MutaGeneSys Project Page

There are several ways to use MutaGeneSys:

• Access it through a web interface (scheduled for release on October 18th, 2007).
• Install the complete system on your own machine (installation information).
• A sub-set of our findings has been incorporated into HapMap GBrowse and James Watson's Personal Genome Sequence browser. Example of a region with multiple OMIM associations: Chr1:194923128..194933127 (check the OMIM_Associations track). James Watson's browser is accessible here.
• You may also download a complete set of our findings in comma-separated format (scheduled for release on October 18th, 2007).

MutaGeneSys is available for use free of charge. If you use our system for scientific research that results in a publication, please cite our most recent publication (see here).

FAQ for the On-Line Version of MutaGeneSys

Q How do I enter query SNPs?
A (short) rs140504:AA, rs140504:AC, rs140504:A are all valid; rs140504:A? is invalid
A (long) SNPs are specified using reference cluster IDs (rs#). See dbSNP for a complete set of reference cluster IDs. An rs# is followed by ":" and then by one or two typed alleles. rs140504:AA, rs140504:AC, rs140504:A are all valid entries. If only one allele was typed, enter rs140504:A, NOT rs140504:A?.
A space-separated list of SNPs may be entered directly into the text field. If you wish to enter more than 1024 characters, please use the file upload feature instead.

Q How do I use the file upload feature?
A Click the "Browse..." button, locate the SNP file, and click "Open". Entries in the file must be space-separater. You may break the file into multiple lines, or enter all SNPs on a single line. A sample snp file is available here.

Q How does MutaGeneSys use population selection?
A If you wish to restrict diagnostic hypotheses to a specific population, please select your group from the population pull-down. We use standard HapMap definitions of populations. EU stands for Utah residents with ancestry from northern and western Europe. JPT+CHB stands for Japanese in Tokyo, Japan and Han Chinese in Beijing, China. YRI stands for Yoruba in Ibadan, Nigeria.

Q What is the coefficient of determination?
A MutaGeneSys uses a whole-genome marker correlation dataset to identify whether any of the query SNPs are linked with causal SNPs reported by OMIM (i.e. whether there are any proxies to causal SNPs in the query set). Correlations between proxies and causal SNPs are associated with a coefficient of determination (squared Pearson's correlation coefficient), a number between 0 and 1 that quantifies the correlation. The closer this coefficient is to 1 -- the more significant the correlation.

Q How does MutaGeneSys use the genotyping technology pull-down?
A MutaGeneSys uses marker association data based on genome-wide SNP arrays. We work with SNP array data from two companies: Affymetrix GeneChip and Illumina HumanHap. If one specific technology, say Affymetrix GeneChip, is selected from the technology pull-down, MutaGeneSys will only use Affymetrix data to estimate disease susceptibility.

Q How do I interpret the output?
A MutaGeneSys processes a query and displays results on the Query Results page. Output is presented in the following columns:

• typed SNP:allele -- these two columns list the SNPs in the input for which a disease association was found. The second column is set to "n/a:n/a" for single-marker associations.
• causal SNP:allele lists the identifier and allele of the causal SNP. Important: We assume that OMIM SNPs are causal. We further assume that the minor allele is associated with the disorder. Which allele is considered minor depends on the population.
• coefficient is Pearson's coefficient of determination that describes the strength of association between the typed SNP(s) and the causal SNP. It is a number between 0 and 1. The higher the value -- the more likely the association.
• zygosity refers to the zygosity of typed SNPs in the input.
• population list the population for which disease susceptibility is estimated. We use standard HapMap populations. CEU stands for Utah residents with ancestry from northern and western Europe. JPT+CHB stands for Japanese in Tokyo, Japan + Han Chinese in Beijing, China. YRI stands for Yoruba in Ibadan, Nigeria.
• OMIM record lists the name of the associated OMIM record. Clicking on the title of the record will load the corresponding OMIM page in a separate browser window.
• HapMap GBrowse is a link to the relevant portion of the genome in the HapMap genome browser. You may need to select the OMIM Disease Associations track in GBrowse to see our annotations. Once on the GBrowse page, check all three OMIM Disease Associations boxes in the track selection area of the page, then click the "Update Image" button.

Q How much data is there in MutaGeneSys?
A MutaGeneSys currently contains 906 single-marker associations and 393 two-marker associations. These are specific to population, and genotyping technology and resolution. Single-marker associations also include the trivial associations of an OMIM SNP with itself. The complete MutaGeneSys dataset can be downloaded from this site.

Q Where can I find more information about MutaGeneSys?
A Please refer to out Publications section. If your questions were not answered after you read the technical report, contact us.

Installing MutaGeneSys

• MutaGeneSys_10202007.tar.gz -- all files needed to install MutaGeneSys
• Load.txt -- installation instructions

Download the MutaGeneSys Dataset

Single_Marker_B36.csv
Two_Marker_B36.csv

Publications

• "MutaGeneSys: Estimating Individual Disease Susceptibility Based on Genome-Wide SNP Array Data", Julia Stoyanovich and Itsik Pe'er. Bioinformatics 2007; doi: 10.1093/bioinformatics/btm587. pdf
• MutaGeneSys poster (MAGNet retreat, April 6th, 2007)

Credits and Fine Print

This material is based in part upon work supported by the National Science Foundation under Grant s IIS-0121239. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.