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.