I am planning exome sequencing for a disease which to find a family is extremely difficult. That is why we have to study on sporadic cases. At this point which approach is better. As we think about our budget 3-fold more affected can be sequenced if it is suitable for analysis or are trios better for evaluating the data.
Well it depends. Are you expecting the condition to be a mendelian, monogenic trait or something more complex?
Assuming a monogenic disease, trio analysis is far more powerful than doing single affected individuals. I've been working on rare conditions and trying to chase down single affecteds is really a needle in a haystack. We're seeing hundreds of potential genes. Sometimes we're lucky and find novel mutations in known causative genes, but often we can't find anything.
With trios the numbers are much smaller, but still not always conclusive. Don't expect to get an answer for all cases.
I agree with Christian, trio's allow you to test all the different models (de novo / recessive (hom and comp-het) / x-linked).
Secondly, as Christian also indicates the number of candidates will be substantially smaller, which is especially useful if you have little control data.
Alternatively, if the lab/center already has hundreds of healthy / differently affected individuals and there is a clear indication that mutations are expected within a single gene / gene family or pathway, multiple individuals could be a better solution. (only works well for mendelian like diseases though)
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