| References |
|
|
Babak T,
Zhang W,
Morris Q et al.
(2004)
Probing microRNAs with microarrays: tissue specificity and functional inference.
RNA
10(11):
1813–1819.
|
|
|
Barbarotto E,
Secchiero P,
Dasgupta A et al.
(2008)
MicroRNAs as new players in the genomic galaxy and disease puzzles.
Clinical and Translational Science
1:
23–29.
|
|
|
Barrett T,
Troup DB,
Wilhite SE et al.
(2007)
NCBI GEO: mining tens of millions of expression profiles–database and tools update.
Nucleic Acids Research
35(Database issue):
D760–D765.
|
|
|
Brazma A,
Hingamp P,
Quackenbush J et al.
(2001)
Minimum information about a microarray experiment (MIAME) – toward standards for microarray data.
Nature Genetics
29(4):
365–371.
|
|
|
Caldwell MD,
Awad T,
Johnson JA et al.
(2008)
CYP4F2 genetic variant alters required warfarin dose.
Blood
111(8):
4106–4112.
|
|
|
Carter NP
(2007)
Methods and strategies for analyzing copy number variation using DNA microarrays.
Nature Genetics
39:
S16–S21.
|
|
|
Chance PF,
Abbas N,
Lensch MW et al.
(1994)
Two autosomal dominant neuropathies result from reciprocal DNA duplication/deletion of a region on chromosome 17.
Human Molecular Genetics
3:
223–228.
|
|
|
Chee M,
Yang R,
Hubbell E et al.
(1996)
Accessing genetic information with high-density DNA arrays.
Science
274(5287):
610–614.
|
|
|
Cheung VG,
Gregg JP,
Gogoli-Ewens KJ et al.
(1998)
Linkage-disequilibrium mapping without genotyping.
Nature Genetics
18(3):
225–230.
|
|
|
Cooper GM,
Nickerson DA and
Eichler EE
(2007)
Mutational and selective effects on copy-number variants in the human genome.
Nature Genetics
39:
S22–S29.
|
|
|
Cowie S,
Drmanac S,
Swanson D et al.
(2004)
Identification of APC gene mutations in colorectal cancer using universal microarray-based combinatorial sequencing-by-hybridization.
Human Mutation
24(3):
261–271.
|
|
|
Cronin MT,
Fucini SMK,
Masino RS et al.
(1996)
Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays.
Human Mutation
7(3):
244–255.
|
|
|
book
Drmanac R and
Drmanac S
(1999)
"cDNA screening by array hybridization".
In: Weissman SM (ed.)
Methods in Enzymology,
vol. 303,
pp. 165–178.
San Diego: Academic Press.
|
|
|
Drobyshev A,
Mologina N,
Shik V et al.
(1997)
Sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations.
Gene
188(1):
45–52.
|
|
|
Eberwine J
(1996)
Amplification of mRNA populations using a RNA generated from immobilized oligo(dT)-T7 primed cDNA.
Biotechniques
20(4):
584–591.
|
|
|
book
Eisen MB and
Brown PO
(1999)
"DNA arrays for analysis of gene expression".
In: Weissman SM (ed.)
Methods in Enzymology,
303,
pp. 179–205.
San Diego: Academic Press.
|
|
|
Ekins RP and
Chu FW
(1991)
Multianalyte microspot immunoassay – microanalytical “compact disk” of the future.
Clinical Chemistry
37(11):
1955–1967.
|
|
|
English SB and
Butte AJ
(2007)
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes.
Bioinformatics
23(21):
2910–2917.
|
|
|
Estivill X and
Armengol L
(2007)
Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies.
PLoS Genetics
3:
1787–1799.
|
|
|
Fan YS,
Jayakar P,
Zhu H et al.
(2007)
Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization.
Human Mutation
28:
1124–1132.
|
|
|
Feuk L,
Carson AR and
Scherer SW
(2006)
Structural variation in the human genome.
