Can Ion Torrent be useful for microRNA sequencing?

aushev · 11-19-2010, 08:18 AM

Dear colleagues,
what do you think about applicability of Ion Torrent for miRNA profiling? They promise "Thousands to Millions of moderate reads per sample". "Moderate reads" is even excessive here, we need just short reads; my question is rather - if we have enough reads for adequate analysis. We have about thousand miRNAs (to be simple, I will not count precursors etc.), but some of them will be much more abundant then others. On my experience of real-time detection, I had Ct difference between highest and lowest about 11..13, i.e. concentration difference about 2000..8000 times, so I am wondering how many of less abundant miRNA species will be detected with this dynamic range.

epistatic · 11-24-2010, 10:01 AM

The spec we have been told is 100K, 100 bp reads. Price aside, our feeling is if we cannot do the project with our 454 Jr., we cannot do it with the ion PGM. I think they are a long way from doing any counting applications and Life is pushing the SOLiD for small RNA assays.

aushev · 11-24-2010, 10:47 AM

Thanks for answer!
But can we really disregard the price? I mean, if single run is many times cheaper, you can simply put more portions to increase the coverage...

epistatic · 11-24-2010, 11:27 AM

Lets start with the library already made, so that cost is the same (or higher if you have to do emPCR with the ion PGM).

If it costs $250-$500/run on ion PGM for 100K reads and $1200/run for SE-43 and ~25M reads on the Illumina GAII, I don't see the ion price being that cheap.

I currently run four yeast RNA-Seq in a single lane of the GAII, so for $300 I get ~6M reads per sample. I may not even need 6M reads per sample, so further multiplexing would bring the price per sample down. With multiplexing on the HiSeq, the price should be even lower.

The current ion machine will be for low output needs, running again and again to get more data from one sample doesn't seem to be the best use.

aushev · 11-25-2010, 09:42 AM

ok, with numbers it became more clear. Thank you for explanation!

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11-19-2010, 08:18 AM	#1
aushev Member Location: Europe Join Date: Nov 2009 Posts: 21	Can Ion Torrent be useful for microRNA sequencing? Dear colleagues, what do you think about applicability of Ion Torrent for miRNA profiling? They promise "Thousands to Millions of moderate reads per sample". "Moderate reads" is even excessive here, we need just short reads; my question is rather - if we have enough reads for adequate analysis. We have about thousand miRNAs (to be simple, I will not count precursors etc.), but some of them will be much more abundant then others. On my experience of real-time detection, I had Ct difference between highest and lowest about 11..13, i.e. concentration difference about 2000..8000 times, so I am wondering how many of less abundant miRNA species will be detected with this dynamic range.

11-24-2010, 10:01 AM	#2
epistatic Senior Member Location: Dronning Maud Land Join Date: Mar 2009 Posts: 129	PGM not ready for counting applications The spec we have been told is 100K, 100 bp reads. Price aside, our feeling is if we cannot do the project with our 454 Jr., we cannot do it with the ion PGM. I think they are a long way from doing any counting applications and Life is pushing the SOLiD for small RNA assays.

11-24-2010, 10:47 AM	#3
aushev Member Location: Europe Join Date: Nov 2009 Posts: 21	Thanks for answer! But can we really disregard the price? I mean, if single run is many times cheaper, you can simply put more portions to increase the coverage...

11-24-2010, 11:27 AM	#4
epistatic Senior Member Location: Dronning Maud Land Join Date: Mar 2009 Posts: 129	Lets start with the library already made, so that cost is the same (or higher if you have to do emPCR with the ion PGM). If it costs $250-$500/run on ion PGM for 100K reads and $1200/run for SE-43 and ~25M reads on the Illumina GAII, I don't see the ion price being that cheap. I currently run four yeast RNA-Seq in a single lane of the GAII, so for $300 I get ~6M reads per sample. I may not even need 6M reads per sample, so further multiplexing would bring the price per sample down. With multiplexing on the HiSeq, the price should be even lower. The current ion machine will be for low output needs, running again and again to get more data from one sample doesn't seem to be the best use.

11-25-2010, 09:42 AM	#5
aushev Member Location: Europe Join Date: Nov 2009 Posts: 21	ok, with numbers it became more clear. Thank you for explanation!