So many ways to analyze genomic DNA methylation, so little time (and money). With so many choices available these days it’s not easy to figure out the best method to use for methylome studies. A new survey of two Nature Biotechnology papers by Stephan Beck from the UK’s University College London puts together the vital stats from head-to-head comparisons, and gives you all of the pros and cons.
Beck compiled the results from two studies that were part of the International Human Epigenome Project, which compared six methylome analysis techniques with an eye towards finding methods to help create accurate reference methylomes for the effort, and pulled out the key features for each. Both papers (Nature Biotechnology, October 2010 Bock et al. and Nature Biotechnolgy, October 2010 Harris et al.) were also featured in this month’s Nature Biotechnolgy issue. The six methods tested were MethylC-seq, MeDIP-seq, MethylCap-seq, MBD-seq, RRBS and Infinium and they were assessed in several categories including:
- Genomic DNA Used– Anywhere from 0.03ug to 5ug
- Readout– Five were sequencing based, one was array based
- Assay– 3 use bisulfite conversion, the rest use antibody, or MBD affinity reagents
- Resolution– Ranging from 1bp to 100-1000bps
- Coverage– Most can cover the whole genome, but RRBS (~10%) and Infinium (~0.1%) are designed to look at only certain areas.
- Cost– Anywhere from $200 for an Infinium array to $20-100k for full coverage MethylC-seq.
The good news is that all methods showed good concordance with the others (anywhere from 84-100%), so you will probably get high quality results regardless of your methylome weapon of choice. Now that we know that performance is probably not an issue, and it no longer costs a king’s ransom to run, researchers are free to choose whatever methylome analysis method they like, or that works best for their particular lab.
If you’re looking to tame the methylome for yourself, check out Dr. Beck’s review, as well as the individual studies at Nature Biotechnology, October 2010 Beck. Most of the work has already been done for you, so what do you have to lose?