Introductory Bioinformatics: Genetic Testing

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

The Introductory 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.

In order for us to measure how our curriculum resources are being used, please take a moment to contact us and let us know the class or classes in which you're using our lessons.  We also welcome feedback about our introductory bioinformatics curriculum. We will not share your contact information with anyone.

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.

Lessons

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.

    Complete Lesson Plans
  • Full "Using Bioinformatics: Genetic Testing" Curriculum Genetic_Testing_FINAL-NWABR.pdf

    This PDF contains the entire “Using Bioinformatics: Genetic Testing” curriculum, including the overview, lessons, and appendix.  For accompanying lesson PowerPoints, please download from the links above.

  • Lesson One: Bioinformatics and Genetic Testing Genetic_Testing_Lesson1_NWABR.pdf

    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.

  • PowerPoint for Lesson One Genetic-Testing-Lesson1-Slides-NWABR.ppt
  • Lesson Two: Navigating the NCBI Genetic_Testing_Lesson2_NWABR.pdf

    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.

  • PowerPoint for Lesson Two Genetic-Testing-Lesson2-Slides-NWABR.ppt
  • Lesson Three: Exploring Genetic Testing: A Case Study Genetic_Testing_Lesson3_NWABR.pdf

    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.

  • PowerPoint for Lesson Three Genetic-Testing-Lesson3-Slides-NWABR.ppt
  • Lesson Four: Understanding Genetic Tests to Detect BRCA1 Mutations Genetic_Testing_Lesson4_NWABR_7.17.15.pdf

    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.

  • PowerPoint for Lesson Four Genetic-Testing-Lesson4-Slides-NWABR.ppt
  • Lesson Five: Learning to Use Cn3D: A Bioinformatics Tool Genetic_Testing_Lesson5_NWABR.pdf

    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.

  • PowerPoint for Lesson Five Genetic-Testing-Lesson5-Slides-NWABR.ppt
  • Lesson Six: Evaluating Genetic Tests: A Socratic Seminar Discussion Genetic_Testing_Lesson6_NWABR.pdf

    In this lesson, students apply the ethical skills and scientific knowledge they have acquired over the previous lessons to determine (1) whether BRCA1 testing meets the standards of a useful genetic test, or (2) whether 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.

  • PowerPoint for Lesson Six Genetic-Testing-Lesson6-Slides-NWABR.ppt
  • Lesson Seven: An Introduction to Bioinformatics Careers Genetic_Testing_Lesson7_NWABR.pdf

    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.

  • PowerPoint for Lesson Seven Genetic-Testing-Lesson7-Slides-NWABR.ppt
  • Lesson Eight: Genetic Testing Unit Assessment: ALAD and SOD1 Genetic_Testing_Lesson8_NWABR.pdf

    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).

  • PowerPoint for Lesson Eight Genetic_Testing_Lesson8_Slides_NWABR.pptx
Resources

Resource Materials FOR Introductory lessons

PowerPoints to accompany each "Using Bioinformatics: Genetic Testing" lesson are found on "Lessons" page, besideeach lesson title.

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

Lesson Four: Understanding Genetic Tests to Detect BRCA1 Mutations

BRCA1 sequences
This Word document file contains Lawler family BRCA1 DNA and protein sequences.

Fluorescent Protein Extension Files:

Comparing Fluorescent Proteins Using BLAST Instructions (PDF)
Using BLAST to Analyze Proteins (PPTX)

DNA Sequences from Various Fluorescent Proteins
Protein Sequences from Various Fluorescent Proteins
These Word documents contain DNA and protein sequences of a variety of fluorescent proteins, including eukaryotic Green Fluorescent Protein (eGFP), the mCherry Red Fluorescent Protein (RFP), the mLemon Yellow Fluorescent Protein (YFP), and other members of the "mFruits" such as mGrape1, and mTangerine 1.5.  This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom." 

Lesson Five: Learning to Use Cn3D: A Bioinformatics Tool

BRCA1 Animation
Authored by the Bio-ITEST team at NWABR.
Animation by Beth Anderson (Arkitek Studios) and Jill DelSordi

DNA Structure File 1NAJ (save to your Desktop and open in Cn3D from the "File" menu)

BRCA1 Structure File 1Y98 (save to your Desktop and open in Cn3D from the "File menu")

BRCA1 VAST alignment:  BRCA_BRCT_vastsrvalignment.val

Protein Structure Music Extension Files:

Primary Structure Song
Secondary Structure Song
Tertiary Structure Song
Quarternary Structure Song

HappyBirthday 
HappyBirthdayImprovisation

Hemoglobin Structure Extension Files:
These structures can be used by teachers to illustrate the consequences of sickle cell mutations on the structure of hemoglobin.  This extension was first developed during the 2012 "Workshop A: An Understanding of DNA: Making the Invisible Visible," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Program, "Easy as ABC: Applications of Biotechnology in the Classroom." 

Wild-type Hemoglobin File  4HHB 
Note:  This is structure is the multimer of four hemoglobin monomers. 
(save to your Desktop and open in Cn3D from the "File" menu)

Sickle Cell Hemoglobin File  2HBS 
Note: This is structure is the multimer of four sickle-type hemoglobin monomers. 
(save to your Desktop and open in Cn3D from the "File" menu)

Hemoglobin VAST alignment    Hemoglobin_VAST_Alignment
Note:  This is an overlay of a single wild-type and a single sickle-type hemoglobin monomer.
(save to your Desktop and open in Cn3D from the "File" menu)

More information about how this sickle cell mutations leads to the sickle cell phenotype:  http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/hbb.shtml

RFP and eGFP Structure Extension Files:
These structures can be used by teachers to illustrate the structural similarities between two unrelated fluorescent proteins: eukaryotic green fluorescent protein (eGFP) and red fluorescent protein (RFP).  This activity can be used in conjunction with the fluorescent protein BLAST comparison activities developed as an extension of Lesson Four.  This extension was first developed during the 2013 "Workshop C: Cloning DNA to Make Protein," part of the three-part partnership series between NWABR and Shoreline Community College's Amgen Bruce Wallace Biotechnology Program, "Easy as ABC: Applications of Biotechnology in the Classroom."

Eukaryotic Green Fluorescent Protein (eGFP) File 1GFL
Note: This is structure is a dimer of two GFP monomers. 
(save to your Desktop and open in Cn3D from the "File" menu)

Red Fluorescent Protein (RFP) File 2H5Q
Note: This is structure is a RFP monomer. 
(save to your Desktop and open in Cn3D from the "File" menu)

Fluorescent Protein VAST Alignment  Fluorescent-Protein_VAST-Alignment
Note:  This is an overlay of a GFP monomer and a single RFP monomer.
(save to your Desktop and open in Cn3D from the "File" menu)

Lesson Eight: Genetic Testing Unit Assessment: ALAD and SOD1

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

 

Resource Materials FOR optional lesson extensions

Share this page   Share Facebook Twitter Email