Abstract
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 COM 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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 528-542 |
| Number of pages | 15 |
| Journal | Nucleic Acids Research |
| Volume | 34 |
| Issue number | 2 |
| DOIs | |
| State | Published - Feb 2006 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Genetics
Cite this
Microarray-based DNA methylation profiling : Technology and applications. / Schumacher, Axel; Kapranov, Philipp; Kaminsky, Zachary A; Flanagan, James; Assadzadeh, Abbas; Yau, Patrick; Virtanen, Carl; Winegarden, Neil; Cheng, Jill; Gingeras, Thomas; Petronis, Arturas.
In: Nucleic Acids Research, Vol. 34, No. 2, 02.2006, p. 528-542.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Microarray-based DNA methylation profiling
T2 - Technology and applications
AU - Schumacher, Axel
AU - Kapranov, Philipp
AU - Kaminsky, Zachary A
AU - Flanagan, James
AU - Assadzadeh, Abbas
AU - Yau, Patrick
AU - Virtanen, Carl
AU - Winegarden, Neil
AU - Cheng, Jill
AU - Gingeras, Thomas
AU - Petronis, Arturas
PY - 2006/2
Y1 - 2006/2
N2 - 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 COM 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.
AB - 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 COM 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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UR - http://www.scopus.com/inward/citedby.url?scp=32644448942&partnerID=8YFLogxK
U2 - 10.1093/nar/gkj461
DO - 10.1093/nar/gkj461
M3 - Article
C2 - 16428248
AN - SCOPUS:32644448942
VL - 34
SP - 528
EP - 542
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 1362-4962
IS - 2
ER -