. 1995 Sep;19(3).

Using oligonucleotide probe arrays to access genetic diversity

R J Lipshutz 1 D Morris  M Chee  E Hubbell  M J Kozal  N Shah  N Shen  R Yang  S P Fodor  
  • PMID: 7495558
  •     55 citations


As the Human Genome Project and related efforts identify and determine the DNA sequences of human genes, it is important that highly reliable and efficient mechanisms are found to access individual genetic variation. It is only through a greater understanding of genetic diversity that the true benefit of the Human Genome Project will be realized. One approach, hybridization to high-density arrays of oligonucleotides, is a fast and effective means of accessing this genetic variation. Light-directed chemical synthesis has been used to generate miniaturized, high-density arrays of oligonucleotide probes. Application-specific oligonucleotide probe array designs have been developed for the rapid screening of characterized genes. Dedicated instrumentation and software have been developed for array hybridization, fluorescence detection and data acquisition and analysis. In a specific and challenging application, oligonucleotide probe arrays have been used to screen the reverse transcriptase and protease genes of the highly polymorphic HIV-1 genome to explore genetic diversity and detect mutations conferring resistance to antiviral drugs. Results from this application strongly suggest that oligonucleotide probe arrays will be a powerful tool for rapid investigations in sequence checking, pathogen detection, expression monitoring and DNA molecular recognition.

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DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides.
S Parinov, V Barsky, +4 authors, A Mirzabekov.
Nucleic Acids Res, 1996 Aug 01; 24(15). PMID: 8760885    Free PMC article.
Covalent attachment of synthetic DNA to self-assembled monolayer films.
L A Chrisey, G U Lee, C E O'Ferrall.
Nucleic Acids Res, 1996 Aug 01; 24(15). PMID: 8760890    Free PMC article.
Fabrication of patterned DNA surfaces.
L A Chrisey, C E O'Ferrall, +2 authors, J M Calvert.
Nucleic Acids Res, 1996 Aug 01; 24(15). PMID: 8760891    Free PMC article.
Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists.
G McGall, J Labadie, +3 authors, W Hinsberg.
Proc Natl Acad Sci U S A, 1996 Nov 26; 93(24). PMID: 8942972    Free PMC article.
Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses.
H M Davey, D B Kell.
Microbiol Rev, 1996 Dec 01; 60(4). PMID: 8987359    Free PMC article.
Highly Cited. Review.
Rapid design of denaturing gradient-based two-dimensional electrophoretic gene mutational scanning tests.
N J van Orsouw, R K Dhanda, +4 authors, J Vijg.
Nucleic Acids Res, 1998 Jun 10; 26(10). PMID: 9580692    Free PMC article.
Line probe assay for detection of human immunodeficiency virus type 1 mutations conferring resistance to nucleoside inhibitors of reverse transcriptase: comparison with sequence analysis.
D Descamps, V Calvez, +7 authors, F Brun-Vézinet.
J Clin Microbiol, 1998 Jul 03; 36(7). PMID: 9650987    Free PMC article.
Preventing antibiotic resistance through rapid genotypic identification of bacteria and of their antibiotic resistance genes in the clinical microbiology laboratory.
M G Bergeron, M Ouellette.
J Clin Microbiol, 1998 Jul 17; 36(8). PMID: 9665984    Free PMC article.
Cellular gene expression altered by human cytomegalovirus: global monitoring with oligonucleotide arrays.
H Zhu, J P Cong, +2 authors, T Shenk.
Proc Natl Acad Sci U S A, 1998 Nov 25; 95(24). PMID: 9826724    Free PMC article.
Highly Cited.
Probing lymphocyte biology by genomic-scale gene expression analysis.
A Alizadeh, M Eisen, +2 authors, L M Staudt.
J Clin Immunol, 1998 Dec 19; 18(6). PMID: 9857281
Genetic methods for assessing antimicrobial resistance.
F R Cockerill.
Antimicrob Agents Chemother, 1999 Jan 30; 43(2). PMID: 9925507    Free PMC article.
Genetics and pulmonary medicine. 5. Genetics of drug resistant tuberculosis.
A Telenti.
Thorax, 1999 May 13; 53(9). PMID: 10319064    Free PMC article.
Performance of the Affymetrix GeneChip HIV PRT 440 platform for antiretroviral drug resistance genotyping of human immunodeficiency virus type 1 clades and viral isolates with length polymorphisms.
M Vahey, M E Nau, +8 authors, S A Wegner.
J Clin Microbiol, 1999 Jul 16; 37(8). PMID: 10405396    Free PMC article.
Automated mutation analysis.
D Ravine.
J Inherit Metab Dis, 1999 Jul 17; 22(4). PMID: 10407782
DNA sequence analysis by hybridization with oligonucleotide microchips: MALDI mass spectrometry identification of 5mers contiguously stacked to microchip oligonucleotides.
