Post on 23-Jan-2016
description
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, 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.
LACTOSE (pre-assess student understanding)
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
• 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?
Pre-assess students on SNPs
What evidence is there that lactose tolerance is due to a genetic polymorphism?
Enattah et al (2002) Nature Genetics (2002) 30:233-237
Which genotype(s) are correlated with lactose tolerance?
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?
• 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?)
Demographic data
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
– 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?
Examine Tiskoff data set from African populations
Example of Tiskoff data
Subject Phenotype SNP 13910 genotype
KEAA001 tolerant C C
KEAA002 tolerant C C
KEAA003 tolerant C C
KEAA005 intolerant C C
KEAA006 intolerant C C
KEAA007 intolerant C C
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.