By: Mandy Butler, Ying-Tsu Loh and Cheryl Ann Peterson 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?

Which genotype(s) are correlated with lactose tolerance? 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 C C KEAA002 KEAA003 KEAA005 intolerant KEAA006 KEAA007

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.