Genomics: A new

Revolution in Science:

An Introduction to promises and
Ethical Considerations by
Genome Alberta
Overview
Genetics/Genomics described
Genomics and Biotechnology
Genome Alberta
Genome Alberta Projects

In the 1850s an Austrian monk Gregory
Mendel started crossing pea varieties
He used pollen from some plants to carefully
fertilize other plants
He was able to observe that characteristics are
inherited in a predictable manner.
He determined that alleles of a single trait segregate
(separate) independently.
He observed that the alleles for different traits assort
independently.
This gave rise to a new discipline that we now call
GENETICS
Anti-parallel strands
Anti-parallel strands
Single Nucleotide Polymorphisms
(SNPs)
Major discovery of human genome project was
single nucleotide polymorphisms (SNPs): points
in genome where 2 or more alternative alleles are
found in >1% of population
93% genes have SNPs
~40% will alter an amino acid
SNPs may have important consequences for
health/disease

SNPs
Collectively, small differences can make a
big difference.
It determines whether you are short or tall,
hair and skin color and
Differences sufficient to make you are
healthy or not

Women who carry a genetic variation
known as BRCA-1 are seven times more
likely to get breast cancer
Persons missing three nucleotides (CTT) at
a very specific spot in have Cystic Fibrosis

Genetics - Genomics
Genetic information is contained with DNA
(deoxyribonucleic acid) and RNA (ribonucleic
acids)
Each plant, animal or bacteria carries its entire
genetic code inside almost every one of its cells
Genomics is the discipline that aims to decipher
and understand the entire genetic information
content of an organism
Genomics marked the beginning of a new age in
biology and medicine

Genetics - Genomics
Metabolomics
Proteomics
Transcriptomics


Genomics marked the beginning of
a new age in biology and medicine






1900
1953
1977
1980
1983
1990
1994-98
1998
2000
2005
Watson and Crick
identify DNA
(the double helix) as
the Chemical basis
of heredity
DNA markers used
to map human
disease genes to
chromosomal
regions
Human Genome
Projects (HPG)
begins-an
international
effort to map and
sequence all the
genes in the
human genome
DNA markers used
to map human
disease genes to
chromosomal
regions
Release
of
Human
Genome
Project
Sanger and Gilbert derive
methods of sequencing
DNA
Huntington
disease gene
mapped to
chromosome 4
Genetic and
physical
mapping
Working Draft of the
human genome
sequencing complete
Rediscovery of
Mendel's laws helps
establish the science
of genetics
Source: Health Policy Research Bulletin, volume 1 issue2, September 2001
A single base change in a gene or the addition of a single gene
from another source can make a crop herbicide resistant
Understanding traits, in particular diseases, some inherited
diseases results from the change of 1 base in a sequence
A gene can be used to make a specific product, for example
insulin
Scientists study the genome
for a variety of reasons.

Simple model of Gene Modification
DNA cut with endonuclease
Sticky ends created
Simple model of Gene Modification
Modified section with similar sticky ends
inserted
DNA ligase reattaches new components

Some Interesting Genome Facts
Human Genome contains about 3 billion
basepairs
Corn Genome contains about 2.6 billion
basepairs
Wheat Genome contains more than 16
billion basepairs
Not all genetic information encodes for
functional molecules or life functions
Some More Interesting Genomics
Facts
Humans only have 20% more genes than worms
Around 99% of our genes have counterparts in mice
Our genetic overlap with chimpanzees is about 97.5%
The genetic difference between one person and
another is less than 0.1 %
But because only a few regions of DNA actively
encode life functions, the real difference between one
person and another is only 0.0003 percent
Sequencing Cost Have been
Dramatically Reduced
A.$10,000
B. $100
C. 1$
D.1 $cts
E. 0.1 $cts
F. 0.001 $cts
G.0.00001 $cts




Some More Interesting Facts
Human Genome:
Took 12 years to complete at a cost of
US$3 Billion
Mouse Genome
Took 3 years to complete at a cost of US
$300 million
Bovine Genome
Took about 1 year at an estimated cost of
US $30 million

Availability of Personal Genetic
Information Poses Challenges
Privacy
Confidentiality
Discrimination
Psychological Impact



Something to Think About:
Who should have access to stored genetic
information? Who owns and controls it?
How can families resolve conflict when some
members want to be tested for a genetic disorder
and others do not?
Should employers be able to require job
applicants to take genetic tests as a condition for
employment?
How would you feel if you tested positive for a
genetic disorder. How would you feel if you tested
negative?

