Presentation for teaching faculty about resources, data, issues, and strategies for including personal genomics in the classroom, within the context of precision medicine as an overarching theme.

1. Personal Genomics For
Teaching Genetic Concepts,
Information, & Resources
PF Anderson, Emerging Technologies Informationist,
Taubman Health Sciences Library, University of Michigan
May 3, 2017

2. Abstract
Precision medicine is a hot new buzzword, radically changing how we look at and use
data and information sources in life sciences research and healthcare. While there are a
lot of different potential data sources to integrate in precision medicine, one of the most
popular is genomic data, and personal genomics is a relatively easy way to start
exploring this space. Have you wanted to use personal genomics in exercises with your
students, but thought it would be too expensive or time-consuming to be practical? Not
necessarily. In this session, you’ll discover personal genomics resources and strategies
for using them, from data to analysis, from easy to expert.

3. Genomics in precision medicine
TRACO 2016
1) Exposome
2) Genome
3) Metabolome
4) Epigenome
5) Transcriptome
6) Microbiome
7) Clinical Information
8) Epidemiological data
<https://youtu.be/3IDpbTveeTo?t=6m28s>
TRACO 2016: Precision Medicine and Nanotechnology. Curtis C. Harris, M.D., NCI, NIH and Marina
Dobrovolskaia, MD, NCI, NIH; Monday, November 28, 2016, 4:00:00 PM

4. Genomics in precision medicine
Amongst the most prominent parameters
of disease are an individual’s:
1. Genome
2. Transcriptome
3. Proteome
4. Metabolome
5. Lipidome
6. Epigenome
Toward Precision Medicine: Building a
Knowledge Network for Biomedical
Research and a New Taxonomy of Disease
<https://www.nap.edu/catalog/13284/tow
ard-precision-medicine-building-a-knowle
dge-network-for-biomedical-research>
“But the prospect of applying this concept
broadly has been dramatically improved by
the recent development of large-scale
biologic databases (such as the human
genome sequence), powerful methods for
characterizing patients (such as proteomics,
metabolomics, genomics, diverse cellular
assays, and even mobile health technology),
and computational tools for analyzing large
sets of data.” F. Collins, NEJM 2015 Feb 26;
372(9): 793–795.
<https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC5101938/>
Image: The Genomics Era: the Future of Genetics in Medicine
<https://www.futurelearn.com/courses/the-genomics-era/0/steps/4923>

5. Personal genomics
in self-tracking
150 of the Best Self-Quantification
Tools (Apps, Sites and Trackers)
Quantified Self / Biohacking Tools
and Resources
https://www.quantifiedbob.com/se
lf-tracking-tools-and-resources/
Images: 150 of the Best Self-Quantification
Tools (Apps, Sites and Trackers). Rezzan
Hussey November 26, 2015.
<http://www.artofwellbeing.com/2015/11/26/self-
quantification/#DNA_microbiome_and_nutritiona
l_testing> | Wikimedia:
File:QuantimetricSelfSensingPrototypeMann199
6inset.jpg
<https://commons.wikimedia.org/wiki/File:Quanti
metricSelfSensingPrototypeMann1996inset.jpg>

6. My personal genomics story
in 25 words or less
BEFORE
● Doctor(s): Tell me where it hurts.
● Me: EVERYWHERE. And ...
● Doctor(s): How long have you hurt?
● Me: 20 years? Forever?
● Doctor(s): It’s probably in your head.
AFTER
What worked? gluten-free diet + new vitamins + exercise
<http://www.slideshare.net/perplexity/celiac-hidden-stories-invisible-disabilities>
Image:
<http://commons.wikimedia.org/wiki/File:Whites%E2%80%99_Physiological_manikin..JPG>

7. What’s YOUR personal genomics story?
1) Curious?
2) I’ve taken a spit test
3) I’m a committed
amateur
4) I’m a professional
geek about this
5) I want to explore this
for teaching
6) Something else
entirely

8. What’s the plan
What is personal genomics (PGen)?
PGen services
How it works
What it can (and can’t do)
Analogies
Risks
Ethics and stuff
Working with data (+ free tools)
Teaching examples

9. What is
personal
genomics?

10. What is personal genomics?
Individual vs. population
<http://www.nature.com/gim/journal/v11/n
8/full/gim200978a.html>
Genetics (heredity) vs genomics (functions &
interactions)
<http://www.who.int/genomics/geneticsVSg
enomics/en/>
Image credits: <https://openclipart.org/detail/181150/shadow-of-person-standing-leg-cross-and-put-hands-in-the-pockets> |
<https://openclipart.org/detail/46141/group-of-people>

