Targeted Genotyping Studies
Progeny is perfectly suited to help you manage targeted region studies. Whether your doing linkage or pure association, load markers specific to certain regions of the genome and combine these genotypes with phenotypes for analysis. Custom imports and exports allow you to import and export files by specifying how they are configured. Full security measures provide the comfort of knowing your data is secure and inaccessible based on userid's. Scheduled backups of the database ensure you can always recover from any disaster.
Work Flow
1. 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. Pedigrees require relationship data in the first few columns, such as mother id and father id, in order to plot the pedigree correctly. You also can import 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 import samples 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 as many marker sets containing specific regions of the genome as you want. Import marker sets from text files provided by the manufacturer (Affymetrix, Illumina, ABI, etc.) or your own files. These files can contain as many SNPs as you want, but need to include certain information such as the positioning of the marker, etc... 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. For each custom marker set you created covering the specific region of interest, you can import genotypes against that set. 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. Prepare output for analysis several times if you like, altering data each time to produce the results you’re looking for. 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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