Title

SNPinProbe_1.0: A database for filtering out probes in the Affymetrix GeneChip® Human Exon 1.0 ST array potentially affected by SNPs

Authors

Shiwei Duan¹, Wei Zhang¹, Wasim Kamel Bleibel¹, Nancy Jean Cox^{1, 2} and M. Eileen Dolan^{1, 3, 4, *}

Affiliation

¹Section of Hematology/Oncology, Department of Medicine; ²Department of Human Genetics; ³Committee on Clinical Pharmacology and Pharmacogenomics; ⁴Cancer Research Center, The University of Chicago, IL 60637, USA

Email

edolan@medicine.bsd.uchicago.edu

773 702 4441

773 702 0963; * Corresponding author

Article Type

Database

Date

received June 18, 2008; revised July 20, 2008; accepted July 23, 2008; published August 01, 2008

Abstract

The Affymetrix GeneChip® Human Exon 1.0 ST array (exon array) is designed to measure both gene-level and exon-level expression in human samples. This exon array contains ~1.4 million probesets consisting of ~5.4 million probes and profiles over 17,000 well-annotated gene transcripts in the human genome. As with all expression arrays, the exon array is vulnerable to SNPs within probes, because these SNPs can affect the hybridization of the probes and thus produce misleading expression values. In some cases, this could result in dramatic fluctuations of the exon-level expression. For this reason, we performed a genome-wide search for SNPs within regions that hybridize to probes by evaluating approximately 18 million SNPs in dbSNP (Build 129) and about 5.4 million probes in the exon array. We identified 597,068 probes within 350,382 probe sets that hybridized to regions containing SNPs. These affected probes and/or probesets can be filtered in the data processing procedure thus controlling for potential false expression phenotypes when using this exon array.

Keywords

database; probes; SNP; Affymetrix GeneChip® human exon 1.0 ST array; human genome

http://cid-fb2a64e541add2be.skydrive.live.com/browse.aspx/Affy%7C_HuEx%7C_1.0ST?uc=2.

Citation

Duan et al., Bioinformation 2(10): 469-470 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.