Lab Features

Complete Genotype Data Management

Designed for large genome-wide studies, Progeny Lab integrates time-saving features to manage genotypes quickly and easily.  We have optimized the database to handle maps as large as the HapMap set (over 4 million SNPs) including any set from Affymetrix or Illumina. 

 

Genotype Data Management

• Marker Management
  Import markers from a genome-wide set, region/chromosome panel, or increase the density of markers in a specific genomic region by inserting fine-mapping markers.
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• Sample Tracking
  Monitor and track samples that come into the lab.  The samples are tied to an individual in the database and can be tracked in any lab process that the user describes.
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• Plate Management
  Designate any size plate (such as 96 or 384-well plates), add samples to the plate using drag and drop, print out the plate layout, and export the layout with additional identifying information for genotyping platforms.
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• Genotype Management
  Import the genotypes directly into Progeny Lab.  Perform multiple error checks including Mendelian errors, control errors, missing markers, zero alleles, and discrepancies between genotype data.
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• Analysis
  Format your data into standard linkage files and generate .pre and .dat files with allele frequencies to be used in a variety of linkage packages. Query individuals along with phenotypic data to include in association analysis exports. Track all exports.
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Benefits

Managing massive amounts of genotypic data is a very arduous task.  Having 3,000 samples using the 500K chip, 650K chip, or 1 mil chip is a lot of data to store and manage and prepare for analysis.  Progeny Lab does all this for you.  Find out why over 100 centers worldwide use us to manage both WGA or targeted regions for their studies.

• Integrate phenotypic and genotypic data in one secure location.
• Specify which users have access to what data and ensure complete confidentiality.
• Natively import chip files from all the major platforms, including Affymetrix, Illumina, ABI, Sequenom, and others. Even import custom files.
• Perform error checking while importing chip files, such as mendelian error checks, missing samples, rejected markers, etc....
• Perform error checks prior to exporting to linkage (missing parents, etc..) preventing iterations of running linkage, receiving errors, correcting them, then running again.
• Perform SNP analysis such as calculating MAF, Hardy-Weinberg p-values, degree of heterozygosity, call rates, and more...
• Prepare outputs for analysis programs such as PLINK, Haploview, Linkage, GeneHunter, Allegro, Phase, and others.