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Exercise: Personal genomics: genotype to phenotype

Introduction

For this exercise, we will use genotype data for two individuals, Greg Mendel and Lilly Mendel, that are freely available through a demo account on 23andme.com, a personal genomics company. We will investigate what we can learn about their traits and medical conditions based on their genotype data using SNPedia and 23andMe.

A step by step example

Navigating a SNP page on SNPedia
SNP search on 23andme
  1. Point your browser to the 23andme.com
  2. Create an account and sign in
  3. Point your browser to SNPedia (http://www.snpedia.com) and search for earwax
  4. Find the corresponding RefSNP accession ID (rs number) for this SNP and follow the link to the SNP page
  5. Point your browser to the 23andme and search for the SNP's rs number or simply click on the SNP's link to 23andMe.
  6. What genotypes do the Mendels have (correcting for dbSNP strand if necessary)?
  7. What can we say about their earwax type?

Hint:

The genotype for a SNP can be reported on eather the plus strand or the minus strand. In 23andMe, it is always reported on the plus strand. Many SNPs in dbSNP are, however, reported on the minus strand and SNPedia uses the same convention and indicates this as "Orientation". If the value is "plus" you don't need to do anything, as the 23andMe agrees with dbSNP and SNPedia. If the value is "minus" you need to change the bases to their complementaries:
  • A → T
  • T → A
  • C → G
  • G → C
Thus, the genotypes of "minus strand" SNPs are changed accordingly (we typically report them alphabetically, e.g. "C;T" instead of "T;C"):
  • A;A → T;T
  • A;T → A;T
  • A;C → G;T
  • A;G → C;T
  • T;T → A;A
  • C;C → G;G
  • C;T → A;G
  • C;G → C;G
  • G;G → C;C
  • G;T → A;C

Search for traits on SNPedia

Preparing the physical traits

You will be looking up the following three traits (and two more of your own choosing):

  • Dyslexia
  • HDL cholesterol level
  • Melanoma (skin cancer)

Assemble in groups and discuss which physical traits (or diseases) you would think could be associated with single nucleotide polymorphisms. Settle on two additional traits and search for these traits on SNPedia and see if any SNP association data exists.

Check what Lilly or Greg Mendel has

Use the information from your chosen traits and search the 23andMe.com for these SNPs and note what (if any) variation they have.

For your traits found to be associated to a SNP, report following:

  1. The rs number and dbSNP orientation
  2. The phenotypic effect associated with the SNP
  3. Greg's or Lilly's genotype (on dbSNP strand)
  4. Their phenotype - if possible to determine

Hint: Use table such as this one: PDF format or XLS format.

Browse traits etc. on 23andme

While SNPedia has a lot of "bleeding edge" information, 23andme is convenient for browsing health and ancestry related topics without leaving their website.

For Greg or Lilly Mendel, see what you can find out about the following traits:

  • Eating behavior (Lilly only)
  • Warfarin sensitivity
  • Alzheimer's disease risk
  • Prostate cancer risk (Greg only)
  • Hemochromatosis
  • HIV resistance

Find one or two additional interesting traits for Greg or Lilly on the website.

For your traits found to be associated to a SNP, report following:

  1. The phenotypic effect associated with the SNP
  2. The rs number
  3. Greg's or Lilly's genotype

Can you say anything about their ancestry?

Possible traits of offspring

Punnet square for rs713598 genotypes (source: 23andMe)

Knowing the parents's genotypes for a given SNP, they can be put in a Punnett square and probabilities of an offspring's possible genotypes can be calculated. If we also know the probabilities with which certain traits are associated with those genotypes, we can combine these numbers to calculate a probality for an offspring having such traits. We will not make those calculations today, but it is explained here. Instead we will focus on a few traits mentioned in 23andMe's Inheritance calculator.

Find the probabilities (in percent) that a child of Lilly and Greg Mendel will have the following traits:

  • Alcohol Flush Reaction
  • Dry Earwax
  • Brown/black eyes
  • Lactose intolerant
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