11. Personal
genomic
services
List of personal genomics
companies (International
Society of Genetic Genealogy:
<http://isogg.org/wiki/List_of_p
ersonal_genomics_companies>

12. Personal genomic
services logos

13. The “Big” (Well Known) Ones

14. And then there’s UM’s “Genes for Good” (FREE!)
● NOTE: Free, but not fast.
● “Genes for Good is a research study
conducted at the University of
Michigan.
● The major goal of the study is to
engage tens of thousands of
individuals in genetic research.
● The primary tool to accomplish this is
the Genes for Good Facebook App.”
<https://genesforgood.sph.umich.edu/> |
<https://genesforgood.sph.umich.edu/face
book_app>

15. How does
personal
genomics work?

16. Basics: what you do, what you get

17. 23andMe (and the FDA)
THEN: NOW:
Images: NATURE > Regulation: The FDA is overcautious on consumer genomics
<http://www.nature.com/news/regulation-the-fda-is-overcautious-on-consumer-genomics-1.14527> NYTimes > F.D.A. Will Allow 23andMe to Sell Genetic Tests for Disease
Risk to Consumers <https://www.nytimes.com/2017/04/06/health/fda-genetic-tests-23andme.html>

18. What personal
genomics CAN’T
do
“*Our tests can be used to determine carrier
status in adults from saliva collected using an
FDA-cleared collection device (Oragene DX model
OGD.500.001), but cannotdetermine if you
have two copies of the genetic variant. Each test
is most relevant for people of certain ethnicities.
The tests are notintended to diagnose a
disease, or tell you anything about your risk for
developing a disease in the future. On their own,
carrier status tests are notintended to tell you
anything about the health of your fetus, or your
newborn child’s risk of developing a particular
disease later in life.” 23andMe,
<https://customercare.23andme.com/hc/en-us/a
rticles/212194308-Health-Reports-and-Ethnicity>

19. Why not?
Personal genomics tends to “cherry pick” genes to
examines throughout the entire “orchard” of the
genome.
Clinical genomics take more of an “apple
harvesting” comprehensive deep dive into the
products of a single “tree.”
Image credits: <https://commons.wikimedia.org/wiki/File:Cherry_picking_201127_(5991855207).jpg> |
<https://commons.wikimedia.org/wiki/File:Apple_Harvest_by_Camille_Pissarro.jpg>

20. A personal
genomics
analogy
Image credits:
<https://commons.wikimedia.org/wiki/File:ATCG.jpg>

21. Our genes are like a score …
They tell us what notes are intended.
Image credits: <https://commons.wikimedia.org/wiki/File:Codons_aminoacids_table.png> |
<https://commons.wikimedia.org/wiki/File:Johann_Sebastian_Bach_-_BWV_Anh._117a_-_Polonaise_in_F_major.pdf>

22. … but they can’t tell us how good the piano is,
or how recently it was tuned, …
Image credits: <https://commons.wikimedia.org/wiki/File:The_Honky_Tonk_Blues_-_geograph.org.uk_-_1625960.jpg> |
<https://commons.wikimedia.org/wiki/File:Steinway_%26_Sons_concert_grand_piano,_model_D-274,_manufactured_at_Steinway%27s_factory_in_Hambu
rg,_Germany.png>

23. … or who is playing, or where, or …
Image credits: <https://commons.wikimedia.org/wiki/File:Student_of_House_of_Piano_Music_Academy.JPG> | Hans Bernhard (Schnobby): Oscar Peterson
Plays Piano <https://commons.wikimedia.org/wiki/Oscar_Peterson#/media/File:Oscar_Peterson_1.JPG> |
<https://commons.wikimedia.org/wiki/File:Arthur_Rubinstein_1906.jpg>

24. What CAN
personal
genomics do?

25. You get clues, to take to a detective
Clues or hints to health puzzles or
mysteries
Image credits: <https://commons.wikimedia.org/wiki/Sherlock_Holmes#/media/File:Basil_Rathbone_Sherlock_Holmes.jpeg> |
<https://commons.wikimedia.org/wiki/File:Cluedo_Game_Board.jpeg>

26. Finding Your Detectives!
Family Physicians:
<http://familydoctor.org/familydoctor/en.html>
Genetic Counselors: <http://www.nsgc.org/>
Genetics Home Reference <https://ghr.nlm.nih.gov/>
And (with caution) patient or public forums like
Patients Like Me and 23andMe, as well as
disease-specific patient forums.

