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Old 11-06-2009, 02:01 AM   #1
Susanne
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Default Success of Solexa-platform

Hi members,
I am currently preparing an overview presentation for my science colleagues (unfamiliar with NGS) on the next- and now-gen sequencing technologies. Obviously, this forum is a great place to fill the gaps in my knowledge - but I was left wondering about one question:
Why is llumina the dominant platform?
As a non-instrument owner, I could think about things like ease-of-use, instument price, popularity, bioinformatics quality, customer support, first on the market, reliability etc.
Don't get me wrong, I don't want to buy an instrument, and I know a little about the advantages of the platforms - but that taken together doesn't help me in understanding why Illumina is the market leader.

So I want to know from you:
What is your notion of the success of Illumina? (Facts welcome )
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Old 11-06-2009, 02:35 AM   #2
francesco.vezzi
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OK... first of all in the lab where I work we have an Illuminna GAII, and I never work on other kind of data....

I can try to answer your question in the following way: the success of illumina are the problems of the others technologies. Solid has the big trouble of color space that oblige to rewrite and rethink all the necessary instruments. Roche 454 has the great advantage of read length but the costs and the throughput is low if compare to illumina.

Illumina output (and I think also technology but don't trust me a lot because I'm a computer scientist) is really similar to sanger output except the length.

I suggest to you to read a really intresting paper that I have discovered yesterday: "Next Generation Gap" by John D. McPherson that is appear on nature methods

Best regards
Francesco
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Old 11-06-2009, 07:52 AM   #3
Susanne
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Thanks, Francesco for your quick and interesting reply. I found the paper & will read it over the weekend.

I researched a bit and read that 454 was first to the market, as far as the 3 big players are concerned. Does anybody have a different information?
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Old 11-06-2009, 08:29 AM   #4
steven
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You will find a confirmation in that paper precisely. 2004: Roche 454 (Margulies et al., Nature, 2005). 2006: Illumina GA. 2007: ABI SOLiD.
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Old 11-06-2009, 08:31 AM   #5
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There was something called MPSS which was developed by Lynx, which eventually became Solexa/Illumina

454 had already sold dozens of machines before Solexa had sold even one

if Illumina had not improved their read lengths from 25nt I don't think they would have become the dominant player
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Old 11-08-2009, 08:52 AM   #6
liu3zhen
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Solexa/Illumina is becoming a dominant platform for many applications (e.g., RNA-seq) due to the below reasons with respect to the technology, I think:

1. deep sequencing (the depth is much higher than Roche 454)
2. affordable cost (the cost per bp is much, much lower than Roche 454)
3. the read quality is good enough for most of applications (Roche 454 has homopolyer problem)
4. the read length is up to 100 bp or a little higher now

Last edited by liu3zhen; 11-08-2009 at 08:59 AM.
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Old 11-08-2009, 01:24 PM   #7
cgb
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Default Lynx

Quote:
Originally Posted by Zigster View Post
There was something called MPSS which was developed by Lynx, which eventually became Solexa/Illumina

454 had already sold dozens of machines before Solexa had sold even one

if Illumina had not improved their read lengths from 25nt I don't think they would have become the dominant player
Solexa ltd existed as a UK company before it reversed into Lynx Therapeutics to form Solexa Inc in 2004. MPSS, the Lynx technology (in many ways pioneering short read sequencing and technically similar to SOLiD) was dropped in favour of the Solexa SBS chemistry -- and other things.

And in fact Solexa (then latterly Illumina) sold ~40 instruments in the first two months, which is roughly equivalent to 454's yearly sales at the time. These were 25-30bp.

Last edited by cgb; 11-09-2009 at 12:57 AM. Reason: afterthought
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Old 11-08-2009, 01:32 PM   #8
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Here is my view on the Illumina(Solexa) dominance as things stand (and could easily change ! - this is a very dynamic space)

1. The overall 'workflow' for the sequencing process on this platform is relatively simple and robust compared to the others.
2. The Solexa system reached a good price/data quality/throughput position quite early on - 454 didn't being only around 3X cheaper than Sanger where Solexa was ~100X. A friend of mine compared 454 to Sputnik and Solexa to the Apollo missions - think on it.
3. The Solexa data ain't funky..... (deliberately so).
4. Most of the platform was 'open' from protocols to source code (previous sequencers were not very open).
5. Uptake was rapid at Genome Centres (and later cores) - also not unplanned and after some relationship building both ways - they provided tech dev, validation, new applications and scientific reference points -
6. DNA sequencing isn't like genotyping. One tech but many applications for DNA sequencing - applications create markets.
7. Performance claims were not over-hyped.

Last edited by cgb; 11-09-2009 at 01:00 AM. Reason: afterthought
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Old 11-21-2009, 06:39 AM   #9
cgb
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I saw a post on another site saying 1500 Solexa systems out.

I would guess that gives it ~70% market, maybe 20% for 454 and 10 for SOLiD ?
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