TreeScan: A bioinformatic application to search for genotype/phenotype associations using haplotype trees

Bioinformatics

Volumn 21, Issue 9, 2005, Pages 2130-2132

  Posada, David ^a,c   Maxwell, Taylor J ^b   Templeton, Alan R ^b  

^a Variagenics Inc ^*  (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c UNIVERSITY OF VIGO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANALYSIS OF VARIANCE; ARTICLE; COMPUTER PROGRAM; CORRELATION ANALYSIS; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENOTYPE; HAPLOTYPE; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURAL BIOINFORMATICS;

EID: 18744390795     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti293     Document Type: Article

References (19)

1. Balciuniene,J. et al. (2002) Investigation of the functional effect of monoamine oxidase polymorphisms in human brain. Hum. Genet., 110, 1-7.
2. Boerwinkle,E. and Sing,C.F. (1986) Bias of the contribution of single locus effects to the variance of a quantitative trait. Am. J. Hum. Genet., 39, 137-144.
3. Clement,M. et al. (2000) TCS: a computer program to estimate gene genealogies. Mol. Ecol., 9, 1657-1659.
4. Crandall,K.A. and Templeton,A.R. (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959-969.
5. Drysdale,C.M. et al. (2000) Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc. Natl Acad. Sci. USA, 97, 10483-10488.
6. Ge,Y. et al. (2003) Resampling-based multiple testing for microarray data hypothesis. Test, 12, 1-44.
7. Knoblauch,H. et al. (2002) Common haplotypes in five genes influence genetic variance of LDL and HDL cholesterol in the general population. Hum. Mol. Genet., 11, 1477-1485.
8. Lam,J.C. et al. (2000) Haplotype fine mapping by evolutionary trees. Am. J. Hum. Genet., 66, 659-673.
9. Oehlert,G.W. and Bingham,C. (2003) MacAnova: a program for statistical analysis and matrix algebra. School of Statistics, University of Minnesota, St Paul, MN.
10. Pfenninger,M. and Posada,D. (2002) Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution Int. J. Org. Evolution, 56, 1776-1788.
11. Seltman,H. et al. (2001) Transmission/Disequilibrium test meets measured haplotypes analysis: family-based association analysis guided by evolution of haplotypes. Am. J. Hum. Genet., 68, 1250-1263.
12. Seltman,H. et al. (2003) Evolutionary-based association analysis using haplotype data. Genetic Epidemiology, 25, 48-58.
13. Templeton,A.R. (1995) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer's disease and the apoprotein E locus. Genetics, 140, 403-409.
14. Templeton,A.R. et al. (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117, 343-351.
15. Templeton,A.R. et al. (2000) Cladistic structure within the human Lipoprotein Lipase gene and its implications for phenotyopic association studies. Genetics, 156, 1259-1275.
16. Templeton,A.R., Maxwell,T., Posada,D., Stengard,J.H., Boerwinkle,E. and Sing,C.F. (in press) Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics, 169, 441-453.
17. Van Eerdewegh,P. et al. (2002) Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness. Nature, 418, 426-430.
18. Westfall,P.H. and Young,S.S. (1993) Resampling-Based Multiple Testing: Examples and Methods for p-value Adjustment Wiley, NY.
19. Zaykin,D.V. et al. (2002) Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered., 53, 79-91.