27. Are there any
risks?
Image credits: <https://openclipart.org/detail/10970/prohibition1> | <https://openclipart.org/detail/10972/prohibition2> |
<https://openclipart.org/detail/10974/prohibition3> | <https://openclipart.org/detail/10976/prohibition4> | <https://openclipart.org/detail/10978/fire-forbidden-sign> |
<https://openclipart.org/detail/10980/prohibition6> | <https://openclipart.org/detail/10982/prohibition7> | <https://openclipart.org/detail/10984/prohibition8>

28. Risks of personal genomics
Finding out something you don’t want to
know
Misunderstanding / misinterpreting what
you find out
Other people finding out something you
don’t want them to know (employers,
insurance, friends, family)
Discovering relatives you don’t know about
Being discovered BY relatives you don’t
know about
Genetics, a double-edged sword
<https://raceandtechnology.wordpress.com/2014/
12/10/genetics-a-double-edged-sword-2/>
GINA - Genetic Information Nondiscrimination Act
<https://www.eeoc.gov/laws/types/genetic.cfm>

29. Risks of personal genomics
● Artificial Insemination Nightmare Revealed by DNA Test
<http://www.yourgeneticgenealogist.com/2014/01/artificial-insemin
ation.html>
● From dream to nightmare: when your sperm donor has secrets
<https://www.theguardian.com/science/2016/aug/29/sperm-donor-
deceivers-dream-turns-nightmare>
● How personal genomics spells the end of donor anonymity
<http://www.bionews.org.uk/page_645114.asp>
● I Got My Personal Genome Mapped and It Was Bullshit
<https://www.vice.com/en_us/article/personal-genomics-companies
-23andme>
● Who’s Your Daddy?
<http://www.slate.com/articles/health_and_science/science/2013/0
5/paternity_testing_personal_genomics_companies_will_reveal_dn
a_secrets.html>
...
Image: Denmark can into mutant sperm donations <https://commons.wikimedia.org/wiki/File:Denmark_can_into_mutant_sperm_donations.png>

30. Data Sources

31. Open access sources of genomic data
● “To find out what's genetically wrong
with me, click over to SNPedia where
I have posted the results of my
23andMe genotype screening tests
for all to see.”
<http://reason.com/blog/2017/04/06
/fda-loosens-its-shackles-on-23andm
e-pers>
● OpenSNP <https://opensnp.org/>
○ Me (yes, REALLY!):
<https://opensnp.org/users/14
17>

32. Open access sources of genomic data
● 69 Genomes Data:
<http://www.completegenomics.com/publ
ic-data/69-genomes/>
● ENSEMBL: Homo sapiens:
<http://www.ensembl.org/Homo_sapiens/I
nfo/Index>
● Genome Databases & Browsers:
<http://www.genenames.org/useful/geno
me-databases-and-browsers>
● Google Genomics
<https://cloud.google.com/genomics/>
● IGSR and the 1000 Genomes Project
<http://www.internationalgenome.org/>

33. Open access sources of genomic data
● Leiden Open (source) Variation Database.
<http://www.lovd.nl/3.0/home>
● NCI Genomic Data Commons
<https://gdc.cancer.gov/>
● Open Personal Genomics Consortium
<http://www.openpgx.org/>
● Personal Genome Project:
<http://www.personalgenomes.org/>
● More (open access data and open sources
bioinformatics tools)
https://www.one-tab.com/page/fbvZfZuyT
zq_XnKUWkOq8g

34. How to get
started with
your 23andMe
data

35. 23andMe: Start at the homepage

36. 23andMe: Check your health reports first

37. 23andMe: Then, if you want more, select
“TOOLS”

38. 23andMe: Under “TOOLS,” choose “Browse
Raw Data”

39. 23andMe: You found the Raw Data … Almost

40. 23andMe: After “Opt In”

