Using the breast cancer susceptibility gene BRCA1 as a model, students are introduced to a collection of bioinformatics tools and explore the ethical issues surrounding genetic testing. As biomedical researchers discover an increasing number of genes associated with susceptibility to disease, the era of “personalized medicine” is increasingly becoming a reality. Students will need to understand disease risks and genetic penetrance, how genetic information is acquired, stored, and used, who has access to their information, and how genetic testing can influence personal and health decisions for themselves and their families. Empowering students to understand the science behind genetic testing also reinforces lessons in evolution, transcription and translation, and the relationship between protein structure and function.

As part of this workshop teachers will receive:
• Basic background in bioethics
• An introduction to the National Center for Biotechnology Information (NCBI)
• Exposure to software for performing multiple sequence alignments
• Instruction on viewing macromolecules using Cn3D

Prior bioinformatics experience is not required.

Stipend, Clock Hours
Teachers will receive a $150 stipend for their participation in the 1.5 day professional development workshop. Nine clock hours will be provided free of charge. Dinner will be provided on Friday, February 4. Breakfast and lunch will be provided at the Saturday session. Teachers will also receive access to various bioinformatics resources.

Contact Jeanne Chowning, NWABR Director of Education, with questions or to request additional information. 206-957-3337, jchowning@nwabr.org

Introductory - Using Bioinformatics: Genetic Testing

Upcoming Introductory Bioinformatics: Genetic Testing Events

This program is made possible by

National Science Foundation