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. 2004 Jan 29:4:4.
doi: 10.1186/1471-2407-4-4.

Genome wide in silico SNP-tumor association analysis

Ping Qiu  1 , Luquan Wang, Mitch Kostich, Wei Ding, Jason S Simon, Jonathan R Greene
Affiliations

Genome wide in silico SNP-tumor association analysis

Ping Qiu et al. BMC Cancer. .

Abstract

Background: Carcinogenesis occurs, at least in part, due to the accumulation of mutations in critical genes that control the mechanisms of cell proliferation, differentiation and death. Publicly accessible databases contain millions of expressed sequence tag (EST) and single nucleotide polymorphism (SNP) records, which have the potential to assist in the identification of SNPs overrepresented in tumor tissue.

Methods: An in silico SNP-tumor association study was performed utilizing tissue library and SNP information available in NCBI's dbEST (release 092002) and dbSNP (build 106).

Results: A total of 4865 SNPs were identified which were present at higher allele frequencies in tumor compared to normal tissues. A subset of 327 (6.7%) SNPs induce amino acid changes to the protein coding sequences. This approach identified several SNPs which have been previously associated with carcinogenesis, as well as a number of SNPs that now warrant further investigation

Conclusions: This novel in silico approach can assist in prioritization of genes and SNPs in the effort to elucidate the genetic mechanisms underlying the development of cancer.

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References

    1. Schuler G. Pieces of the puzzle: expressed sequence tags and the catalog of human genes. J Mol Med. 1997;75:694–698. doi: 10.1007/s001090050155. - DOI - PubMed
    1. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schonbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y, RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium Functional annotation of a full-length mouse cDNA collection. Nature. 2001;409:685–690. doi: 10.1038/35055500. - DOI - PubMed
    1. Irizarry K, Kustanovich V, Li C, Brown N, Nelson S, Wong W, Lee CJ. Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nat Genet. 2000;26:233–236. doi: 10.1038/79981. - DOI - PubMed
    1. Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchell-Olds T, Weisshaar B. Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res. 2003;13:1250–1257. doi: 10.1101/gr.728603. - DOI - PMC - PubMed
    1. Barker G, Batley J, O' Sullivan H, Edwards KJ, Edwards D. Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics. 2003;19:421–422. doi: 10.1093/bioinformatics/btf881. - DOI - PubMed