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The foundational publications describing the fabrication of microarrays
using a photolithographic process are illustrated in the following
publications:
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Fodor S.P., et al. Light-directed, spatially addressable
parallel chemical synthesis. Science. 1991, 251(4995):767-73.
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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. |
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Fodor S.P., et al. Multiplexed biochemical assays with
biological chips. Nature. 1993, 364(6437):555-6. |
Expression analysis using Affymetrix microarrays was first described
in a study of gene expression after induction of cytokine in mouse
lymphocyte:
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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:
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Golub, T. R., et al. Molecular classification of cancer:
class discovery and class prediction by gene expression monitoring.
Science. 1999, 286(5439), 531-7.
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Winzeler, E. A. et al. Functional characterization
of the S. cerevisiae genome by gene deletion and parallel
analysis. Science. 1999, 285(5429), 901-6.
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The fundamentals of DNA sequence analysis using Affymetrix microarrays
can be found in the following review article:
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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:
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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.
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Cronin, M.T., et al. Cystic fibrosis mutation detection
by hybridization to light-generated DNA probe arrays. Hum
Mutat. 1996, 7(3):244-55.
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Chee, M., et al. Accessing genetic information with
high-density DNA arrays. Science. 1996, 274(5287):610-4.
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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.
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Kapranov, P. et al. Large-scale transcriptional activity
in chromosomes 21 and 22. Science. 2002, 296(5569), 916-9. |
The Microarray Suite 5.0 statistical algorithm is presented in Liu,
et al. 2002 and in Hubbell, et al. 2002.
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Liu, W.M., et al. Analysis of high density expression
microarrays with signed-rank call algorithms. Bioinformatics.
2002, 18(12):1593-9.
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Hubbell, E., et al.Robust estimators for expression
analysis. Bioinformatics. 2002, 18(12):1585-92.
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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.
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Liu, G., NetAffx: Affymetrix probesets and annotations. Nucleic
Acids Res. 2003, 31(1):82-6.
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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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