Deep Analysis of 300 Samples on 454

[gavin.oliver]

Hi,

I have a colleague who is interested in deep-sequencing of the transcriptome of 300 patient samples (liver cells I think) and looking for everything (expression profiling, SNPs, INDELs, novel variants etc). Also, they wish to do this with 454 sequencing technology.

Is it just me, or does this sound like a huge project? Would the expense with 454 especially not be prohibitive?

Any input would be appreciated.

Gavin

[nickloman]

Sounds like it might need a run per sample and even then you are likely not to capture all the "deep" variation present. So one would be looking at £2-3 million UKP to do that. And that's before someone actually gets to analysing the data. I would have thought a higher-throughput technology like Solexa would be a better option.

[gavin.oliver]

Lol.

I thought it sounded like a pretty ridiculous undertaking - I just wanted confirmation

[elaney_k]

might not be such a mad idea if they were looking to use a different platform like Illuminas new HiSeq 2000. I think the type of project you're talking about would be significantly cheaper on that system and not such a ridiculous undertaking..

[gavin.oliver]

Yeah, this was my first thought also.

I might advise him to look into this as an alternative. The analysis could still be a pretty huge undertaking though!