Nature Reviews. Genetics
7:
85–97.
|
|
|
Fodor SP,
Read JL,
Pirrung MC et al.
(1991)
Light-directed, spatially addressable parallel chemical synthesis.
Science
251(4995):
767–773.
|
|
|
Freeman JL,
Perry GH,
Feuk L et al.
(2006)
Copy number variation: new insights in genome diversity.
Genome Research
16:
949–961.
|
|
|
Gerry NP,
Witowski NE,
Day J et al.
(1999)
Universal DNA microarray method for multiplex detection of low abundance point mutations.
Journal of Molecular Biology
292(2):
251–262.
|
|
|
Golub TR,
Slonim DK,
Tamayo P et al.
(1999)
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.
Science
286(5439):
531–537.
|
|
|
Grant GR,
Manduchi E and
Stoeckert CJ Jr
(2007)
Analysis and management of microarray gene expression data.
Current Protocols Molecular Biology
Supplement 77: 19.6.1.
|
|
|
Greshock J,
Feng B,
Nogueira C et al.
(2007)
A comparison of DNA copy number profiling platforms.
Cancer Research
67:
10173–10180.
|
|
|
Gunderson KL,
Huang XC,
Morris MS et al.
(1998)
Mutation detection by ligation to complete n-mer DNA arrays.
Genome Research
8(11):
1142–1153.
|
|
|
Hacia JG,
Brody LC,
Chee MS et al.
(1996)
Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays, two color fluorescence analysis.
Nature Genetics
14(4):
441–447.
|
|
|
Hanahan D and
Meselson M
(1980)
Plasmid screening at high colony density.
Gene
10(1):
63–67.
|
|
|
Hardenbol P,
Banér J,
Jain M et al.
(2003)
Multiplexed genotyping with sequence-tagged molecular inversion probes.
Nature Biotechnology
21(6):
673–678.
|
|
|
Hehir-Kwa JY,
Egmont-Petersen M,
Janssen IM et al.
(2007)
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.
DNA Research
14(1):
1–11.
|
|
|
Heller MJ,
Forster AH and
Tu E
(2000)
Active microeletronic chip devices which utilize controlled electrophoretic fields for multiplex DNA hybridization and other genomic applications.
Electrophoresis
21(1):
157–164.
|
|
|
Khrapko KR,
Lysov YuP,
Khorlin AA et al.
(1991)
A method for DNA sequencing by hybridization with oligonucleotide matrix.
DNA Sequence
1(6):
375–388.
|
|
|
Kim VN and
Nam JW
(2006)
Genomics of microRNA.
Trends in Genetics
22(3):
165–173.
|
|
|
Koltai H and
Weingarten-Baror C
(2008)
Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction.
Nucleic Acids Research
36(7):
2395–2405.
|
|
|
Kozal MJ,
Shah N,
Shen N et al.
(1996)
Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays.
Nature Medicine
2(7):
753–759.
|
|
|
Landegren U,
Nilsson M and
Kwok P-Y
(1998)
Reading bits of genetic information: methods for single-nucleotide polymorphism analysis.
Genome Research
8(8):
769–776.
|
|
|
Lemmo AV,
Rose DJ and
Tisone TC
(1998)
Inkjet dispensing technology: applications in drug discovery.
Current Opinion in Biotechnology
9(6):
615–617.
|
|
|
Lindroos K,
Sigurdsson S,
Johansson K et al.
(2002)
Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system.
Nucleic Acids Research
30(14):
e70.
|
|
|
Liu CG,
Calin GA,
Meloon B et al.
(2004)
An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues.
Proceeding of the National Academy of Science of the USA
101(26):
9740–9744.
|
|
|
Livache T,
Bazin H,
Caillat P and
Roget A
(1998)
Electroconducting polymers for the construction of DNA or peptide arrays on silicon chips.
