Frühling Rijsdijk & Pak Sham, June 2001

MPIC calculates the Multipoint Polymorphism Information Content of a group of markers, using a new sib-pair specific method that takes into account the informativeness of the marker genotype data (parental mating types). MPIC can be evaluated at any location along a marker map, and is proportional to the noncentrality parameter for linkage. The MPIC index of map quality can be used across a marker map to assess the adequacy of marker density for linkage analyses, especially if SNPs are used.

Reference: F.V. Rijsdijk & P.C. Sham. Estimation of Sib-Pair IBD Sharing and Multipoint Polymorphism Information Content by Linear Regression, Behavioral Genetics, 32, 211-220, 2002.

In the first window, paste or type data in the following format: the first line contains the number of markers (n); the next n lines contain the number of alleles, followed by their frequencies. In the second window, enter the marker distances (in cMorgan).

Example:

Locus specification

6

9 0.2875 0.0125 0.1375 0.1125 0.2375 0.0125 0.1375 0.0375 0.025

11 0.075 0.0875 0.0125 0.075 0.1375 0.0875 0.2375 0.0125 0.1375 0.025 0.1125

11 0.175 0.025 0.0125 0.0625 0.0375 0.1 0.3375 0.15 0.0625 0.0125 0.025

11 0.0125 0.0125 0.0125 0.275 0.25 0.0875 0.05 0.075 0.025 0.125 0.075

7 0.2875 0.2 0.175 0.125 0.175 0.0125 0.025

9 0.5 0.0125 0.0625 0.2375 0.075 0.05 0.0375 0.0125 0.0125

Map distance

5.9 9.8 11.8 12.8 7

The maximum number of alleles and markers in this version of the program is 25.

The next example illustrates how map quality (MPIC) of a set of markers on the X chromosome (6 loci, 10 cM grid) increases when a denser map, containing 8 additional markers, is used.

Output of MPIC values after running the two different maps (input files) separately: