Below you can find an overview of frequently asked questions about our technology and services
1) How does MBD-based sequencing compare to MeDIP?
MeDIP uses antibodies to pick up methylated C’s independent from CpG context. This results in picking up a lot of biologically irrelevant methylated Cs or regions. MBD-based sequencing on the other hand uses the MBD of the NuRD complex. This complex plays a crucial role in living cells since it triggers chromatin remodeling resulting in the actual silencing of DNA regions.
Secondly MBD-based sequencing focuses more on CpG dense regions instead of individual methylated Cs like MeDIP does. Since silencing occurs in densily methylated regions instead of at individual methylated C-sites, MBD-based sequencing picks up the biologically relevant sites which is not the case for MeDIP.
Thirdly after comparison we have seen that MBD-based sequencing is 100 times more sensitive than MeDIP.
Finally we have compared our MBD-based sequencing approach to BSS. This has shown that more than 95% of the info found with BSS is also found with our MBD-based sequencing approach.
2) What is included in your offering?
Our offering includes everything from sample shipment to data delivery. This means that we send our customers a sampling kit in which they can ship their samples to our lab in Belgium, paid by NXT-Dx. Upon delivery the samples are checked for quality and sonicated. Afterwards MBD-capture, library prep and sequencing are performed. The bio-informatics services entail cleansing and mapping. The data will be delivered on the one hand as raw data on a hard disk and on the other hand through our Genome Browser software, which allows easy visualization and analysis of your results.
3) What do we need to provide to NXT-Dx?
The only thing that our customers need to provide is 500ng of genomic DNA in a maximum volume of 75µl. The DNA quality should be checked preferably using a fluorescence-based quantitation method (e.g. using the quant-it picogreen dsDNA assay kit -Invitrogen-). UV spectrometer methods (based on 260 OD readings) are prone to overestimate genomic DNA concentration due to the presence of RNA and other contaminants commonly found in genomic DNA preparations. All plastic ware should be DNase-free and Lo-bind !
4) How much time does it take to analyze my samples?
The entire process usually takes around 1,5 months.
5) Are there any papers available on the MBD-based sequencing technology used by NXT-Dx?
For the moment several papers discussing the technology are being reviewed.
6) Does NXT-Dx offer genome-wide bisulfite sequencing (BSS)?
NXT-Dx has not yet performed full genome BSS experiments. However NXT-Dx can offer customers the possibility to do this if this is absolutely necessary. NXT-Dx would not advise customers to take this approach since genome-wide BSS remains very expensive until this date (tens of thousands of euros per samples). NXT-Dx advises customers to do MBD-based genome-wide methylation sequencing, since this technology finds more than 95% of the information found by BSS and is much more economical. Afterwards if needed customers can validate their results by region-specific BSS for their regions/genes of interest. This approach will give customers the same end result but for much lower cost.
7) What coverage can I expect if NXT-Dx performs MBD-based sequencing on my samples?
Customers can chose between 10 million unmapped paired end reads per sample and 20 million unmapped paired end reads per sample. If customers, for a very specific reason, want to have a higher coverage for their samples, this can be discussed. However keep in mind that this results in a higher cost price per sample.