dChipSNP: Significance curve and clustering of SNP-array-based loss-of-heterozygosity data

Bioinformatics

Volumn 20, Issue 8, 2004, Pages 1233-1240

  Lin, Ming ^a   Wie, Lee Jen ^a   Sellers, William R ^a   Lieberfarb, Marshall ^a   Wong, Wing Hung ^a,b   Li, Cheng ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; AUTOMATION; BREAST CANCER; CHROMOSOME ANALYSIS; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; GENETIC ANALYSIS; HETEROZYGOSITY LOSS; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROBABILITY; PROSTATE CANCER; SAMPLING; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 2542548405     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth069     Document Type: Article

References (19)

1. Affymetrix Inc. (2000) GeneChip® HuSNP™ Mapping Assay User's Manual. Technical Report.
2. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc., B57, 289-300.
3. Cargill,M., Altshuler,D., Ireland,J., Sklar,P., Ardlie,K., Patil,N., Shaw,N., Lane,C.R., Lim,E.P., Kalyanaraman,N. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet., 22, 231-238.
4. Chee,M., Yang,R., Hubbell,E., Berno,A., Huang,X.C., Stern,D., Winkler,J., Lockhart,D.J., Morris,M.S. and Fodor,S.P. (1996) Accessing genetic information with high-density DNA arrays. Science, 274, 610-614.
5. Cutler,D.J., Zwick,M.E., Carrasquillo,M.M., Yohn,C.T., Tobin,K.P., Kashuk,C., Mathews,D.J., Shah,N.A., Eichler,E.E., Warrington,J.A. et al. (2001) High-throughput variation detection and genotyping using microarrays. Genome Res., 11, 1913-1925.
6. Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis. Cambridge University Press, Cambridge.
7. Eisen,M.B., Spellman,P.T., Brown,P.O. and Botstein,D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci., USA, 95, 14863-14868.
8. Golub,T.R., Slonim,D.K., Tamayo,P., Huard,C., Gaasenbeek,M., Mesirov,J.P., Coller,H., Loh,M.L., Downing,J.R., Caligiuri,M.A. et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
9. Hacia,J.G., Fan,J.B., Ryder,O., Jin,L., Edgemon,K., Ghandour,G., Mayer,R.A., Sun,B., Hsie,L., Robbins,C.M. et al. (1999) Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet., 22, 164-167.
10. Halushka,M.K., Fan,J.B., Bentley,K., Hsie,L., Shen,N., Weder,A., Cooper,R., Lipshutz,R. and Chakravarti,A. (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet., 22, 239-247.
11. Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci., USA, 98, 31-36.
12. Lieberfarb,M., Lin,M., Lechpammer,M., Li,C., Tanenbaum,D.M., Wright,R., Shim,J., Kantoff,P.W., Loda,M., Meyerson,M. et al. (2003) Genome-wide loss-of-heterozygosity analysis from laser-capture microdissected prostate cancer using SNP arrays and a novel bioinformatics platform dChipSNP. Cancer Res., 63, 4781-4785.
13. Lindblad-Toh,K., Tanenbaum,D.M., Daly,M.J., Winchester,E., Lui,W.O., Villapakkam,A., Stanton,S.E., Larsson,C., Hudson,T.J., Johnson,B.E. et al. (2000) Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol., 18, 1001-1005.
14. Lipschutz,R.J., Fodor,S.P.A., Gingeras,T.R. and Lockhart,D.J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet., 21, 20-24.
15. Mei,R., Galipeau,P.C., Prass,C., Berno,A., Ghandour,G., Patil,N., Wolff,R.K., Chee,M.S., Reid,B.J. and Lockhart,D.J. (2000) Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res., 10, 1126-1137.
16. Schubert,E.L., Malone,K., Hsu,L., Daling,J.D., Cousens,L.G. and Porter,P. (2001) Whole genome LOH analysis of lobular and ductal breast cancers by Hu-SNP array. Breast Cancer Res. Treatment, 69, 232.
17. Wang,D.G., Fan,J.B., Siao,C.J., Berno,A., Young,P., Sapolsky,R., Ghandour,G., Perkins,N., Winchester,E., Spencer,J. et al. (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 280, 1077-1082.
18. Wang,Z.C., Lin,M., Wei,L.J., Li,C., Miron,A., Lodeiro,G., Harris,L., Ramaswamy,S., Tanenbaum,D.M., Meyerson,M., Iglehart,J.D. and Richardson,A. (2003) Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Res., in press.
19. Westfall,P.H. and Young,S.S. (1993) Resampling-Based Multiple Testing: Examples and Methods for P-value Adjustment. Wiley, New York.