Biosensors & Bioelectronics
13(6):
629–634.
|
|
|
Lockhart DJ,
Dong H,
Byrne MC et al.
(1996)
Expression monitoring by hybridization to high-density oligonucleotide arrays.
Nature Biotechnology
14(13):
1675–1680.
|
|
|
Lu J,
Getz G,
Miska EA et al.
(2005)
MicroRNA expression profiles classify human cancers.
Nature
435(7043):
834–838.
|
|
|
Lucito R,
Healy J,
Alexander J et al.
(2003)
Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation.
Genome Research
13:
2291–2305.
|
|
|
MAQC Consortium,
Shi L,
Reid LH et al.
(2006)
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
Nature Biotechnology
24(9):
1151–1161.
|
|
|
Matson RS,
Rampal JB and
Coassin PJ
(1994)
Biopolymer synthesis on polypropylene supports. I. Oligonucleotides.
Analytical Biochemistry
217(2):
306–310.
|
|
|
McCarthy JJ and
Hilfiker R
(2000)
The use of single-nucleotide polymorphism maps in pharmacogenomics.
Nature Biotechnology
18(5):
505–508.
|
|
|
other
Molinari RJ
(1999) Flexible DNA chips for DNA microarrays. IBC's 6th Annual Biochip Technology Conference: Chips to Hit ‘99. November 2–5, Berkeley, CA. Vol. II, IBC, Southborough, MA, USA.
|
|
|
Nelson PT,
Baldwin DA,
Scearce LM et al.
(2004)
Microarray-based, high-throughput gene expression profiling of microRNAs.
Nature Methods
1(2):
55–61.
|
|
|
Nilsson M,
Malmgren H,
Samiotaki M et al.
(1994)
Padlock probes: circularizing oligonucleotides for localized DNA detection.
Science
265(5181):
2085–2088.
|
|
|
O'Donnell-Maloney MJ and
Little DP
(1996)
Microfabrication and array technologies for DNA sequencing and diagnostics.
Genetic Analysis
13(6):
151–157.
|
|
|
Okamoto T,
Suzuki T and
Yamamoto N
(2000)
Microarray fabrication with covalent attachment of DNA using Bubble Jet technology.
Nature Biotechnology
18:
438–441.
|
|
|
Pease AC,
Solas D,
Sullivan EJ et al.
(1994)
Light-generated oligonucleotide arrays for rapid DNA sequence analysis.
Proceedings of the National Academy of Sciences of the USA
91(11):
5022–5026.
|
|
|
Perry GH,
Tchinda J,
McGrath SD et al.
(2006)
Hotspots for copy number variation in chimpanzees and humans.
Proceeding of the National Academy of Science of the USA
103:
8006–8011.
|
|
|
Pinkel D,
Segraves R,
Sudar D et al.
(1998)
High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.
Nature Genetics
20(2):
207–211.
|
|
|
Pollack JR,
Perou CM,
Alizadeh AA et al.
(1999)
Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
Nature Genetics
23(1):
41–46.
|
|
|
Rayner TF,
Rezwan FI,
Lukk M et al.
(2009)
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB.
Bioinformatics
25(2):
279–280.
|
|
|
Redon R,
Ishikawa S,
Fitch KR et al.
(2006)
Global variation in copy number in the human genome.
Nature
444:
444–454.
|
|
|
Roda A,
Musiani M,
Pasini P et al.
(2000)
In situ hybridization and immunohistochemistry with enzyme-triggered chemiluminescent probes.
Methods Enzymology
305:
577–590.
|
|
|
Rodriguez-Revenga L,
Mila M,
Rosenberg C et al.
(2007)
Structural variation in the human genome: the impact of copy number variants on clinical diagnosis.
Genetics Medicine
9:
600–606.
|
|
|
Schena M,
Shalon D,
Davis RW and
Brown PO
(1995)
Quantitative monitoring of gene expression patterns with a complementary DNA microarray.
