Exploring the Genotype Networks of Human Variation

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Exploring the Genotype Networks of Human Variation

In a recently published paper (Dall’Olio et al, 2014), we described a new method to look at genome variation based on the concept of genotype networks.

Genotype networks are described extensively in the group “The origins of Evolutionary Innovations” by Andreas Wagner, and they provide a method to estimate the robustness of a phenotype to mutations, and its ability of its underlying genotypes to evolve towards different phenotypes.

The data from this study are also available as a UCSC tracks. Click on this link to load them in the UCSC browser, or use this suffix (db=hg19&hubUrl=http://bioevo.upf.edu/~gdallolio/genotype_space/hub.txt) to add them to any other genome browser url.

Reference: Dall’Olio GM, Bertranpetit J, Wagner A, Laayouni H. Human genome variation and the concept of genotype networks. PLoS One. 2014 Jun 9;9(6):e99424. doi: 10.1371/journal.pone.0099424. eCollection 2014. PubMed PMID: 24911413; PubMed Central PMCID: PMC4049842. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0099424

 

An easier way to download the raw scores

An easier way to download the raw scores

It is now possible to download all the raw scores used in our browser, from this web server: http://hsb.upf.edu/hsb_data/

The whole dataset weights about 13 GB in total.

The files contain 5 or 6 columns, depending on whether the test is calculated by SNP (e.g. iHS, FST, DAF, XP.EHH), or by region (e.g. CLR, Omega, Fay and Wu, XP-CLR).

Here is a description of the columns:

  • snp or region id
  • chromosome
  • start and end positions, or snp position
  • raw score of the test
  • ranked scores, as described in http://hsb.upf.edu/?page_id=594

Our paper is now available online!

Our NAR paper is now available online!

Our paper presenting the 1000 Genomes selection browser is now available online! You can access it from here: http://nar.oxfordjournals.org/content/42/D1/D903.long

The paper will appear in the next Nucleic Acid Research Database issue, in January 2014.

Here is the full citation:

1: Pybus M, Dall'olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P,
Laayouni H, Bertranpetit J, Engelken J. 1000 Genomes Selection Browser 1.0: a
genome browser dedicated to signatures of natural selection in modern humans.
Nucleic Acids Res. 2014 Jan 1;42(1):D903-9. doi: 10.1093/nar/gkt1188. Epub 2013
Nov 25. PubMed PMID: 24275494. Available at http://nar.oxfordjournals.org/content/42/D1/D903.short