41. 23andMe: You may also download the data

42. 23andMe: Options prior to download

43. Tools to analyze
your 23andMe
data
Image: Genetic Genie <http://geneticgenie.org/>

44. 23andMe > 23andYOU: 3rd Party Tools
<http://www.23andyo
u.com/3rdparty>

45. 23andMe: 3rd Party Tools
23and You: <http://www.23andyou.com/3rdparty>
ISOGG: Autosomal DNA Tools: <http://isogg.org/wiki/Autosomal_DNA_tools>
A few of my (FREE) favorites:
● GEDmatch: <http://gedmatch.com/>
● Genetic Genie: <http://geneticgenie.org/>
● Promethease: <http://snpedia.com/index.php/Promethease>
● David Pike's DNA Comparison Utilities:
<http://www.math.mun.ca/~dapike/FF23utils/>
● Interpretome: <http://esquilax.stanford.edu/>
Not free:
● Strategene <http://go.strategene.org/genetic-analysis/>

46. Talking with
your doctor(s)
about your
results
(i.e. ethics and stuff)
Images: <https://openclipart.org/detail/262573/doctor-holding-clipboard> |
<https://openclipart.org/detail/261044/doctor-holding-clipboard>

47. Doctors can react in different ways …
OMG, it’s a real genetic test!
Wow! Let’s change all your
meds!
OMG, it’s a
personal
genomic
test. Not
another
one! I
don’t have
time for
this.
OMG, it’s a real genetic
test! Wow! Let’s
change all your meds!
OMG, it’s a personal genomic
test. Not another one! I don’t
have time for this.
Image credits:
<https://openclipart.org/detail/242102/surprised> |
<https://openclipart.org/detail/213625/facepalm-as-
gesture>

48. Best is
something
like this —>
Not this —> OMG! (too much
action, too little data)
Or this —> OMG! (not enough
action, not enough conversation
about why it’s important)
Hmmmm. Well, this is interesting,
and while it really doesn’t tell us
anything definitive yet, it does
suggest some areas we might
want to explore. Let’s talk more.
Would you be willing to have some
more tests? Or see a genetic
counselor? I’m thinking of …
Image credits:
<https://openclipart.org/detail/242102/surprised> |
<https://openclipart.org/detail/245805/Doctors-and-
nurses-and-hospital-staff> |
<https://openclipart.org/detail/213625/facepalm-as-
gesture>

49. More
information &
resources
● DIYgenomics: <http://www.diygenomics.org/index.php>
● DNA.Land: <https://dna.land/>
● Genetics Home Reference (NIH):
<https://ghr.nlm.nih.gov/>
● GeneKnot: <https://geneknot.com/>
● Genomes Unzipped: <http://genomesunzipped.org/>
● Infinome: <https://www.infino.me/welcome>
● Patients Like Me: <https://www.patientslikeme.com/>
● Your Genome: <http://www.yourgenome.org/>

50. Teaching
examples
Search:
23andMe|personal-genomics|pers
onal-genetics
courses|class|syllabus|lesson-plan
Image: DNA alignment written in paper
<https://commons.wikimedia.org/wiki/File:DNA_alignment_written_in_p
per.jpg>

51. Teaching Examples
23andMe for Education <https://education.23andme.org/>

52. Teaching Examples
● Genetics Home Reference: Primer: <https://ghr.nlm.nih.gov/primer>

53. Teaching Examples
● BYU: PWS168 Personal Genomics (John Chaston)
● Carnegie Mellon: Human Genetics and Personal Genomics (Javier Lopez and
Linda Visomirski-Robic) (Press)
● Cornell: Personal Genomics and Medicine -- Why Should You Care About
What's in Your Genes? (Press)
● Drury U.: Advanced Molecular Genetics 322 (Roger J. Young)
● Duke U.: N562 Applied Genomics and Personalized Medicine in Clinical Care
● Duke U.: N563 Trends in Genetics and Genomics for Health Care and Society
(Jennifer R. Dungan, Allison Vorderstrasse, Sara H. Katsanis)
● Georgetown U.: GNMX201: Personalized Genomics: An Exploration into the
Heritable Elements of Disease (About, Press)
● John Hopkins: Computational Personal Genomics. BME 580.689 (Steven
Salzberg)
● MIT: Personal Genomics and Medicine: What's in Your Genome?
Image: Berlin Naturkundemuseum DNA <https://commons.wikimedia.org/wiki/File:Berlin_Naturkundemuseum_DNA.jpg>

