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Nucleic Acids Research 2004 32(20):6104-6110; doi:10.1093/nar/gkh937
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Published online 23 November 2004

Nucleic Acids Research, Vol. 32 No. 20 © Oxford University Press 2004; all rights reserved

The impact of SNPs on the interpretation of SAGE and MPSS experimental data

Ana Paula M. Silva, Jorge E. S. De Souza1,2, Pedro A. F. Galante1,3, Gregory J. Riggins4, Sandro J. De Souza1 and Anamaria A. Camargo*

Laboratory of Molecular Biology and Genomics and 1 Laboratory of Computational Biology, Ludwig Institute for Cancer Research, 01509-010, São Paulo, SP, Brazil, 2 Interunit in Bioinformatics and 3 Department of Biochemistry, University of São Paulo, 05508-900, São Paulo, SP, Brazil and 4 John Hopkins University School of Medicine, 21224, Baltimore, MD, USA

* To whom correspondence should be addressed at Rua Prof. Antonio Prudente 109, 4th floor, 01509-010 São Paulo, SP, Brazil. Tel: +55 11 3388 3248; Fax: +55 11 3207 7001; Email: anamaria{at}compbio.ludwig.org.br

Received August 5, 2004; Revised September 24, 2004; Accepted October 25, 2004

Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for ~8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.


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