Distortion of quantitative genomic and expression hybridization by Cot-1 DNA: Mitigation of this effect

Nucleic Acids Research

Volumn 33, Issue 22, 2005, Pages

  Newkirk, Heather L ^a   Knoll, Joan H M ^a   Rogan, Peter K ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; REPETITIVE DNA;

ARTICLE; CONTROLLED STUDY; CROSS HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION; GENE PROBE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC VARIABILITY; MEASUREMENT; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY;

DNA; GENE EXPRESSION PROFILING; GENOMICS; MICROSPHERES; NUCLEIC ACID HYBRIDIZATION; NUCLEIC ACID PROBES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS;

EID: 31144444397     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni190     Document Type: Article

References (18)

1. Oostlander,A., Meijer,G. and Ylstra,B. (2004) Microarray-based comparative genomic hybridization and its applications in human genetics. Clin. Genet., 66, 488-495.
2. van Hijum,S.A., de Jong,A., Baerends,R.J., Karsens,H.A., Kramer,N.E., Larsen,R., den Hengst,C.D., Albers,C.J., Kok,J. and Kuipers,O.P. (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics, 6, 77.
3. Bammler,T., Beyer,R.P., Bhattacharya,S., Boorman,G.A., Boyles,A., Bradford,B.U., Bumgarner,R.E., Bushel,P.R., Chaturvedi,K., Choi,D. et al. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods, 2, 351-356.
4. Sherlock,G. (2005) Of FISH and chips. Nature Methods, 2, 329-330.
5. Dobbin,K.K., Beer,D.G., Meyerson,M., Yeatman,T.J., Gerald,W.L., Jacobson,J.W., Conley,B., Buetow,K.H., Heiskanen,M., Simon,R.M. et al. (2005) Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin. Cancer Res., 11, 565-572.
6. Li,X., Weikuan,G., Mohan,S. and Baylink,D. (2002) DNA microarrays: Their use and misuse. Microcirculation, 9, 13-22.
7. Wren,J., Kulkarni,A., Joslin,J., Butow,R. and Garner,H. (2002) Cross-hybridization on PCR-spotted microarrays. IEEE Eng. Med. Biol., 71-75.
8. Marshall,E. (2004) Getting the noise out of gene arrays. Science, 306, 630-631.
9. Zakharkin,S., Kim,K., Mehta,T., Chen,L., Barnes,S., Scheirer,K., Parrish,R., Allison,D. and Page,G. (2005) Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics, 6, 214-225.
10. Britten,R. and Kohne,D. (1968) Repeated sequences in DNA. Science, 161, 529-540.
11. Rogan,P.K., Pan,J. and Weissman,S.M. (1987) L1 repeat elements in the human epsilon-G gamma globin gene intergenic region: Sequence analysis and concerted evolution within this family. Mol. Biol. Evol., 4, 327-42.
12. Carter,N., Fiegler,H. and Piper,J. (2002) Comparative analysis of comparative genomic hybridization microarray technologies: Report of a workshop sponsored by the Wellcome Trust. Cytometry, 49, 43-48.
13. Rogan,P., Cazcarro,P. and Knoll,J. (2001) Sequence-based design of single-copy genomic DNA probes for fluorescence in situ hybridization. Genome Res., 11, 1086-1094.
14. Rogan,P. and Knoll,J. (2003) Sequence-based in situ detection of chromosomal abnormalities at high resolution. Am. J. Med. Genet., 121, 245-257.
15. Knoll,J.H.M. and Rogan,P.K. (2004) US Patent 6,828,097.
16. Knoll,J. and Lichter,P. (2005) In situ hybridization to metaphase chromosomes and interphase nuclei. In Dracopoli,N., Haines,J., Korf,B., Moir,D., Morton,C., Seidman,C., Seidman,J. and Smith,D. (eds), Current Protocols in Human Genetics. Green-Wiley, NY, Vol. 1, Unit 4.3.
17. Kent,W. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
18. Dong,S., Wang,E., Hsie,L., Cao,Y., Chen,X. and Gingeras,T.R. (2001) Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res., 11, 1418-1424.