Process Description

SNP Power

The SNP Power process assists you in the planning of your experiments. Starting with some basic information about the hypothesized genetic model for the trait of interest, it enables you to calculate the sample size needed to obtain results with the needed statistical power. Conversely, this process also enables you to calculate the statistical power of an experiment, given a specified sample size. This process should be run before you run your experiment.

The power and sample size calculations involve estimating the mean and variance of the appropriate test statistic under the alternative hypothesis that alleles (for the allele test) or genotypes (for the genotype and trend tests) come from independent multinomial distributions for cases and controls as opposed to a single distribution for the combined sample. Details for the trend test are given by Slager and Schaid (2001) and for Pearson chi-square tests by Agresti (1990).

What do I need?

To successfully run the SNP Power process, you must have some knowledge of the genetic model that you are working with. Required information includes:

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the frequency of the trait in both the entire population and the sample of individuals being analyzed, and the frequency with which the trait allele occurs in the population,

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the likelihood that an individual having one ( heterozygous) or two ( homozygous) copies of the trait allele also has the trait, relative to an individual without the allele,

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whether the marker locus and the trait locus are, in fact, identical or are separate but linked. In that case, you also need an estimate of linkage disequilibrium, and

•

the level of inbreeding in the population.

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 SNP Power output documentation for detailed descriptions and guides to interpreting your results.