It turns out that not all heritable traits (those that can be passed on to your offspring and beyond) are located within the nucleotide sequence of the DNA.  Experiences during your lifetime that do not mutate the ACTGs of your DNA can still have an effect that can be passed along to your future generations.  These changes are called epigenetic changes and offer fascinating new insights and possibilities in the world of genetics.  Go to my wiki page on epigenetics and follow the links to read several articles on epigenetics, genomic imprinting and new research findings.

Epigenetics wiki page

You will have a genetics test on Wednesday, 4/22/15.  The test will include genetic crosses, pedigrees, karyotypes, inheritance patterns, DNA replication, transcription/translation and any other topics covered in class or assigned readings.

There is a practice test located at

http://www.docfleetwood.net/biology/studyguides/geneticspracticetest.htm

While not all-inclusive, the practice test should give you a good idea of what to expect on the actual test. The test is for practice only and it is your responsibility to check the accuracy of any answers.  The crosses on the real test will be more extensive than on the practice test.

Go to my wiki page located here.  You will see two links (Exploring DNA and DNA Structure).  You should visit these pages in the order presented and view the JMOL interactive models at those sites.  These are very cool 3-D models that you can manipulate to understand the structure of DNA.  After you view the first site (Exploring DNA) and while you are viewing the second site (DNA Structure), you should answer the questions from the Question Sets shared with you in your Google Drive folder  Please don’t just rush to answer the questions.  Take your time to investigate and appreciate the beauty of DNA and of these modeling programs.

Due:  Tuesday, 3/31/15

Finish the NCBI BLAST tutorial and practice Google Doc so that we can apply that knowledge to Drake genetics 🙂

You should also try to finish up the Geniverse cases.

We will tie it all together at our next class and it will be helpful if you have tried your very best to work these things out before we meet.

Complete by Wednesday, 3/4/15

You will have a test on cancer, imperfect testing, pharmacogenetics and personalized medicine on Friday, 2/6/15.  For a more specific list, see the goals and objectives handout provided in class.

Complete the ‘Ethical Issues’ section of my Pharmacogenetics page in my wiki.  Answer the associated questions (on the wiki page) in your notebook.  Be prepared to defend your choices regarding the case study and whether or not Elizabeth should tell her children and what her children should do if she does tell them.

On March 9, 2014, The-Scientist reported on a new screening test for Alzheimer’s disease.  According to the abstract of the study,

Herein, we describe our lipidomic approach to detecting preclinical Alzheimer’s disease in a group of cognitively normal older adults. We discovered and validated a set of ten lipids from peripheral blood that predicted phenoconversion to either amnestic mild cognitive impairment or Alzheimer’s disease within a 2–3 year timeframe with over 90% accuracy. This biomarker panel, reflecting cell membrane integrity, may be sensitive to early neurodegeneration of preclinical Alzheimer’s disease.

Note the 90% accuracy claim of the test.  Now that we have looked at ways to measure a test’s value (i.e. sensitivity, specificity, PPV and NPV), you might wonder what a 90% accuracy means in the context of this study.  Others wondered the same thing and there are a few articles discussing this research finding in the context of medical screenings and being careful about the conclusions one should draw.

1. Screen the Healthy? – read this page for a quick overview of the issue.
2. How a “90% accurate” Alzheimer’s test can be wrong 92% of the time – see a good infographic here that visually displays the problem.
3. On the hazards of significance testing. Part 1: the screening problem – finish by reading this page that shows the issue with screening via probability trees, Baye’s Rule, prevalence affects, and several examples.  An excellent summary of many of the issues we have discussed with screening tests.

Read the mammogram FAQ and cancer FAQ in the ‘Class View’ folder of our class in your Google Drive.  Come to class prepared to discuss these documents and/or ask clarifying questions.

Due: Monday, 12/8/14