ExGenotype2PhenotypeLite

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Exercise: Genotype to Phenotype

Introduction

In this exercise you will reconstruct the past by analysing the DNA of the first ancient human genome sequence — a paleo-eskimo, dug out from permafrost in northern Greenland. You will analyse the genome to find single nucleotide polymorphisms (SNPs) — differences in single DNA base pairs that exist between individual genomes, and that may act as markers of an individual's physical traits. (more introductionary info about SNPs and the SNP database dbSNP)

Rasmussen et al. [1] have sequenced the genome of a man from the Saqqaq culture, using DNA from hair preserved in permafrost in Greenland. They analysed the genome to find single nucleotide polymorphisms (SNPs) — differences in single DNA base pairs that exist between individual genomes, and that may act as markers of an individual's physical traits. a, Here, a short stretch of human DNA is shown that is a marker for normal earwax. b, In the analogous DNA from the Saqqaq individual, there is a SNP in which a C in the lower strand has been replaced by a T (C, G, T and A denote the four kinds of DNA base). This SNP shows that the Saqqaq man had dry earwax. Rasmussen and colleagues identified other SNPs indicating that the ancient human had, among other things, brown eyes, non-white skin, thick dark hair and an increased susceptibility to baldness. (From Nature News & Views)



You will start by searching for different physical traits (or diseases) which are associated to SNPs. Each SNP has a unique RefSNP accession ID (rs number) which you can use to search the SNP in the Saqqaq Genome Database (http://www.cbs.dtu.dk/cgi-bin/saqqaq.cgi).


Hint:

The genotype for a SNP can be reported on eather the plus strand or the minus strand. For Mr. Inuk, 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 Saqqaq Genome Database 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 genotype of "minus strand" SNP 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


A step by step example - the exciting story about wet vs dry earwax

Navigating a SNP page on SNPedia
Earwax SNP on the Saqqaq Genome Database


From the NCBI Coffee Break Bookshelf:

Don't put anything smaller than your elbow in your ear: the genetics of ear wax
Recently, an exciting genetic discovery was made in the field of ear wax. It appears that a change in a single nucleotide of your DNA can determine whether your ear wax is wet or dry. This marks the first time that a single-nucleotide polymorphism (SNP) has been found to determine a visible genetic trait.
  1. Point your browser to SNPedia (http://www.snpedia.com) and search for earwax and follow the link.
  2. Read the full earwax story (NCBI coffeebreak introduction, also here) and note what changes determine the type of human earwax.
  3. Find the corresponding RefSNP accession ID (rs number) for this SNP and note the location of this SNP.
  4. Point your browser to the Ancient Genome Database (http://www.cbs.dtu.dk/cgi-bin/saqqaq.cgi) and search either for the location (chromosome and position) or the rs number.
  5. What genotype does the Saqqaq genome (Mr. Inuk) have? What is the reference genotype? How does that fit in the genetics of earwax story?

SNP genotype to phenotype

Preparing the physical traits

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

Check what Inuk had

Use the information from your chosen traits and search the Ancient Genome Database for these SNPs and note what (if any) variation Inuk had. If you fail to find physical traits with enough data on Mr Inuk, then try hair colour, eye colour, tooth-shape.

Compare amongst populations

Search for the same rs number in dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP) and note the distribution of this SNP amongst following populations (scroll down to the population diversity part):

  • HapMap-CEU European
  • HapMap-HCB Chinese
  • HapMap-JPT Japanese
  • HapMap-YRI African

In which population fits the Saqqaq genotype?

Reporting

For at least three different traits found to be associated to to a SNP, report following:

  1. The rs number and dbSNP orientation
  2. The phenotypic effect associated with the SNP
  3. Inuk's genotype - and how you interpreted the reads at this location
  4. Inuk's phenotype - if possible to determine
  5. The distribution of Inuk's genotype amongst the HapMap populations

Hint: Use table such as this one (use first sheet/page): PDF format or XLS format.

Combinations of genotypes

More complex traits

Not all, in fact only a few phenotypes are easily defined by a single SNP (like the earwax type). By far the most are constituted of multiple SNPs, which in SNPedia is called a genoset - defined as the combination of alleles at 2 or more distinct SNP locations.

For this exercise, it is easier browse through SNPedia's genosets (http://www.snpedia.com/index.php/Genoset) and settle for one or two phenotypes/disease/conditions and find out what our friend Inuk had... (Whereas you in the above exercise started out by searching for phenotypes).

Hint: Click at the Criteria link on the genoset page.

Reporting

For at least two genosets with an interesting phenotype, report following:

  1. The rs number and dbSNP orientation
  2. The phenotypic effect associated with the genoset
  3. Inuk's genotypes - and how you interpreted the reads at this location
  4. Inuk's phenotype - does he fulfill all the genoset criteria? (otherwise we cannot tell based on this genoset)
  5. The distribution of Inuk's genotype amongst the HapMap populations

Hint: Use table such as this one (use second sheet/page): PDF format or XLS format.

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