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203.343!Advanced Genetics
and Genomics!
Austen Ganley, Course coordinator
[email protected] ext.43619/room 14.05
!
Course outline!
Class rep!
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203.343!Outline of the Course!
Austen Ganley, July 13th, 2015
You are going to
be thought
leaders in the
place of personal
genetic DATA in NZ
society
Changes to the Paper Outline
Changes to the Paper Outline
Course Outline • Week 1 - Introduction to
Personal Genomics. !• Week 2 - Gene Linkage
and Linkage Disequilibrium.!
• Week 3 - GWAS Methods.!
• Week 4 - GWAS Results. !• Week 5 - Concepts of
GWAS – Missing Heritability. !
• Week 6 - Concepts of GWAS – Nutrigenomics, Nutrigenetics, and the Microbiome.!
• Week 7 - Personal Genomics in Cancer Treatment. !
• Week 8 - The Ethics of Personal Genomics I. !
• Week 9 - The Ethics of Personal Genomics II. !
• Week 10 - Determining Ancestry from Genetic Data. !
• Week 11 - Personal Genomics in Society.!
• Week 12 - Producing a Consensus Opinion Editorial on Personal Genetics in Society.!
Course Structure - Lectures
Course Structure - Labs
Good Meeting Behaviour • Principles:!
• Everyone is a member and deserves respect!• Everyone has something to contribute!• Questions are the best learning tool!
• Goal: Equal participation and understanding!• How to achieve: Be aware of your contributions!
• Are you contributing more than others? If so, take a back seat for a bit!
• Are you contributing less than others? If so, make an active decision to contribute!
• If you don’t understand, ASK!!
Course Structure - Assessment
203.343!Introduction to Personal
Genomics!Week 1!
Austen Ganley, July 13th, 2015
The DNA Sequencing Revolution – Cost per Human Genome
Personal Genomics and Personal Genetic Data
• “Personal genomics is the branch of genomics concerned with the sequencing and analysis of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips…, or partial or full genome sequencing.” [Wiki]!
• “Personal genetic data is genotype data for one or more loci from an individual” [Austen]!
Personalized Medicine and Genome Services
• “Personalized medicine is a medical model that proposes the customization of healthcare - with medical decisions, practices, and/or products being tailored to the individual patient.” [Wiki] A major part of this is the use of genotyping data!
• “Direct-to-consumer (DTC) genetic testing is a type of genetic test that is accessible directly to the consumer without having to go through a health care professional. ” [Wiki]!
DTC example: 23andme • Private company based in California!• For US$99 (excluding postage) they do a SNP-
Chip analysis of your genome. This gives you:!• until 2013, health and trait-based interpretations
of your data!• ancestry interpretations of your data!• access to your raw data!
• They run a research program for those who agree, and have published a number of papers!
• Their genome service was named Invention of the Year by Time magazine in 2008!
Why is this a Big Deal? • If we know our DNA sequence, we can
potentially:!• Know our risk of diseases and how to avoid or
take action against them!• Know how we’ll respond to nutrition, drugs,
exercise, etc!• Identify new mutations that have caused a new
disease (e.g. cancer)!• This is potentially cheaper and better than the
current system of generalised post-disease treatment!
BF McAllister, University of Iowa https://wiki.uiowa.edu/pages/viewpage.action?pageId=126977171
But… • This is new – society has never had to deal with
the issues that this raises before!• The issues include personal, family, expectation,
moral, economic, discrimination, and equity issues!
• Thus, how society should navigate the potential advantages and disadvantages to provide the greatest benefit has never been dealt with before!
• Your job is to lead the debate on this!• To do this, you will need a comprehensive
understanding of the science behind personal genomics, and of our current understanding of the negative issues!
Opinion Editorial • The way this will be achieved is by producing an
Opinion Editorial on personal genetic data!• An OpEd is published in a newspaper or
magazine: written by an outside “expert”!• Aim is to promote debate on an issue – to lead
discussion!• The topic of your OpEd is how personal genetic
data should be approached in NZ society!• This is a major component of the course, and
much of the lecture/lab component of this course will be directly relevant for your OpEd. It is important that its an informed OpEd.!
Opinion Editorial - Background • There are potential benefits of these data, and
potential disadvantages, but in NZ there is little control over how these data are used!
• Other countries have introduced legislation around the use of these data, for example in insurance and employment!
• To know what approach we should take to these data, we should have realistic ideas about the benefits and disadvantages!
• We want to be thought leaders in NZ by ensuring we make clear where and how science can help us to understand these issues better!
Opinion Editorial - Structure • The key is to take an angle to stimulate debate,
and the core of this is to provoke discussion of the advantages versus the disadvantages of accessibility to personal genetic data!
• There are the consequences of the advantages and disadvantages to consider!
• However, there are also the chances of the advantages and disadvantages eventuating to consider!
• Science and research often helps us to understand these factors better, allowing us to offer a more informed perspective!
Opinion Editorial - Approach • The key is that your OpEd must be appealing,
and appealing to an “average” person!• It is not designed to convey information, but
instead to promote thought, discussion, debate, controversy!
• So, do NOT write it as a scientific document – it’s a totally different beast!
• It should be interesting, understandable, and appealing to anyone – so think if everyone you know would be interested (and give it to them to see for sure)!
• There are resources available on Stream!
Opinion Editorial – Assignment 1 • The first assignment is to write an OpEd on your
views of how personal genetic data should be approached in NZ society as a practice!
• You probably don’t have very strong or informed views – that is fine – the job is to write a good OpEd, even if the opinion you provide is completely unjustified!
• If you have views currently, then write one on these. If not, it might be easier to write it from an extreme perspective, even if what you say is not justified – you won’t be marked on how reasonable your arguments are, only on whether your OpEd achieves its goal of being appealing and promoting debate!
Opinion Editorial – Assignment 1 • This assignment is due on Friday, July 31st. I will set
up a Stream assignment submission box for you to submit to. Read the “Opinion Editorial Assignments” document for more information!
• Your OpEd MUST be between 600 and 750 words and it should have a title (12 words or less) that does not contribute to the word count!
• Read the resources and read some OpEds to get an idea of what you are supposed to be doing !
• Swapping ideas and providing comment on others’ OpEds is fine: plagiarism of any sort is not!!
• Same rules will apply to your final OpEd!