Privacy and Confidentiality of
Genetic Test Results
Clinical test results are normally included in
a persons medical records, this could have
serious complications
For example, when applying for medical, life,
or disability insurance, people may be asked to
reveal their medical history.

Calgary Herald. Monday, Feb 12, 2007

Genome Alberta
Independent not-for-profit corporation
One of the six regional Genome Centers supported by
Genome Canada
Genome Canada receives its funds from Industry Canada
Supports research in plant, animal and human genomics,
bioinformatics, instrumentation development and bioethics
additional information is available at www.genomalberta.ca
Genome Albertas
Areas of Interest
Nutrigenomics

Study of the Link between
our Diet and our Genes
The burden of obesity
Cardiovascular disease
$20 billion
Diabetes
$13 billion
Self esteem
? billion
Slide Courtesy
David Wishart
U of A
Food and Phenotype
Same Junk Food Diet - Different Outcomes -- Why?
Slide Courtesy
David Wishart
U of A
Genomics may have the answer
C
G
C
T
C
C
C/G polymorphism
In PPAR gamma
C/T polymorphism
In PPAR gamma
No polymorphism
In PPAR gamma
Slide Courtesy
David Wishart
U of A
Metabolomics could have the
answer as well
Fat challenge
S
e
r
u
m

o
x
y
-
l
i
p
i
d
s

Time
Slide Courtesy
David Wishart
U of A
Food & phenotype
Genomics and metabolomics allows at-risk
individuals to be identified before
symptoms appear
Allows lifestyle changes to be made early
on (prevention)
Allows customization of diet and nutrition
to match genotype or metabotype
(personalized nutrition)
Food and phenotype - 2
Different Diet - Different Outcomes -- Why?
Slide Courtesy
David Wishart
U of A
Genomics may have the answer !
Gut microflora & metagenomics
Slide Courtesy
David Wishart
U of A
Metabolomics may have an answer
too
Diet + metabolism
monitored via urine
Slide Courtesy
David Wishart
U of A
Food & phenotype - 2
Genomics and Metabolomics allow detailed
characterization of gut microflora and their
nutritional or phenotypic consequences
Allows customization of diet and nutrition
to change gut microflora to a better type
(personalized nutrition)
Environmental
Genomics
Metagenomics or
Environmental Genomics
Creating Novel Opportunities for Enhanced
Recovery and Reduced Environmental Impact in
the Alberta Oil Sands through Metagenomics
Oilsands Environmental Genomics
Concept
Oilsands Environmental Genomics
Concept
Describes a new approach to reduce the environmental and
improve production and footprint of present and future oil
sands operations by harnessing the activity of indigenous
microbial communities active in oil sands deposits and
tailings ponds
Sets out a program area based on creation of a microbial
genomics resource for the oil sands as a springboard for
innovation
Reduction of Green House Gas
Emissions and I mproved Water
Recycling
Tailings ponds dont settle and release
methane, a potent greenhouse gas
Manipulation of the indigenous microbial
community could prevent methane release and
accelerate settling
Reduced Energy and Water Use,
Higher Recovery, More Producible
Reserves
Pre-treatment of target deposits by fostering
biosurfactant production, CO
2
, reactive
intermediates in the indigenous microbial
community could soften deposits prior to
steam injection

Methane Where we Need it!

Final energy harvest from residual
hydrocarbon left in situ after SAGD or other
production technologies have been exhausted
Based on in situ biomethanation
Process active in heavy oil and oil sands formation
Luca Technologies, Colorado, USA has estimated 37
TCF of methane could be produced from Athabasca Oil
Sands*
Opportunities Create Challenges
Creation of a Synthetic Organisms
Could solve Energy challenges and address
Global warming
What are the risks?
Mountain Pine Beetle
The Mountain Pine Beetle Epidemic:
A Disease System of Three Genomes
Host
Pine Trees
Bark Beetle
Fungal Pathogens
Slide Courtesy
Joerg Bohlmann
U BC
Mountain Pine Beetle
Project Deliverables
1. The first complete genome sequence for a tree-
killing, bark beetle-associated fungal pathogen.
2. Expressed genome sequences for the MPB and
the pine host.
3. Identification of genes that are linked to bark
beetle fitness, fungal pathogenicity, and tree
resistance.
4. Application of information from (1) - (3) to
improve forest pest management practices by
making predictive forest management models
more accurate, and developing diagnostics for
forest pests and diseases.