Linkage Studies
Progeny has been the leader in managing family studies since 1996. In 2005, we launched Progeny Lab to specifically manage genotypic data for linkage studies. This was a natural evolution of our software. Combining pedigrees, phenotypic data, and genotypic data allows you to access the power you need to reach meaningful conclusions. Automating the process of outputting to linkage analysis programs such as GeneHunter, Allegro, and others is a major time saver. There is no better fit in the world when it comes to managing linkage studies.
Work Flow
1. Loading Pedigrees into the Database
If you have existing pedigrees and 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. In addition, the file needs to have the relationship data (mother id, father id, etc…) in the first few columns so we can plot the pedigree correctly. Samples can be imported 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, for instance the Affymetrix 100K marker set for Affy 100K chip files. You can load marker sets by importing them directly from the manufacturer (such as Affymetrix, Illumina, etc.) via text file or from your own custom text file. The file should contain the positioning of the marker as well as additional info (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 platforms such Affymetrix, Illumina, ABI, Sequenom, or even your own custom text files. 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 FBAT, QTDT, Phase, 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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