A A Stomakhin, V A Vasiliskov, +3 authors, A D Mirzabekov.
Nucleic Acids Res, 2000 Feb 10; 28(5). PMID: 10666462    Free PMC article.
Comparison of sequencing by hybridization and cycle sequencing for genotyping of human immunodeficiency virus type 1 reverse transcriptase.
G J Hanna, V A Johnson, +5 authors, R T D'Aquila.
J Clin Microbiol, 2000 Jul 06; 38(7). PMID: 10878069    Free PMC article.
Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes.
P V Riccelli, F Merante, +4 authors, A S Benight.
Nucleic Acids Res, 2001 Feb 13; 29(4). PMID: 11160933    Free PMC article.
Development of a 950-gene DNA array for examining gene expression patterns in mouse testis.
J C Rockett, J Christopher Luft, +5 authors, D J Dix.
Genome Biol, 2001 Apr 18; 2(4). PMID: 11305942    Free PMC article.
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.
Ron Edgar, Michael Domrachev, Alex E Lash.
Nucleic Acids Res, 2001 Dec 26; 30(1). PMID: 11752295    Free PMC article.
Highly Cited.
Oligonucleotide arrays for high-throughput SNPs detection in the MHC class I genes: HLA-B as a model system.
Zhen Guo, Mark S Gatterman, +2 authors, Effie W Petersdorf.
Genome Res, 2002 Mar 05; 12(3). PMID: 11875033    Free PMC article.
Single nucleotide polymorphism seeking long term association with complex disease.
Brian W Kirk, Matthew Feinsod, +2 authors, Francis Barany.
Nucleic Acids Res, 2002 Jul 26; 30(15). PMID: 12140314    Free PMC article.
Microarray results: how accurate are they?
Ravi Kothapalli, Sean J Yoder, Shrikant Mane, Thomas P Loughran.
BMC Bioinformatics, 2002 Aug 27; 3. PMID: 12194703    Free PMC article.
Exo-proofreading, a versatile SNP scoring technology.
Patrick Cahill, Michele Bakis, +6 authors, Douglas R Smith.
Genome Res, 2003 Apr 16; 13(5). PMID: 12695330    Free PMC article.
Genome informatics: current status and future prospects.
Raimond L Winslow, Mark S Boguski.
Circ Res, 2003 May 17; 92(9). PMID: 12750305    Free PMC article.
Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study.
Wuxiong Cao, Charles Epstein, +16 authors, Asher Zilberstein.
BMC Genomics, 2004 Apr 29; 5(1). PMID: 15113399    Free PMC article.
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information.
Yian A Chen, David J McKillen, +5 authors, Jonas S Almeida.
BMC Bioinformatics, 2004 Dec 09; 5. PMID: 15585062    Free PMC article.
Metabolic engineering in the -omics era: elucidating and modulating regulatory networks.
Goutham N Vemuri, Aristos A Aristidou.
Microbiol Mol Biol Rev, 2005 Jun 10; 69(2). PMID: 15944454    Free PMC article.
A multivariate prediction model for microarray cross-hybridization.
Yian A Chen, Cheng-Chung Chou, +5 authors, Jonas S Almeida.
BMC Bioinformatics, 2006 Mar 03; 7. PMID: 16509965    Free PMC article.
Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes?
Naftali Kaminski, Ivan O Rosas.
Proc Am Thorac Soc, 2006 Jun 02; 3(4). PMID: 16738198    Free PMC article.
Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions.
M T Horne, D J Fish, A S Benight.
Biophys J, 2006 Sep 12; 91(11). PMID: 16963510    Free PMC article.
Nanoliter high throughput quantitative PCR.
Tom Morrison, James Hurley, +9 authors, Colin J H Brenan.
Nucleic Acids Res, 2006 Sep 27; 34(18). PMID: 17000636    Free PMC article.
Microarray-based analysis of ventilator-induced lung injury.
Mark M Wurfel.
Proc Am Thorac Soc, 2007 Jan 05; 4(1). PMID: 17202295    Free PMC article.
Microarray-based DNA resequencing using 3' blocked primers.
Jakub Sram, Steve S Sommer, Qiang Liu.
Anal Biochem, 2007 Nov 21; 374(1). PMID: 18023400    Free PMC article.
Application of DNA array technology for diagnostic microbiology.
S A Booth, M A Drebot, G A Tipples, L K Ng.
Can J Infect Dis, 2007 Dec 27; 11(6). PMID: 18159302    Free PMC article.
In silico approach to identify the expression of the undiscovered molecules from microarray public database: identification of odorant receptors expressed in non-olfactory tissues.
Atsuhiko Ichimura, Tadashi Kadowaki, +3 authors, Gozoh Tsujimoto.