Science
270(5235):
467–470.
|
|
|
Schirinzi A,
Drmanac S,
Dallapiccola B et al.
(2006)
Combinatorial sequencing-by-hybridization: analysis of the NF1 gene.
Genetic Testing
10(1):
8–17.
|
|
|
Schoumans J,
Ruivenkamp C,
Holmberg E et al.
(2005)
Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation. Array-CGH.
Journal of Medical Genetics
42:
699–705.
|
|
|
Sharp AJ,
Cheng Z and
Eichler EE
(2006)
Structural variation of the human genome.
Annual Review of Genomics and Human Genetics
7:
407–442.
|
|
|
Sharp AJ,
Locke DP,
McGrath SD et al.
(2005)
Segmental duplications and copy-number variation in the human genome.
American Journal of Human Genetics
77:
78–88.
|
|
|
Shaw CJ,
Bi W and
Lupski JR
(2002)
Genetic proof of unequal meiotic crossovers in reciprocal deletion and duplication of 17p11.2.
American Journal of Human Genetics
71:
1072–1081.
|
|
|
Shumaker JM,
Metspalu A and
Caskey CT
(1996)
Mutation detection by solid phase primer extension.
Human Mutation
7(4):
346–354.
|
|
|
Singh-Gasson S,
Green RD,
Yue Y et al.
(1999)
Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array.
Nature Biotechnology
17(10):
974–978.
|
|
|
Southern EM,
Maskos U and
Elder JK
(1992)
Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models.
Genomics
13(4):
1008–1017.
|
|
|
Spellman PT,
Miller M,
Stewart J et al.
(2002)
Design and implementation of microarray gene expression markup language (MAGE-ML).
Genome Biology
3(9): RESEARCH0046.
|
|
|
Stankiewicz P and
Lupski JR
(2002)
Genome architecture, rearrangements and genomic disorders.
Trends in Genetics
18:
74–82.
|
|
|
Stillman BA and
Tonkinson JL
(2000)
FAST slides: a novel surface for microarrays.
Biotechniques
29(3):
630–635.
|
|
|
Trask BJ,
Friedman C,
Martin-Gallardo A et al.
(1998)
Members of the olfactory receptor gene family are contained in large blocks of DNA duplicated polymorphically near the ends of human chromosomes.
Human Molecular Genetics
7:
13–26.
|
|
|
Veltman JA
(2006)
Genomic microarrays in clinical diagnosis.
Current Opinion in Pediatrics
18:
598–603.
|
|
|
Whetzel PL,
Parkinson H,
Causton HC et al.
(2006)
The MGED Ontology: a resource for semantics-based description of microarray experiments.
Bioinformatics
22(7):
866–873.
|
|
|
Winzeler EA,
Shoemaker DD,
Astromoff A et al.
(1999)
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
Science
285(5429):
901–906.
|
|
|
Wong KK,
deLeeuw RJ,
Dosanjh NS et al.
(2007)
A comprehensive analysis of common copy-number variations in the human genome.
American Journal of Human Genetics
80:
91–104.
|
| Further Reading |
|
|
Cahan P,
Rovegno F,
Mooney D et al.
(2007)
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization.
Gene
401(1–2):
12–18.
|
|
|
Colantuoni C,
Henry G,
Zeger S et al.
(2002)
SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.
Bioinformatics
18(11):
1540–1541.
|
|
|
Hoheisel JD
(2006)
Microarray technology: beyond transcript etprofiling and genotype analysis.
Nature Reviews. Genetics
7(3):
200–210.
|
|
|
Simon R
(2008)
Challenges of microarray data and the evaluation of gene expression profile signatures.
Cancer Investigation
26(4):
327–332.
|
|
|
Yauk CL and
Berndt ML
(2007)
Review of the literature examining the correlation among DNA microarray technologies.
Environmental and Molecular Mutagenesis
48(5):
380–394.
|
