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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.
• How is lactose intolerance measured?
• What are the symptoms of lactose
intolerance?
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 polymorphism effects gene
regulation
• Use 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
http://alfred.med.yale.edu/alfred/mvograph.asp?siteuid=SI00
1784U
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
KEAA00
1
tolerant
CC
KEAA00
2
tolerant
CC
KEAA00
3
tolerant
CC
KEAA00
5
intolerant
CC
KEAA00
6
intolerant
CC
KEAA00
7
intolerant
CC
Floyd Reed and Sarah Tishkoff University of Maryland January 2007
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.