The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Microarray-based DNA methylation profiling: technology and applications
Open accessAbstract
This work is dedicated to the development of a technology for unbiased, high-throughput DNA methylation profiling of large genomic regions. In this method, unmethylated and methylated DNA fractions are enriched using a series of treatments with methylation sensitive restriction enzymes, and interrogated on microarrays. We have investigated various aspects of the technology including its replicability, informativeness, sensitivity and optimal PCR conditions using microarrays containing oligonucleotides representing 100 kb of genomic DNA derived from the chromosome 22 COMT region in addition to 12 192 element CpG island microarrays. Several new aspects of methylation profiling are provided, including the parallel identification of confounding effects of DNA sequence variation, the description of the principles of microarray design for epigenomic studies and the optimal choice of methylation sensitive restriction enzymes. We also demonstrate the advantages of using the unmethylated DNA fraction versus the methylated one, which substantially improve the chances of detecting DNA methylation differences. We applied this methodology for fine-mapping of methylation patterns of chromosomes 21 and 22 in eight individuals using tiling microarrays consisting of over 340 000 oligonucleotide probe pairs. The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.
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Cites
CpG-rich islands and the function of DNA methylation
Bird, A. P. (1986) · Nature · doi:10.1038/321209a0 · Cited by 3,777
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Epigenetic Reprogramming in Mammalian Development
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A vision for the future of genomics research
Collins, F. S., Green, E. D., Guttmacher, A. E., Guyer, M. S., & on behalf of the US National Human Genome Research Institute (2003) · Nature · doi:10.1038/nature01626 · Cited by 1,752
The power and the promise of DNA methylation markers
Laird, P. W. (2003) · Nature Reviews Cancer · doi:10.1038/nrc1045 · Cited by 1,562
Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse
Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., Gingeras, T. R., et al. (2005) · Cell · doi:10.1016/j.cell.2005.01.001 · Cited by 1,527
Epigenetics: Regulation Through Repression
Wolffe, A. P., & Matzke, M. A. (1999) · Science · doi:10.1126/science.286.5439.481 · Cited by 1,239
Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. (2005) · Science · doi:10.1126/science.1108625 · Cited by 1,178
Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095
Cited by
DNA methylation landscapes: Provocative insights from epigenomics
Suzuki, M. M., & Bird, A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2341 · Cited by 3,039
High density DNA methylation array with single CpG site resolution
Bibikova, M., Barnes, B., Tsan, C., Ho, V., Klotzle, B., Le, J. M., Delano, D., Zhang, L., Schroth, G. P., Gunderson, K. L., et al. (2011) · Genomics · doi:10.1016/j.ygeno.2011.07.007 · Cited by 1,727
SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
Maksimovic, J., Gordon, L., & Oshlack, A. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r44 · Cited by 826
Epigenomic Profiling Reveals DNA-Methylation Changes Associated with Major Psychosis
Mill, J., Tang, T., Kaminsky, Z., Khare, T., Yazdanpanah, S., Bouchard, L., Jia, P., Assadzadeh, A., Flanagan, J., Schumacher, A., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.01.008 · Cited by 773
Self-citationDNA methylation profiles in monozygotic and dizygotic twins
Kaminsky, Z. A., Tang, T., Wang, S.-C., Ptak, C., Oh, G. H. T., Wong, A. H. C., Feldcamp, L. A., Virtanen, C., Halfvarson, J., Tysk, C., et al. (2009) · Nature Genetics · doi:10.1038/ng.286 · Cited by 668
Metadata
- Authors
- Schumacher, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-30
- Volume
- 34
- Issue
- 2
- Pages
- 528-542
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2104429441
- Cited by
- 294
- References
- 40
- FWCI
- 14.12
- Type
- journal article
- Language
- en
- Open access
- gold
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