Summary of Research Project Results under JSPS FY2004
"Research for the Future Program"

1. Research Institution   Tokyo Women's Medical University
2. Research Area Life Sciences
3. Research Field Genome Research
4. Term of Project FY 2000 - FY 2004
5. Project Number 00L01410
6. Title of Project Development and Application of Computer Programs for Mapping Disease-related Genes Using Polymorphic Markers

7. Project Leader

Name Institution, Department Title of Position
Naoyuki, Kamatani Institute of Rheumatology Tokyo Women's Medical University Professor

8. Core Members

Names Institution, Department Title of Position
Shigeru, Kotake Institute of Rheumatology Tokyo Women's Medical University Lecturer

9. Summary of Research Results

  1.   Development and use of algorithms and computer programs for statistical genetics. We have developed 8 algorithms to analyze the genetic data using statistics of which 6 have been published as follows. 1. Checkfam (Saito et al. J Hum Genet 47:377-379, 2002) which detects contradictions in the genotypic data in pedigrees. 2. SimPack (Saito et al. J Hum Genet 47:360-365, 2002) which performed simulations of various linkage analyses and linkage disequilibrium analyses and evaluate the study designs. 3. Ldsupport (Kitamura et al. Ann Hum Genet 66: 183-193, 2002) which infers population haplotypes and diplotype configurations based on maximum-likelihood nalysis. 4. Penhaplo (Ito et al. Genetics 168: 2339-2348, 2004) which performs tests and inference based on haplotypes and diplotype configurations for the data from cohort, clinical trial, and case-control samples. 5. AssignHaplo (Kamatani et al. Am J Hum Genet 75: 190-203, 2004) which assign rare SNPs in LD blockto major haplotypes. 6. Popstruct (Nakamura et al. J Hum Genet 50:53-61, 2005) which detects the population structuring of case control, cohort and clinical trial samples and performs tests based on such structures. 7. Mctable which performs test of linkage disequilibrium analysis for microsatellite polymorphisms using MCMC method and calculates the confidence interval of P value. 8. Ldinterval Calculate confidence interval of coefficient of linkage disequilibrium. As stated above, we have developed many computer programs and used them for many studies. We have requested by many researchers to send them the programs.
  2.   We have opened a home page in which various techniques for statistical genetics are explained ( ).
  3.   We have provided computer programs we made and analyzed data for other researchers. 34 different reports have been published (See reference). The contents of the reports included cause of diabetes, the involvement of diabetes, drug reactions, APRT deficiency, AMP deaminase deficiency, the metabolism of a cancer drug (Irinotecan), prion gene in cattles, cause of schizophrenia, dystonia, systemic sclerosis, BMI, colon cancer, the involvement of rheumatoid arthritis, case of chronic renal failure, adverse events of rheumatic diseases (See reference).

10. Key Words

( 1 ) Statistics ( 2 ) Statistical genetics ( 3 ) Linkage analysis
( 4 ) Linkage disequilibrium ( 5 ) Haplotype ( 6 ) SNP
( 7 ) Microsatellite ( 8 ) Pharmacogenetics ( 9 ) Algorithm