Naunyn Schmiedebergs Arch Pharmacol, 2008 Jan 30; 377(2). PMID: 18228002
A copula method for modeling directional dependence of genes.
Jong-Min Kim, Yoon-Sung Jung, +3 authors, Insuk Sohn.
BMC Bioinformatics, 2008 May 02; 9. PMID: 18447957    Free PMC article.
Making a new technology work: the standardization and regulation of microarrays.
Susan Rogers, Alberto Cambrosio.
Yale J Biol Med, 2008 May 02; 80(4). PMID: 18449388    Free PMC article.
Translational bioinformatics: coming of age.
Atul J Butte.
J Am Med Inform Assoc, 2008 Aug 30; 15(6). PMID: 18755990    Free PMC article.
Gene expression profiling of breast cancer.
Ting Bao, Nancy E Davidson.
Adv Surg, 2008 Oct 29; 42. PMID: 18953822    Free PMC article.
Real-time, multiplexed electrochemical DNA detection using an active complementary metal-oxide-semiconductor biosensor array with integrated sensor electronics.
Peter M Levine, Ping Gong, Rastislav Levicky, Kenneth L Shepard.
Biosens Bioelectron, 2008 Dec 05; 24(7). PMID: 19054661    Free PMC article.
Differential gene expression in vertebrate embryos.
Igor B Dawid.
J Biol Chem, 2009 Jan 23; 284(20). PMID: 19158075    Free PMC article.
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Michael Dondrup, Stefan P Albaum, +14 authors, Alexander Goesmann.
BMC Bioinformatics, 2009 Feb 10; 10. PMID: 19200358    Free PMC article.
Translational bioinformatics applications in genome medicine.
Atul J Butte.
Genome Med, 2009 Jul 02; 1(6). PMID: 19566916    Free PMC article.
Disease signatures are robust across tissues and experiments.
Joel T Dudley, Robert Tibshirani, Tarangini Deshpande, Atul J Butte.
Mol Syst Biol, 2009 Sep 17; 5. PMID: 19756046    Free PMC article.
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.
Erdem Arslan, Ian J Laurenzi.
BMC Bioinformatics, 2009 Dec 17; 10. PMID: 20003312    Free PMC article.
Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.
David Gresham, Bo Curry, +4 authors, David Botstein.
Proc Natl Acad Sci U S A, 2010 Jan 19; 107(4). PMID: 20080586    Free PMC article.
Simple PCR-based DNA microarray system to identify human pathogenic fungi in skin.
Tomotaka Sato, Atsushi Takayanagi, +7 authors, Nobuyoshi Shimizu.
J Clin Microbiol, 2010 Apr 28; 48(7). PMID: 20421438    Free PMC article.
Metabolomics in premature labor: a novel approach to identify patients at risk for preterm delivery.
Roberto Romero, Shali Mazaki-Tovi, +10 authors, Chris Beecher.
J Matern Fetal Neonatal Med, 2010 May 28; 23(12). PMID: 20504069    Free PMC article.
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions.
Rong Chen, Tara K Sigdel, +11 authors, Atul J Butte.
PLoS Comput Biol, 2010 Oct 05; 6(9). PMID: 20885780    Free PMC article.
Discovery and preclinical validation of drug indications using compendia of public gene expression data.
Marina Sirota, Joel T Dudley, +5 authors, Atul J Butte.
Sci Transl Med, 2011 Aug 19; 3(96). PMID: 21849665    Free PMC article.
Highly Cited.
Overview of DNA microarrays: types, applications, and their future.
Roger Bumgarner.
Curr Protoc Mol Biol, 2013 Jan 05; Chapter 22. PMID: 23288464    Free PMC article.
Snord 3A: a molecular marker and modulator of prion disease progression.
Eran Cohen, Dana Avrahami, +9 authors, Ruth Gabizon.
PLoS One, 2013 Jan 26; 8(1). PMID: 23349890    Free PMC article.
Cancer-testis antigens PRAME and NY-ESO-1 correlate with tumour grade and poor prognosis in myxoid liposarcoma.
Kunio Iura, Kenichi Kohashi, +6 authors, Yoshinao Oda.
J Pathol Clin Res, 2016 Aug 09; 1(3). PMID: 27499900    Free PMC article.
"Multi-Omics" Analyses of the Development and Function of Natural Killer Cells.
Yonggang Zhou, Xiuxiu Xu, Zhigang Tian, Haiming Wei.
Front Immunol, 2017 Sep 21; 8. PMID: 28928751    Free PMC article.
The use of high-dimensional biology (genomics, transcriptomics, proteomics, and metabolomics) to understand the preterm parturition syndrome.
R Romero, J Espinoza, +7 authors, G Tromp.
BJOG, 2007 Jan 09; 113 Suppl 3. PMID: 17206980    Free PMC article.