Process Description

IBS Sharing Regions

This process identifies regions of consecutive SNPs that are shared IBS between a set of affected individuals. Columns of parents or founders can be specified from the Input Data Set to only examine loci for which all parents are heterozygous. Sample genotypes can be in separate data sets (one for each chromosome, for example) or combined into a single data set. "Runs" (denoted "streaks" by Leibon, Rockmore, and Pollak (2008)) can be determined in terms of a set of at least a certain number of individuals (offspring) sharing an allele (Thomas et al. 2007), only those sharing at least one variant allele, or only sharing two variant alleles.

What do I need?

At least one tall SAS Input Data Set is required. This data set must contain genotype and location information for the markers on one or more chromosome. This tall data set has markers listed in rows and individual sample subjects listed in columns. The chr1_geno.sas7.dat data set, shown below, has genotype data at 612,864 markers from chromosome 1 from 10 individuals.

Note: These data sets should be in tall format, where samples are in columns and SNPs are in rows. SNP genotypes must be coded numerically (0, 1, or 2) based on the variant alleles.

Data can be contained in one data set or across multiple data sets. All of the data sets must be located in the same folder. The chr1_geno.sas7.dat data set, shown above, and eight additional data sets containing genotype data from chromosomes 2 - 9 for the same 10 individuals, are located in the Sample Data folder.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output generated by this process is summarized in a Tabbed report. Refer to the IBS Sharing Regions output documentation for detailed descriptions and guides to interpreting your results.