Transcript Document 7821702

SNPing Lactose
By: Mandy Butler, Ying-Tsu Loh and
Cheryl Ann Peterson
A mother and father and their two young children
walk into an ice-cream bar. The two youngsters
order delicious 100% whole milk milkshakes,
while their parents look on enviously and order
non-dairy fruit smoothies. Why do you think the
parents didn’t order milkshakes?
LACTOSE (pre-assess student
understanding)
• Lactose, the primary sugar in milk, is hydrolyzed by an
enzyme called lactase into the more absorbable
monosaccharides, glucose and galactose.
• Virtually all humans are born with ability to digest lactose
but many lose this ability as they age.
• In lactose tolerant individuals, the lactase gene is
expressed into adulthood, so eating a milkshake is a
pleasant experience. But in people who are lactose
intolerant, that lactase gene is switched off, and the
consumption of milk products can lead to unpleasant
effects.
Lactase
Survey class on lactose
tolerance/intolerance
• Show map of lactose tolerance
geographically
• Ask for ideas about why certain
populations are lactose tolerant and others
are not
• Is there consistency between the map and
their condition/experiences?
• Introduce concept of phenotype
LacIntol-World.png
Pre-assess students on SNPs
• What might account for this difference in
phenotype on a genetic level?
• Idea of genetic polymorphisms?
– What kinds of polymorphisms are there?
– What is a SNP?
What evidence is there that lactose
tolerance is due to a genetic polymorphism?
Which genotype(s) are correlated with lactose
tolerance?
Enattah et al (2002) Nature Genetics (2002) 30:233-237
What is the percentage of the different
genotypes in the Finnish population?
Enattah et al (2002) Nature Genetics (2002) 30:233-237
Conclusions:
– What is the predominant phenotype in the
Finnish population?
– What does this tell you about evolutionary
selection process at this locus?
– (Why would this trait have been selected for in
the Finnish population?)
How could a SNP change the
phenotype of an individual?
– Develop some hypotheses
• The SNP induces a change amino acid sequence?
• The SNP causes a change in expression of the
gene?
• Anything else
Possible avenues of exploration:
• Look into how change effects gene
regulation
• Data on reporter constructs?
• What is an enhancer?
Demographic data
• What is the frequency of the SNP variant associated with
lactose tolerance in the Finnish in other ethnic groups?
– Use HapMap data as example
• What is your prediction about lactose tolerance in these
other groups?
• What other information can students find on lactose
tolerance demographics (use own families?)
Populations being studied in Hapmap project:
• 30 trios (two parents and an adult child) from Yoruba,
Nigeria
• 30 trios from Utah with European ancestry
• 45 unrelated Japanese from Tokyo
• 45 unrelated Chinese from Beijing
http://snp.cshl.org/whatishapmap.html.en
Allele Frequencies from NCBI
and HapMap
ALlele FREquency Database
Examine Tiskoff data set from
African populations
– Does the same SNP determine lactose
tolerance in these populations?
– If not, what does this suggest about the
evolution of the phenotype in these
populations (idea of convergent evolution)
– When did these variants arise?
Example of Tiskoff data
Subject
Phenotype
SNP 13910 genotype
KEAA001
tolerant
CC
KEAA002
tolerant
CC
KEAA003
tolerant
CC
KEAA005
intolerant
CC
KEAA006
intolerant
CC
KEAA007
intolerant
CC
LAB
• Use PCR and RFLP to determine genotype of students
at this C/T 13910 SNP
– Students will isolate cheek cell DNA and use PCR to
generate product containing SNP
– Incubate PCR product with restriction enzyme Hinf1
– Run agarose gel to size fragments after digestion with
Hinf1
– If T allele, PCR product will cut with Hinf and generate
two fragments; product with C allele will not cut
Create database of student results
– Correlate ethnic background both genotype
and phenotype
– Data may be messy, but will accumulate over
time
• Extend discussion to importance of SNPs
and individual predisposition to disease
– See next slide for example
deCODE Genetics
• deCODE is a genetics company that has gathered genotypic and
medical data from more than 100,000 volunteer participants in
Iceland - over half of the adult population. They are using this
information to find correlations between SNPs and diseases.
• For example, scientists at deCODE Genetics and academic
colleagues from the U.S. identified a SNP on chromosome 9 that
confers increased risk of heart attacks. Of the 17,000 patients and
control subjects in the study, more than 20% of participants carried
two copies of the variant, which corresponded to an increased risk of
more than 60%.
• deCODE plans to use this type of information in the development of
a DNA-based tests to identify individuals who are at elevated risk fro
various diseases, thereby facilitating the implementation of
preventive measures.