If you have a chance to ask questions to the CEO of Illumina, what would you do?

Question

[zhuosong]

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.

Thanks,
Zhuo

[zhuosong]

Thanks for the questions.

Answer 1

[Istvan Albert]

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

[zhuosong]

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.

[Istvan Albert]

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

[Matt Shirley]

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

[Michael]

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

[Istvan Albert]

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

Answer 2

[Irsan]

Does it really have to be that expensive?

[zhuosong]

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

Answer 3

[5heikki]

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

[Adrian Pelin]

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

[Xingyu Yang]

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

Answer 4

[pld]

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.

[zhuosong]

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.

[pld]

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.

Answer 5

[Ann]

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