Haplotype analysis by novel algorisms.
sole application by StaGen |
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| Patent No. | JP 2003-130638 (Japan) US2005050129 (USA) |
| Project Name | PEN haplo |
| Title | Method of estimating a penetrance and evaluating a relationship between diplotype configuration and phenotype using genotype data and phenotype data. |
| Abstract | A method of simultaneously estimating a diplotype-based penetrance as well as haplotype frequencies and diplotype configurations on the basis of observed genotype and phenotype data. The method includes a step a of calculating, on the basis of genotype data and phenotype data with haplotype frequencies and penetrance used as parameters, the maximum likelihood (L 0max ) obtained by maximizing likelihood under the hypothesis that there is no association between predetermined diplotype configurations and a predetermined phenotype, the maximum likelihood estimates of haplotype frequencies and penetrances, the maximum likelihood (L max ) obtained by maximizing likelihood under the hypothesis that there is an association between the predetermined diplotype configurations and the predetermined phenotype; and a step b of calculating the penetrance from the maximum likelihood estimate obtained in said step a. |
| Working example | Software |
| Information | 1. Ito T, Inoue E, Kamatani N. Association test algorithm between a qualitative phenotype and a haplotype or haplotype set using simultaneous estimation of haplotype frequencies, diplotype configurations and diplotype-based penetrances. Genetics. 2004;168(4):2339-48. 2. Furihata S, Ito T, Kamatani N. Test of association between haplotypes and phenotypes in case-control studies: Examination of validity of the application of an algorithm for samples from cohort or clinical trials to case-control samples using simulated and real data. Genetics. 174:1505-1516, 2006. |
sole application by StaGen |
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| Patent No. | JP 2003-340598 (Japan) No.10/944,821(USA) |
| Project Name | QTL haplo |
| Title | Algorithm for Estimating and Testing Association between Haplotype and Quantitative Phenotype |
| Abstract | A method of estimating, in addition to haplotype frequencies and diplotype configurations, a means and a standard deviation determining a distribution of a quantitative phenotype by the diplotype on the basis of data on observed genotypes and phenotype data taking a continuous value. The method includes a step a of calculating the maximum likelihood (L 0max ) on the basis of genotype data and phenotype data taking a continuous value by using as parameters haplotype frequencies and a means and a standard deviation determining a distribution of a quantitative phenotype, under the hypothesis that there is no association between a diplotype configuration including a predetermined haplotype and a predetermined phenotype, and maximum likelihood estimates and the maximum likelihood (L 0max ) of haplotype frequencies and penetration rate obtained by maximizing the likelihood under the hypothesis that there is an association between the diplotype configuration including the predetermined haplotype and the phenotype distribution taking a continuous value, and a step b of obtaining the means and the standard deviation determining a distribution of a quantitative phenotype from the maximum likelihood estimates obtained in the step a. |
| Working example | Software |
| Information | Shibata K, Ito T, Kitamura Y, Iwasaki N, Tanaka H, Kamatani N. Simultaneous estimation of haplotype frequencies and quantitative trait parameters: applications to the test of association between phenotype and diplotype configuration. Genetics. 2004 Sep;168(1):525-39. |