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ANTH/BIOL 460 Human Genetics – Spring 2014

 

Class time and place:

T R 4:15-5:30pm, 113 Carnegie Building

 

Professor:

Dr. George (PJ) Perry

Departments of Anthropology and Biology

513 Carpenter Building

ghp3@psu.edu

Office hours: Thursday 2:00-3:00

 

Teaching assistant:

Arslan Zaidi

Interdisciplinary Graduate Program in Genetics

510 Carpenter Building

saz5078@psu.edu

Office hours: Monday 11:15-12:15 & Tuesday 3:00-4:00

 

Prerequisites:

This is an advanced course. You are expected to have basic knowledge of genetics through an introductory course that covered this topic in at least part of the semester. Some intuition about statistics and probability is also helpful, although we will not spend much time in the course or on the exams directly applying statistical analysis. If necessary, some additional reading can be done early on to ensure an adequate background in these areas.

 

Course overview:

This course will cover the nature and contents of the human genome and the basic principles of evolution. We will also carefully consider the processes by which we can identify how information contained within our genomes may affect physical and behavioral phenotypes, and what other factors may be involved (e.g., the environment). The points will be illustrated by a variety of examples of human evolution and important biomedical issues. The lectures will be posted on ANGEL prior to class. Attendance records will not be taken. However, it will likely be difficult to comprehend the material and especially the key concepts (on which the exams will focus) without consistently attending class. To supplement your own studying, prior to each exam there will be a class period devoted to a brief review of selected key concepts (~45 minutes; the review will be high level and will not comprehensively cover all of the details and concepts for which you will be responsible on the exams) and ample opportunity for asking specific questions (~30 minutes). Come prepared with questions.

 

Textbook:

Jobling et al. 2013 Human Evolutionary Genetics (2nd edition). This book does a great job introducing many fundamentals and key concepts of the human genome and human genome variation. These principals are relevant for all downstream aspects of the course. The book itself then focuses on evolutionary genetics, but as we will discuss, there is a major intersection between human evolutionary and medical genetics, and the Jobling et al. book also includes much material related to the latter. Short reading assignments, with the specific, most relevant pages, are provided for each lecture. For additional context and help with broader concepts, you may wish to read the entire book. As a second book for those who desire some additional reference material, consider Vogel and Motulsky 2010 Human Genetics. The PSU library has an institutional copy Vogel and Motulsky for online downloading of chapters.

 

23andMe personal genomics opportunity:

We have moved into a personal genomics era, in which individuals can now spend surprisingly small amounts of money to obtain dense genome-wide single nucleotide polymorphism (SNP) data (eventually this will move to whole genome sequencing), either on their own or as part of medical treatment. From these data, and benefitting from published evolutionary, population history, and medical genomics studies (of the sort that will be emphasized throughout this course), it is in turn possible to obtain detailed ancestry information and an understanding of your genetic risk for certain common diseases. This semester, for the first time, we will integrate student (and professor) individual genomic data and profiles into the course, through the best company offering a personal genomic service, 23andMe (funded by Google). The service will cost you $99 – and thus it is completely optional. But for $99 you receive genotypes for ~1 million of your SNPs spread across the genome (the same data costs researchers >$400 per individual; 23andMe is able to offer a steep discount in part because they process so many samples), and a very well done web-based presentation of the analysis of those data, which then updates going forward as relevant new scientific studies are published.

When you order the service, 23andMe mails a “kit” that contains a tube for saliva collection. You send that back by return mail and create an online account. They notify you when the results are ready for your review. In the meantime, you can choose (optionally) to answer phenotypic questions about yourself, which 23andMe then is able to use, as part of its huge customer database, to advance our knowledge of SNPs associated with complex traits. By reviewing your own genetic information and profile, you will solidify your understanding of the key evolutionary and medical genetics concepts that we cover throughout the semester. There will be an extra credit opportunity related to your interpretation of your personal genomic analysis and how you connect this to the material from the course (see below for details). The information may also be of personal value to you. Finally, we will spend a period at the end of the semester to discuss these results and this experience, and the future outlook for personal genomics. If you wish to participate in the 23andMe opportunity, you need to order the service during the first week of the class, and then return your saliva sample immediately after it arrives, because the genotyping process can take several months and you will want to have your results before the end of the semester. Again, participation is completely optional, and there is an alternate extra credit assignment, based on papers that have been published by 23andMe (see below for details), so that those who do not order the personal genomics service are not disadvantaged.

 

Grading for UNDERGRADUATE students:

There will be 3 multiple-choice exams during the semester (50 questions each) and a comprehensive final exam (75 questions). The final may be very slightly weighted towards the material presented not covered on the first three exams, but otherwise it will be very much comprehensive. As this is an upper division course, to the greatest extent possible the multiple choice questions will require basic knowledge of the information presented in class and (most importantly) a strong grasp of relevant underlying concepts. The questions are designed to be challenging but not tricky. Still, some past students have found it difficult to know what to expect and how to study for the exams before experiencing the first one. In response, and because there are few opportunities for earning and raising grades in a course of this nature, of the 3 exams offered during the semester, the 2 highest scores will count towards the overall course grade. In addition, in the review sessions prior to each exam we will review and walk through the logic and the material used to answer multiple questions from past years’ exams.

