We have some DNA samples that I would like to run whole genome sequencing on. Unfortunately these samples only contain very little DNA (too little for WGS). It has then been suggested to do whole genome amplification of the DNA before sequencing. This approach is commonly used before doing genotyping of a specific SNP.
Do you think that the pre-amplification will create a lot of bias in the seqeuncing (i.e generate many false postive genotype call, indell calls, CNV, etc.)?
Another approach could be to do single cell sequencing. What are the pros and cons when applying this?
Thanks a lot for any comments!
best wishes, Thomas
Thanks to all the comments/concerns you have provided below. This is indeed very helpfull. I will talk to the lab about applying MALBAC to small amounts of DNA (not single Cell). If anyone has hands on experience with MALBAC I would very much like more comments. Thanks again. Thomas
MALBAC is pretty recent...the paper was only published at the end of last year, and I first heard of it about two months ago. It may be hard to track down people with hands on experience outside of the lab that developed the technique.