Hi SEQanswer community,
Firstly, hi everyone, I'm so glad that I've found this forum. I'm currently doing a research project where I compare different technology on detecting different types of mutations from single cells.
Detection of gene deletions/duplications from single cells is quite difficult using conventional methods and I am interested to see whether next-gen would be good at it. I am planning to whole genome amplify my single cell, do a PCR on my gene of interest and send my samples off for library generation and sequencing. (We do not have a sequencer in our lab and we'll be sending them to another lab to be put in an Ion Torrent sequencer.)
My question is that would next-gen be able to detect these duplications/deletions? Especially, heterozygous deletions. I've read some papers where they mention that it is possible to detect them by means of normalised depth of coverage and split-read analysis but it would be great if you can give some more insights. Also, do you think just carrying out a targetted PCR will be OK or do I need to follow a different route? Thanks a lot.
Firstly, hi everyone, I'm so glad that I've found this forum. I'm currently doing a research project where I compare different technology on detecting different types of mutations from single cells.
Detection of gene deletions/duplications from single cells is quite difficult using conventional methods and I am interested to see whether next-gen would be good at it. I am planning to whole genome amplify my single cell, do a PCR on my gene of interest and send my samples off for library generation and sequencing. (We do not have a sequencer in our lab and we'll be sending them to another lab to be put in an Ion Torrent sequencer.)
My question is that would next-gen be able to detect these duplications/deletions? Especially, heterozygous deletions. I've read some papers where they mention that it is possible to detect them by means of normalised depth of coverage and split-read analysis but it would be great if you can give some more insights. Also, do you think just carrying out a targetted PCR will be OK or do I need to follow a different route? Thanks a lot.