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Foundation Publications

Foundational GeneChip Technology Publications

Review key manuscripts describing the fabrication, analysis, and application of GeneChip arrays.


The foundational publications describing the fabrication of microarrays using a photolithographic process are illustrated in the following publications:

  • Fodor S.P., et al. Light-directed, spatially addressable parallel chemical synthesis. Science. 1991, 251(4995):767-73.
  • Pease A.C., et al. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A. 1994, 91(11):5022-6.
  • Fodor S.P., et al. Multiplexed biochemical assays with biological chips. Nature. 1993, 364(6437):555-6.

Expression Analysis with GeneChip Arrays

Expression analysis using Affymetrix microarrays was first described in a study of gene expression after induction of cytokine in mouse lymphocyte:

  • Lockhart D.J., et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996, 14(13):1675-80.

Subsequent publications further demonstrated that Affymetrix microarrays are well suited for this task:

  • Golub, T. R., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999, 286(5439), 531-7.
  • Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science. 1999, 285(5429), 901-6.

DNA Analysis with GeneChip Arrays

The fundamentals of DNA sequence analysis using Affymetrix microarrays can be found in the following review article:

  • Lipshutz, R.F. et al. Advanced DNA sequencing technologies. Curr Opinion in Structural Biology. 1994, 4:376-380.

Some of the early applications of Affymetrix microarrays to detect SNPs have been cited for genes including HIV-1 in Kozal, et al. 1996, cystic fibrosis (CFTR) in Cronin, et al. 1996, human mitochondrial sequence in Chee, et al. 1996, and breast cancer in BRCA1 Hacia et al. 1996:

  • Kozal, M.J., et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med. 1996, 2(7):753-9.
  • Cronin, M.T., et al. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum Mutat. 1996, 7(3):244-55.
  • Chee, M., et al. Accessing genetic information with high-density DNA arrays. Science. 1996, 274(5287):610-4.
  • Hacia, J.G., et al. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nat Genet. 1996, 14(4):441-7.

Whole Genome / Chromosome Tiling Arrays

  • Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 2002, 296(5569), 916-9.

Software and Informatics

  • The Microarray Suite 5.0 statistical algorithm is presented in Liu, et al. 2002 and in Hubbell, et al. 2002.
  • Liu, W.M., et al. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics. 2002, 18(12):1593-9.
  • Hubbell, E., et al.Robust estimators for expression analysis. Bioinformatics. 2002, 18(12):1585-92.

The url for the NetAffx Analysis Center is http://www.affymetrix.com/analysis/index.affx and a description of the annotations and the software system can be found in Liu, et al. 2003.

  • Liu, G., NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003, 31(1):82-6.

Additional Resources

Many other publications by Affymetrix scientists and microarray researchers around the world can be found in our searchable Database of Scientific Publications. Affymetrix continues to generate new publications on the latest applications of GeneChip technology through a continued commitment to molecular biology and related technology.

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