A typical grading scale will be used: (90-100% = A; 80-89% = B, 70-79% = C; 60-69% = D, < 60% = F). Depending on the overall performance of the class, a curve may be (likely will be) applied to the scores for each exam. A curve can only help your grade on an exam, not hurt it. For example, if you correctly answer 43 of 50 questions on an exam, for a percent score of 86%, your curved percent score could possibly improve your grade on the exam to an A, but you would not receive credit for less than 86% (B), even if everyone else in the class answered 44 or more questions correctly. Your overall grade will be calculated as 30% from each of the two highest in-semester exam grades, and 40% from the final exam.

There will be one opportunity for extra credit, connected to the 23andMe opportunity described above. The assignment is a 3-5 page report (11 point Arial font, 1 inch margins, 1.5 line spacing) not including references or figures, of one or two personally interesting or valuable results from your 23andMe profile, explained in the context of your family or personal history (i.e., why is the result interesting or valuable to you?), and using what you have learned over the course of the semester to describe the methods likely used by 23andMe to obtain that result from your genome-wide SNP data. Provide screenshots of the relevant 23andMe pages from your profile as part of your report (the figures do not count towards the page requirements). It is not required, but you may enhance your report by also reading, discussing, and referencing relevant articles from the primary literature (journals only – no webpage citations). Alternatively (for students who chose to not order the 23andMe personal genotyping service), you may write a report describing the methods and results from one of the multiple papers published by 23andMe based on their analysis of the genotype and phenotype data from their database of customers (papers to choose from will be uploaded to ANGEL). The extra credit assignment is due (electronically) by April 24, with no extensions. This is two days following the third exam. Your submission of this assignment indicates your consent for the potential use of your results and information from your paper (without your name) in the final lecture of the semester, when we discuss the overall 23andMe experience and the outlook for the personal genomics future. Students submitting truly outstanding extra credit reports will have a 3% bonus applied to their final, overall grade (i.e., sufficient to raise your final grade from a B to a B+, from a B+ to an A-, or from an A- to an A, etc.). Good reports will lead to a 2% bonus, fair reports a 1% bonus, and reports with minimal effort or thought will not be rewarded with a final grade bonus.

 

Grading for GRADUATE students ONLY:

Your grades from each of the three in-semester exams will be counted towards your final grade (the lowest score will not be dropped). You will not take the final exam. Instead, a term paper will be due (electronically) by April 24. The term paper will follow the format of the extra credit opportunity for the undergraduate students (i.e., either detailing results from your own 23andMe profile, or a report inspired by one of the published 23andMe GWAS papers), except that it should be 5-10 pages in length (11 point Arial font, 1 inch margins, 1.5 line spacing) not including references or figures, and it must cite the primary literature more extensively (at the level as would a manuscript that you would submit for publication to an academic journal). Your overall grade will be calculated as 25% from each of the three in-semester exam grades, and 25% from the term paper. There will be no extra credit opportunities for graduate students.

 

Other:

All general Penn State policies (academic integrity, accommodations for students with disabilities, make up exams, etc.) will be applied strictly to the course, so I will not repeat them here. Please contact me, as appropriate, should you have any questions or points to discuss on these matters.

 

Approximate schedule (topics subject to change):                            Jobling et al. pages:

 

January:

14     Introduction

16     1. Evolutionary concepts and the history of human genetics   3, 160

21     2. Organization of the human genome                                      22-27, 34-40

23     3. Sources of variation in the genome                                       48, 55-6, 66-9, 76, 83, 140-1

28     4. Phenotypic effects of genome variation                               57-60

30     5. Genomics technology (how we measure variation/effects) 98-104, 116-8

 

February:

4       6. Simple and complex traits                                                     43-6, 483-4

6       7. Environmental effects and the human microbiome

11     Review session for exam 1

13     Exam 1 – Human genome organization and variation.

18     8. Evolutionary theory and population genetics                         141-5, 159, 523-6

20     9. Human variation and race                                                     147, 300-2, 443-6, 464-6, 485-93

25     10. Recent human evolution                                                      209-12, 215-16, 335-8, 500-3

27     11. Human evolution and disease                                             529-38, 546-9, 560-2

 

March:

4       12. Ancient DNA and human evolution                                     123-8, 272-3, 276-8, 303-13

6       13. Comparative genomics                                                       160-1, 237-8, 241, 265-71

11     Spring Break – No class

13     Spring Break – No class

18     Review session for exam 2

20     Exam 2 – Human evolutionary genetics.

25     14. Simple trait mapping and admixture mapping                     462-3, 517-9

27     15. Complex trait mapping                                                        553, 558

 

April:

1       16. Human medical genetics and pharmacogenomics             564-6

3       17. Behavioral genetics                                                             555

8       18. Cancer genetics                  

10     Guest lecture or movie - TBD (AAPA meeting)

15     19. Animal models for human disease

17     Review session for exam 3

22     Exam 3 – Medical genetics.

24     20. Biomedical research and ethics; forensic genetics             572-80

29     21. 23andMe data analysis; the personal genomics future       594, 596, article posted on ANGEL

 

May:

1       Review session for final exam

TBD  Final exam – comprehensive.