Unreliable Microarray Probes Hamper Research

Molecular biologists who were concerned about the poor reproducibility of results in their field evaluated commercially available microarray biochips and found that greater than 19% of the probes on each platform did not correspond to their appropriate mRNA reference sequence (RefSeq)

The Reference Sequence (RefSeq) database provides a biologically nonredundant collection of DNA, RNA, and protein sequences. Each RefSeq represents a single, naturally occurring molecule from a particular organism. RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses.

RefSeqs are frequently based on the records of GenBank (NCBI, U.S. National Center for Biotechnology Information) but differ in that each RefSeq is a synthesis of information, not a piece of a primary research data in itself. Similar to a review article in the literature, a RefSeq is an interpretation by a particular group at a particular time. RefSeqs can be retrieved in several different ways: by searching the Entrez Nucleotide or Protein database, by BLAST (basic local alignment search tool) searching, by FTP (file transfer protocol), or through links from other NCBI resources.

Investigators at Harvard Medical School (Boston, MA, USA) and Washington University (St. Louis, MO, USA) inspected commercially available microarray biochips in order to assess the accuracy of individual probe sequences used to query gene expression. They reported in the August 2004 issue of Physiological Genomics that more than 19% of the probe sequences failed to perfectly correspond with the appropriate mRNA as defined by the reference sequence. Furthermore, and not surprisingly, they found that sequence-verified probes performed more consistently, and with higher accuracy, within replicates and across different versions of the technology.




Related Links:
National Center for Biotechnology Information
Harvard University
Washington University