Workshop:Vancouver2011:Compartmentalization

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You have viral sequences from different patients, and the samples come from either plasma or cerebrospinal fluid. You want to investigate whether the viral sequences show compartmentalization to try to correlate this characteristic with clinical data.

Contents

Data sets

FASTA files

File:C align.fas

File:D align.fas

File:K align.fas

File:Q align.fas

File:S align.fas


Outgroup FASTA files

File:C align out.fas

File:D align out.fas

File:K align out.fas

File:Q align out.fas

File:S align out.fas


Newick tree string files

File:C tree.nwk

File:D tree.nwk

File:K tree.nwk

File:Q tree.nwk

File:S tree.nwk

Distance based methods

Using the data sets for patients C, D, K, Q and S, determine their level of compart- mentalization using the FST and Snn tests.

  1. In order to achieve this go to the HyPhy Standard analysis menu and choose “Compartmentalization”, followed by “F ST”.
  2. For the purpose of these exercises, we are going to use a distance based matrix built using the TN93 nucleotide substitution model.
  3. Be sure to perform a bootstrap test to determine the certainty of the FST estimates, as well as a permutation test to asses the level of significance of the obtained scores.

Tree-based methods

Using the data sets for patients C, D, K, Q and S, determine their level of compartmentalization using the Slatkin-Maddison, Association Index and Correlation coefficients tests.

Slatkin-Maddison test

  1. In order to achieve this go to the HyPhy Standard analysis menu and choose “Compartmentalization”, followed by “SlatkinMaddison”
  2. For this method you will need to use the phylogeny rather than the alignment
  3. Follow the instructions and remember to carry out the significance test.

Association Index test

  1. In order to achieve this go to the HyPhy Standard analysis menu and choose “Compartmentalization”, followed by “SimmondsAI”
  2. For this method you will need to use an alignment that includes an outgroup. For this purposes you were given a series of alignments in a folder named “Outgroup”.
  3. Follow the instructions and remember to carry out the significance test. Use the default values given by the program.

Correlation coefficients test (r and rb)

  1. In order to achieve this go to the HyPhy Standard analysis menu and choose

“Compartmentalization”, followed by “TreeCorrelationCoefficients”

  1. For this method you will need to load a tree.
  2. Follow the instructions and remember to carry out the significance test.

Result interpretation

Using the table bellow discuss if you can use it, at least in some of the patients to interpret the results from the compartmentalization tests.

C D K Q S
Current CD4 (cells/mL) 312 55 221 68 32
Plasma RNA (log10 copies/mL) 5.7 5.9 5.7 5.1 6.0
CSF RNA (log10 copies/mL) 5.2 4 4.4 3.5 3.2
CSF WBC (cells/mL) 312 2 16 2 3
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