Whole Genome Amplification for Cancer Study

[kenosaki]

I’d like to sequence the tumor sample that material is very limited amount. My goal is to find a structural variant like large inversion and deletion (translocation if possible) in a single tumor cell. The problem is that whole genome amplification by Multiple Displacement Amplification will produce many inversion false positives as this article says;

“Jiao et al., Structural Alterations from Multiple Displacement Amplification of a Human Genome Revealed by Mate-Pair Sequencing” (http://www.plosone.org/article/info%...l.pone.0022250)

Do you know any methods that are capable to amplify whole genomes with minimum conformational change in the sample genome?

Or shouldn’t I use the amplification method for structural analysis of genome?

I understand amplification bias is inevitable is these kind of technologies.

Best,
Ken

[kenosaki]

I found that MALBAC (Multiple Annealing and Looping Based Amplification Cycles; PMID 23258894) may be an alternative method

[bman]

I know that this post is pretty old but I was wondering if the MALBAC procedure worked well. Also, were your tumor samples fresh or FFPE?

Thanks.