Question: If you have a chance to ask questions to the CEO of Illumina, what would you do?
3
gravatar for zhuosong
3.1 years ago by
zhuosong60
zhuosong60 wrote:

Hi,there

There is a chance to ask a few questions to the CEO of Illumina, Jay Flately, face to face tomorrow. I'm working in Bioinformatics and would like to gather some questions from the Bioinformatics community.

If you have questions, please leave a comment. No guarantee that the question will be asked. But if it is, I'll reply Jay's answer to you.

Thank,

Zhuo

bioinformatics illumina • 2.0k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 3.1 years ago by zhuosong60

Thanks for the questions.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by zhuosong60
11
gravatar for Istvan Albert
3.1 years ago by
Istvan Albert ♦♦ 71k
University Park, USA
Istvan Albert ♦♦ 71k wrote:

Why doesn't Illumina fund open source software that helps analyze sequencing data.

ADD COMMENTlink written 3.1 years ago by Istvan Albert ♦♦ 71k
1

I can't quote Jay word by word. But based on Jay's answer and my understanding, ILMN wants to build the their BaseSpace as an App Store. So they won't fund any open source outside the platform.

ADD REPLYlink written 3.1 years ago by zhuosong60

Intriguing. Thanks for following up on this. We are getting a peek into the future here folks!

ADD REPLYlink written 3.1 years ago by Istvan Albert ♦♦ 71k

If I could up vote this more than once I would.

ADD REPLYlink written 3.1 years ago by Matt Shirley7.2k

Maybe they do, at least a little? https://github.com/sequencing

ADD REPLYlink written 3.1 years ago by Michael Dondrup41k

true, forgot about that, what I really meant something that is not necessarily an in-house tool, instead to give out  grants/support to the community at large

ADD REPLYlink written 3.1 years ago by Istvan Albert ♦♦ 71k
6
gravatar for Irsan
3.1 years ago by
Irsan6.2k
Amsterdam
Irsan6.2k wrote:
Does it really have to be that expensive?
ADD COMMENTlink written 3.1 years ago by Irsan6.2k

It'll get cheaper and cheaper, as more and more people to buy.

ADD REPLYlink written 3.1 years ago by zhuosong60
5
gravatar for 5heikki
3.1 years ago by
5heikki6.3k
Finland
5heikki6.3k wrote:

I'd ask about the possible future plans of >1kb and >10kb and beyond read lengths..

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by 5heikki6.3k
1

Yes. I would ask whatever happened to the "moleculo" technology. There is barely any info on it.

ADD REPLYlink written 3.1 years ago by Adrian Pelin2.0k

Yes. I'm really curious about illumina's plan in developing 3rd generation sequencing.

ADD REPLYlink written 3.1 years ago by Xingyu Yang240
1
gravatar for pld
3.1 years ago by
pld4.5k
United States
pld4.5k wrote:

I'd ask about:

-Illumina's road map for moving away from reaction based sequencing to solid state sequencing.

-Developing portable sequencing equipment to replace qPCR based assays for diagnostics in non-hospital disease outbreak settings.

-Illumina's road map for moving away from technologies that require cDNA library generation but will still work with more sensitive RNA molecules like mRNA, single stranded viral genomes, etc.

-Illumina's road map for improving throughput of clinical sample types, especially liquids such as whole blood, plasma, saliva, semen. (If it exists).

-Efforts to improve the ability of sequencing technologies to deal with complex secondary and tertiary structure, such as what is found in the 5' and 3' NTRs of viral genomes.

 

 

 

ADD COMMENTlink written 3.1 years ago by pld4.5k
2

1. ILMN tried the same tech as ion torrent privately, but never release the product, since they don't believe in emulsion PCR.

2. ILMN invented in new sequencing tech, like nano-pore. But there is a long way for the new tech to go.

3. ILMN is semi-conductor based as well, but they won't throw away the optical system. The simplified the optical system on NextSeq 500 and put more effort on CMOS tech.

ADD REPLYlink written 3.1 years ago by zhuosong60
2

Everything but Maxam-Gilbert sequencing requires semiconductors, so that is not what I meant by solid state sequencing. I mean moving to non-reaction based sequencing. There's a distinct difference between sequencing using semi-condictors to in a sense, copy information generated by a biochemical reaction, and the sequencing event being totally solid state. I don't care how fancy their digital cameras get, it has not moved any closer to becoming solid state sequencing.

I'd wager that they do believe in emulsion PCR, but there is no longer IP space for it with with Roche holding 454, and Thermo-Fisher holding Life Technologies. Although Roche almost managed to buy Life Tech.

Same probably goes with nanopores and so on, the IP space is probably small. There are a few start ups with bio-molecule nanopores, most notably Oxford Nanopore. Then you have Roche teaming up with IBM to develop a semi-conductor based nanopore. So there's probably not much room left. I think Agilent still holds a ton of nanopore IP, they were one of the earlier ones.

If anything illumina seems to be dead set on staying where they are. They've done a good job in making dye based sequencing work, but in the end it is still dye based sequencing. Although I hope they survive, Roche seems determined to take over.

ADD REPLYlink written 3.1 years ago by pld4.5k
1
gravatar for Ann
3.1 years ago by
Ann2.1k
Concord NC USA
Ann2.1k wrote:

I'd ask about Illumina's plans for BaseSpace. Then I'd ask about internships for my students.

ADD COMMENTlink written 3.1 years ago by Ann2.1k
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