LESSON 1: What is Genetic Research?

1. LESSON 1: What is Genetic Research? PowerPoint slides to accompany Using Bioinformatics: Genetic Research Chowning, J., Kovarik, D., Porter, S., Grisworld, J., Spitze, J., Farris, C., K. Petersen, and T. Caraballo.  Using Bioinformatics: Genetic Research.  Published Online October 2012. figshare. http://dx.doi.org/10.6084/m9.figshare.936568

2. Genetic Research Deals with Inherited Traits Genetic researchers study inherited traits by analyzing DNA sequences. Use bioinformatics to research differences in DNA sequences. How are we similar? How are we different? DNA isolation.

3. Scientific Practices Ask a Question Based on Observations: Plants grow in soil. What do plants use to grow larger? Hypothesis & Prediction: If – and – then Hypothesis: Plants use materials in the soil to gain mass. Prediction: If my hypothesis is correct, and I measure the mass of soil & plants over time, then I predict the soil mass will decrease as plant mass increases. Gather and Analyze Data (Methods): Measure mass of bean seeds and soil at Day 1 and Day 15. Results: Bean plants increased in mass by 24.6 grams. Soil mass stayed the same. Conclusions: Minerals from the soil do not affect the mass of plants. Hypothesis is contradicted. New Hypothesis: Plants use something in the air to gain mass. Image Source: Wikipedia Commons

4. The Practices of Scientific Research Observations of Nature Interpretation and Evaluation The Scientist Hypothesis and Prediction Data Collection and Analysis

5. What is Bioinformatics? Bioinformatics is the application of computer science and information technology to biology and medicine. Bioinformatics makes it possible to analyze large quantities of complex biological data and can be used to search biological databases, compare sequences, and draw molecular structures.

6. Bioinformatics Tools Help Scientists:Organize, Process, and Make Sense of Complex Biological Data Sets DNA RNA Protein Bioinformatics Tools: DNA Sequencing Identify Mutations in DNA. Bioinformatics Tools: RNA Sequencing Identify tissue specific gene expression. Bioinformatics Tools: Protein 3D Structure visualization. Question: What kinds of scientific questions can we answer with bioinformatics tools? Image Source: Wikipedia Commons

7. The Practices of Scientific Research Do families with higher rates of cancer also have higher rates of DNA damage? Observations of Nature DNA sequences from tumors contain genetic mutations. Interpretation and Evaluation Studies by other scientists demonstrate that genes X and Y are involved in DNA repair, which could explain the increased cancer risk. The Scientist Hypothesis and Prediction Genetic differences contribute to the development of cancer. Data Collection and Analysis Comparisons of genomes from different cancers identify variants in genes X and Y.

8. DNA Sequencing Core Lab ManagerELLEN SISK, MS Place of Employment: Seattle Biomedical Research Institute Type of Work: Manages the DNA Sequencing “Core.” The Core lab is a centralized facility that provides DNA sequencing for all the researchers at the Institute. The Seattle BioMed Sequencing Core facility has been in operation for over 18 years and offers DNA sequencing and analysis to Seattle's scientific community, as well as international scientists and organizations. Our service provides cost-effective solutions for small laboratories that lack access to sequencing technology.

9. Which Animals are Most Closely Related to One Another? Coyote Jack Russell English Shepherd Toy Poodle Labradoodle Red fox Cocker Spaniel Gray wolf Image Source: Wikipedia Commons

10. Inside the Gene Machine: How Information from DNA is Acquired and Used for Genetic Testing Genetic Counselors work with patients to help them decide whether or not to have a genetic test, and help them understand the results of the test. Patient Sample: Blood or Saliva. Lab Technicians work with patient samples in the lab, purifying and sequencing the DNA. Extract DNA from Cells. …TTCACCAACAGGCCCACA… Bioinformatics programmers create computer programs to help biologists analyze data. Sequence DNA. Biomedical Researchers perform experiments with patient samples to find different variations of genes that might cause disease. Bioinformatics tools like BLAST and ClustalW are used to compare sequences. Reference …TTCACCAACATGCCCACA… F T N M P T Patient …TTCACCAACAGGCCCACA… F T N R P T Compare Patient DNA Sequence to Reference Sequence. Search Database to Determine if Patient Mutation is Associated with Disease. Medical Doctors and Veterinarians use the knowledge gained from genetic testing to care for their patients. Image Source: Microsoft Clip Art

11. How DNA Sequence Data is Obtained for Genetic Research Genetic Data Obtain Samples: Blood , Saliva, Hair Follicles, Feathers, Scales. Compare DNA Sequences to One Another. Extract DNA from Cells. …TTCACCAACAGGCCCACA… Sequence DNA. TTCAACAACAGGCCCAC TTCACCAACAGGCCCAC TTCATCAACAGGCCCAC Image Source: Wikipedia Commons

12. Which Animals are Most Closely Related to One Another? Coyote Jack Russell English Shepherd Toy Poodle Labradoodle Red fox Cocker Spaniel Gray wolf Image Source: Wikipedia Commons

13. Multiple Sequence Alignment of Canine DNA Sequences

14. Color Coding Reveals Differences

15. DNA Sequencing Core Lab ManagerELLEN SISK, MS Place of Employment: Seattle Biomedical Research Institute Type of Work: Manages the DNA Sequencing “Core.” The Core lab is a centralized facility that provides DNA sequencing for all the researchers at the Institute. The Seattle BioMed Sequencing Core facility has been in operation for over 18 years and offers DNA sequencing and analysis to Seattle's scientific community, as well as international scientists and organizations. Our service provides cost-effective solutions for small laboratories that lack access to sequencing technology.

16. CAREERS IN SPOTLIGHT:DNA Sequencing Core Lab Manager What do they do? The manager oversees the core lab facility. These types of facilities make it possible to perform DNA sequencing reactions and analysis for many different researchers at a given institution, company, or university. The Core lab facility makes it possible for many researchers to share the same DNA sequencing facility and expertise of technicians and the Core Lab Manager. What kind of training is involved? Bachelor’s degree in biology, molecular biology, biochemistry, or related discipline. Some have a Master’s degree or a PhD. What is a typical salary for a Core Manager? Salaries vary with experience and range from $50-$100,000 per year ($25-$50/hour). Source: Genome Technology Salary Survey 2010