The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data
Abstract
Motivation: Oligonucleotide microarrays allow genotyping of thousands of single-nucleotide polymorphisms (SNPs) in parallel. Recently, this technology has been applied to loss-of-heterozygosity (LOH) analysis of paired normal and tumor samples. However, methods and software for analyzing such data are not fully developed. Result: Here, we report automated methods for pooling SNP array replicates to make LOH calls, visualizing SNP and LOH data along chromosomes in the context of genes and cytobands, making statistical inference to identify shared LOH regions, clustering samples based on LOH profiles and correlating the clustering results to clinical variables. Application of these methods to prostate and breast cancer datasets generates biologically important results. Availability: The software module dChipSNP implementing these methods is available at http://biosun1.harvard.edu/complab/dchip/snp/ Supplementary information: The breast cancer data are provided by Andrea L. Richardson, Zhigang C. Wang and James D. Iglehart.
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Cites
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 16,184
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.
Li, C., & Wong, W. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.1.31 · Cited by 3,133
Self-citation
Cited by
Molecular characterization of the tumor microenvironment in breast cancer
Allinen, M., Beroukhim, R., Cai, L., Brennan, C., Lahti-Domenici, J., Huang, H., Porter, D., Hu, M., Chin, L., Richardson, A., et al. (2004) · Cancer Cell · doi:10.1016/j.ccr.2004.06.010 · Cited by 1,299
Self-citationCharacterizing the cancer genome in lung adenocarcinoma
Weir, B. A., Woo, M. S., Getz, G., Perner, S., Ding, L., Beroukhim, R., Lin, W. M., Province, M. A., Kraja, A., Johnson, L. A., et al. (2007) · Nature · doi:10.1038/nature06358 · Cited by 1,105
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy
Barretina, J., Taylor, B. S., Banerji, S., Ramos, A. H., Lagos-Quintana, M., DeCarolis, P. L., Shah, K., Socci, N. D., Weir, B. A., Ho, A., et al. (2010) · Nature Genetics · doi:10.1038/ng.619 · Cited by 735
Self-citationLaFramboise, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp552 · Cited by 467
Kerkel, K., Spadola, A., Yuan, E., Kosek, J., Jiang, L., Hod, E., Li, K., Murty, V. V., Schupf, N., Vilain, E., et al. (2008) · Nature Genetics · doi:10.1038/ng.174 · Cited by 441
Metadata
- Authors
- Lin, M., Wei, L.-J., Sellers, W. R., Lieberfarb, M., Wong, W. H., & Li, C.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-02-10
- Volume
- 20
- Issue
- 8
- Pages
- 1233-1240
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2104241530
- Cited by
- 374
- References
- 2
- FWCI
- 11.48
- Type
- journal article
- Language
- en
- Open access
- closed
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- Lin, M., Wei, L.-J., Sellers, W. R., Lieberfarb, M., Wong, W. H., & Li, C. (2004). dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics. https://doi.org/10.1093/bioinformatics/bth069
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