54. Teaching Examples
● Penn State: Genes and Human Biology, Behavior, and Evolution, Anthropology
297A (David Puts, Mark Shriver)
● Stanford U.: Personal Genomics and Your Health (XGEN205)
● UCLA: MGMT 275 Current Topics In Emerging Technologies: Healthcare
Technology (Roy Doumani, Jennifer McCaney)
● U. Illinois-UC: The Molecular Me (Jeff Moore)
● U. Iowa: Who are you? Revelations from The Personal Genome G4G (Bryant
Alexander)
● U. Michigan: HBHE 669: Genetics, Health Behavior, & Health Education (Scott
Roberts)
● U. Minnesota: “LL X028 - Genomes: Understanding Your Body's Ancestry”
(David Matthes)
● U. New Hampshire: GEN 714 (M1) - Personal Genomics (Sarah Prescott)
● Vanderbilt: School of Medicine course lets students test own DNA (Ellen
Wright-Clayton, MD, JD, Dan Roden, MD)
Image: MTHFR
<https://commons.wikimedia.org/wiki/Fil
e:MTHFR.jpg>

55. Issues Teaching with Personal Genomics
COST (& Time):
“McAllister's seminar is open to students from
all areas of study, and submitting a test to
23andMe is optional. He uses his seminar
budget to pay for the $199 DNA kits, so
there's no added course fee. Over the course
of the semester, students also take part in class
discussions on the societal impact of
commercial genetics testing, write blog posts
on the course webpage, and learn how to
analyze their genetic data beyond the reports
provided by 23andMe.”
<http://www.iowalum.com/magazine/nov16/fi
ndingthemselves.cfm>

56. Issues Teaching with Personal Genomics
LEGAL:
● CON: “The University’s original plan was to allow students to elect to receive the
results of their tests as part of the program. Two weeks ago, however, the California
Department of Public Health (CDPH) ruled that if Berkeley wanted to return
personalized genetic data to some of its freshmen, the testing must be conducted at
the direction of a physician and performed by a licensed clinical laboratory.”
● PRO: “If personal genomics is ever to live up to its name, at some point we must allow
individuals – including the future leaders of our society, as embodied by Berkeley’s
incoming freshmen – to decide for themselves whether and how to participate. To do
otherwise, and to continue to aggressively criticize and thereby discourage personal
genomics innovation in our zeal to render it a riskless enterprise, would be a
mistake.”
○ <https://www.genomicslawreport.com/index.php/2010/09/08/getting-serious-
about-personal-genomics-risks/>
Image: Gender equality icon
<https://openclipart.org/detail/244113/ge
nder-equality-icon-2>

57. Issues Teaching with Personal Genomics
● “Stanford and Berkeley faced the same essential ethical dilemmas
in creating their programs: avoiding coercion, protecting students'
privacy and adequately preparing students to interpret the results
of their tests. But the two universities took markedly different
approaches to designing and executing their respective projects.”
<https://www.scientificamerican.com/article/exposing-the-student
-body/>
○ Outsourcing vs. testing on campus
○ Consulting with campus bioethics committee/IRB/etc.
■ What is asked for
■ What happens with information
■ How students are asked to respond to the info
○ Privacy concerns
○ Student reactions & nature of population
Image: COI
<https://commons.wikimedia.org/wiki/Fil
e:UserpageCOI.svg>

58. More Teaching Examples & Resources
● Higher ed
○ 23andMe: A Fresh Take on Genetics for Freshmen
<https://blog.23andme.com/education/a-fresh-take-on-genetics-for-freshman/>
● Any educational level
○ Genetics Lesson Plans
<http://www.teach-nology.com/teachers/lesson_plans/science/biology/genetics/>
○ PBS: The Ethical Considerations of Personal Genomics
<https://dptv.pbslearningmedia.org/resource/cygc12.sci.life.gen.lpethics/the-ethical-considerations-
of-personal-genomics/>
● General resources
○ 23andMe for Education <https://education.23andme.org/>
○ Genetics Home Reference <https://ghr.nlm.nih.gov/>
○ NIH: Genetics, Education, & Discovery <https://geneed.nlm.nih.gov/topic_subtopic.php?tid=35> |
Teacher Resources <https://geneed.nlm.nih.gov/specialty.php?spageID=2>
○ Personal Genetics Education Project <https://pged.org/> | Lesson Plans
<https://pged.org/lesson-plans/>
○ Smithsonian Institution: Genome Educator Guide:
<https://naturalhistory.si.edu/exhibits/genome/Genome-Educator-Guide.pdf>
○ Virtual Genome Project: Lesson Plans: <http://people.ibest.uidaho.edu/~etop/vgp/lessonPlans.html>
Image:
<https://commons.wikimedia.org/wi
ki/File:Brokechromo.jpg>

59. Next, the
microbiome?

60. Contact
Patricia F. Anderson, @pfanderson
<pfa@umich.edu>