Whole Genome Association
Managing Whole Genome Association studies requires the ability to import extremely large data sets from varied platforms and to combine that data with phenotypes. With Progeny Lab, you have all of this and more. Our software tracks individuals with unlimited phenotypic data, samples for these individuals, SNPs and STRs from multiple platforms, and the ability to output your data to several analysis packages including your own custom exports. See for yourself below.
Work Flow1. Loading Individuals into the Database
If you have existing data on individuals in an Excel Spreadsheet or in a database, you need to output that data to a text (tab delimited) file. The file needs to be one row per individual with as many columns of data as you want. Number of individuals is not limited, nor is the number of columns. Trios require mother id and father id in order to plot the pedigree correctly. You also have the option of importing sample ID’s at this time as well.
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2. Importing Samples
For each individual in the database, you need to have a corresponding sample id in order to import genotypes. Genotype files are based on sample ID and therefore, require the sample ID to be associated with an individual in the database. Samples can be imported while you import individuals in step 1. You simply need to specify how you want the samples imported. If the individuals are already in Progeny, you can simply just import the samples only as shown in the video below.
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3. Loading Marker Sets
All genotype data stored in Progeny Lab needs to correlate with a marker set. You can load marker sets by importing them from text files, usually provided by the manufacturer (Affymetrix, Illumina, ABI, etc.). You can also import your own files and can contain as many SNPs as you want, but needs to contain certain info such as the positioning of the marker. You can import additional information for each SNP such as the original allele A value, allele B value, call rate, etc.. As you import genotypes, checks are performed against the corresponding marker set stored in Progeny. SNP statistics (Hardy Weinberg p-values, allele counts, call rates, etc…) are also constantly updated and calculated within Progeny Lab.
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4. Importing Genotypes
You can import genotype files directly from Affymetrix, Illumina, ABI, Sequenom, or your own custom text files as well. Large arrays such as the 500K or 550K are not a problem at all. We provide the entire HapMap data set if you want, consisting of over 4.2 million SNPs. Thousands of samples with billions of genotypes is not a problem with Progeny Lab.
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5. Output to Analysis
Once all of the data has been entered into Progeny Lab, you can begin to prepare your data for output to several different analysis packages instantaneously. Supported packages include, but are not limited to, Haploview, Phase, FBAT, QTDT, PLINK, Allegro, Genehunter, MLINK, etc…We even provide the ability to create your own custom output in case you have a special program we don’t know about.
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