Is It Possible To Use Different Amounts Of Dna For An Acgh?

Question

[Saskia]

For an experiment I am using tumour DNA and commercially available control DNA.

For the result of my aCGH, would it possible to use a different ratio of tumour DNA vs control DNA? E.g. tumour:control = 2:1 or visa versa tumour:control = 1:2

For example, if I were to use 500ng tumour DNA and 800ng control DNA for an array CGH, would this influence the result? Intuitively I would think using more control DNA than tumour DNA would bring down any amplifications and increase deletions... Am I correct? And if so, could this be corrected in the analysis?

Answer 1

[Istvan Albert]

The expectation is that, for multiplexed samples (I believe that is what you are asking about) the number of sequenced reads will correlate directly with the amount of DNA for each sample.

I would try to keep both of these equal - trying to improve the power of statistical analysis by adding more data to one group data while taking away from the other is not a good strategy.

Having to correct for unequal coverage will introduce a whole other set of problems.

[Chris Miller]

The poster is asking about array-based CGH, which doesn't involve sequencing at all.