How many exomes with good coverage (30x) can sequenced in 454/Roche with US$ 30,000??
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All of the solution phase methods used for exome capture have a small insert size to increase the amount of on target sequencing. All exomes we do cheaply and well on the Illumina HiSeq. Even Roche Nimblegen's EZ exome kits are designed for the HiSeq. The solution phase work well and are easy to automate.
Roche has the 2.1M exome array that works with 454 but out of a single run with ~1.2M reads (~350 Mb) you can only get 8-9X median coverage of a single sample. For a 50 Mb exome @ 50X you can easily run eight samples in a single lane of a HiSeq for a fraction of the cost of a 454 run.
We have found the 454 better suited for 250 kb - 1Mb custom panels to use the longer reads to get better information on indels and haplotype SNPs. With the 1Mb using the 385K array ~50X median coverage using 1/4 PTP. This is useful in addition to exomes/genomes done on the HiSeq and for follow-up validation. This step likely will move to the MiSeq especially with the PE-250 coming.
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Hello anoopmandaher, I am a sales rep with Axeq Technologies. The prices have gone down a little bit, but not too much. You can see our current promotions at www.axeq.com
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