Overview of available platforms for large-scale analysis of DNA methylation
| Technology . | Applications . | Advantages . | Limitations . | References . |
|---|---|---|---|---|
| Illumina bead arrays | Methylation polymorphism discovery and analysis | Quantitative | Requires design of a primer library | (Bibikova et al., 2006a; Bibikova et al., 2006b; Fan et al., 2006) |
| Rapid analysis of up to 96 samples | Only 1536 sites can be assayed simultaneously | |||
| Affymetrix arrays | Whole-genome methylation mapping | High feature density | Short oligonucleotide probes produce noisier data | (Dalma-Weiszhausz et al., 2006; Schumacher et al., 2006; Zhang et al., 2006) |
| Readily available mouse, human and Arabidopsis arrays | `Single channel' hybridization | |||
| Accessible to researchers with access to a microarray facility | Custom arrays prohibitively expensive | |||
| Reasonable price | ||||
| NimbleGen arrays | Whole-genome methylation mapping | Long oligonucleotide probes produce cleaner data | Lower feature density than Affymetrix | (Khulan et al., 2006; Nuwaysir et al., 2002; Weber et al., 2007; Zilberman et al., 2007) |
| `Dual channel' hybridization | ||||
| Inexpensive custom arrays | ||||
| Hybridization available as a service at a reasonable price | ||||
| Agilent arrays | Large-scale methylation mapping | Long oligonucleotide probes produce cleaner data | Substantially lower feature density than Affymetrix and NimbleGen | (Wolber et al., 2006) |
| `Dual channel' hybridization | ||||
| Solexa sequencing | Whole-genome methylation mapping | Quantitative | New technology | (Barski et al., 2007; Bentley, 2006) |
| Analysis of imprinted loci | Does not require hybridization | Requires purchase of an expensive instrument | ||
| Concurrent genotype information |
| Technology . | Applications . | Advantages . | Limitations . | References . |
|---|---|---|---|---|
| Illumina bead arrays | Methylation polymorphism discovery and analysis | Quantitative | Requires design of a primer library | (Bibikova et al., 2006a; Bibikova et al., 2006b; Fan et al., 2006) |
| Rapid analysis of up to 96 samples | Only 1536 sites can be assayed simultaneously | |||
| Affymetrix arrays | Whole-genome methylation mapping | High feature density | Short oligonucleotide probes produce noisier data | (Dalma-Weiszhausz et al., 2006; Schumacher et al., 2006; Zhang et al., 2006) |
| Readily available mouse, human and Arabidopsis arrays | `Single channel' hybridization | |||
| Accessible to researchers with access to a microarray facility | Custom arrays prohibitively expensive | |||
| Reasonable price | ||||
| NimbleGen arrays | Whole-genome methylation mapping | Long oligonucleotide probes produce cleaner data | Lower feature density than Affymetrix | (Khulan et al., 2006; Nuwaysir et al., 2002; Weber et al., 2007; Zilberman et al., 2007) |
| `Dual channel' hybridization | ||||
| Inexpensive custom arrays | ||||
| Hybridization available as a service at a reasonable price | ||||
| Agilent arrays | Large-scale methylation mapping | Long oligonucleotide probes produce cleaner data | Substantially lower feature density than Affymetrix and NimbleGen | (Wolber et al., 2006) |
| `Dual channel' hybridization | ||||
| Solexa sequencing | Whole-genome methylation mapping | Quantitative | New technology | (Barski et al., 2007; Bentley, 2006) |
| Analysis of imprinted loci | Does not require hybridization | Requires purchase of an expensive instrument | ||
| Concurrent genotype information |