Forum:Bioinformatics startup market analysis
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3 months ago
gtechbio ▴ 30

Dear Biostars  Community,

We are planning to launch a small bioinformatics SaaS (Software-as-a-Service) startup that will develop IT solutions for biomedical research/diagnostics labs and sequencing facilities. Our main focus will be implementation of software and IT infrastructure helping to organize and optimize sequencing-related projects and tasks. For example, we developed an algorithm allowing to optimize sequencing strategy (based on sample multiplexing), which by our estimates can significantly reduce the cost of sequencing benefiting both the end users (researchers, patients, etc) and facilities.

To assess the viability of the start-up, we are now performing a market analysis. So if there are people in Biostars who work(ed) in genomics facilities, we'd appreciate very much any cooperation to get an idea about sequencing volumes that are processed by an average size genomics facility.

In particular, how many samples per year (or month) are sequenced, what type of sequencing (RNAseq, DNAseq, ATACseq, etc) is performed, technology (Illumina, Nanopore, etc) and what species are sequenced.

We can discuss it in this thread, but if there are people willing to share some data, please drop an email to gtechbio@gmail.com or let us know how to get in touch with you.

Thanks in advance for cooperation

startup • 1.1k views
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That information should be made public from public genomics facilities. Apart from a rampant double moral from people who otherwise criticize private initiative, it's incompatible with transparency laws of many countries. People are taking private advantage of public investment not subject to public tender. That's morally unacceptable. But that's how it is and doesn't seem that's going to change.

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agreed, especially if no private information (names, clinical status, etc) is needed, this information should be freely accessible.

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Dear @juanjo75es, thank you for your input. We do agree that NGS data/metadata should be more accessible to public, in part also due to initiatives like ours, which aims to benefit all parties. If you know any facility or centre which has these data publicly available, we'd appreciate if you can point to it. Kind regards, gtechbio team

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Well, I am in a similar case than you (also developing software that could help genomics facilities) and the lack of public NGS data has not been a problem for now... There are lots of data on the NCBI portal and other ones. But I can't either get any cooperation from any genomics facility and that's what I was talking about.

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Dear jaunjo75es, by "NGS data/metadata" we meant the data directly from public genomics facilities.

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I guess it could be more effective if you ask/partner with a local genomics facility. People can be reluctant here to share this info

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Dear @grant.hovhannisyan, thank you for the advice. In fact we are already in touch with two local genomics facilities, though as you have commented we do see some reluctance in sharing these data. This is one of the reasons why we also decided to post our initiative and request in Biostars, knowing that bioinformatics and NGS community is very active here.

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good luck!

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3 months ago

Think of it this way, you are proposing to be a competitor to an organization - but you are asking them to share information that allows you to compete even more efficiently. Morality or fairness aside, it is easy to see why people are not all that motivated to cooperate.

From my (limited) understanding the cost structures in many educational and non-profit organizations are distorted by various externalities that an organization has to account for. For example at a university a genomics core may not "profit" from performing sequencing - basically, everything has to be "at cost".

Anyone that has ever run a business knows, that you make money on some customers and lose money on some others, difficult to predict which. Fixing costs at "no-profit" will always lead to more inefficient operations overall.

I for one observed that outsourcing sequencing to third parties often leads to worse quality of data and worse support than when doing it in-house, here at PSU. For that reason, for PSU scientists I recommend the PSU facilities, even if these happen to be more expensive. (Usually, the saving are like $1,500 on a project that already cost maybe $100K in total, sample collection, tuition, etc) Thus the savings ought to be substantial to warrant the additional risks.

Long story short, like grant.hovhannisyan pointed out you should team up with a local genomics facility but not in "asking them for sales information" but in providing them services that may make them more efficient. Now all of a sudden you will know how much they are willing to pay.

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I don't think that makes sense. First, if you limit business opportunities to people who have a local facility willing to cooperate with them, you are not in a free market. That usually goes against progress and in the long term even against the economic return for those opposing progress. Second, in the actual business environment, you usually can't create a product without knowing previously the market. Nobody is going to invest and your only chance is if you can develop the product by your own means (and hoping to be lucky to get the right product). Against that's anti-competitive. Also letting morality apart...This is just protectionism and protectionism not towards the country but towards some people working for(?) the country. I understand that people working there have an interest not to cooperate, the question is if they should be allowed by the political leaders to impose their personal interests. But we already have an answer to that question, therefore not much left to discuss.

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I for one observed that outsourcing sequencing to third parties often leads to worse quality of data and worse support than when doing it in-house

Loosely related to this thread, in my opinion and limited experience the main improvement I would ask to sequencing facilities is to reduce turn-around time. With benchtop sequencers taking just a matter of hours to run it's frustrating to wait weeks or months to get a few million reads for a handful of RNAseq or ChIPseq libraries that you hand-in ready to sequence.

As you correctly say, these days the cost of sequencing is not that much but time is really the limiting factor. A student or anyone on short contracts (< 2-3 years - most of us I bet) effectively has to choose between analyzing existing data or producing it. I don't know... but for many projects I would gladly trade, cost, quantity and, to some extent, quality for faster turn-around. Any thoughts...?

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dear dariober, thanks for your comment. Delays in sequencing can be due to various reasons, and while some of them can be controlled (hiring more technicians, automating different processes), others are harder to handle becaue they don't depend on the facility. For example, paradoxically the increasing throughput of sequencing machines is also causing delays, because sequencing units usually need to fill the flowcells before running a machine, and in our experience the longest delays were due to exactly that (there were simply not enough samples with the same read length configuration that matched our request). Effective sample multiplexing coupled with data management systems is one of the solutions (e.g. users (or facility managers) can see the load of sequencing machines and design a sequencing configuration that can minimize the turn-around time), and it is one of the issues tackled with our algorithms.

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Dear @Istvan, thank you for your input!

Quoting your comment - "not in "asking them for sales information" but in providing them services that may make them more efficient", then this is exactly what we do. We plan to be a SaaS startup, and so we do not compete with genomics facilities, but provide them with software solutions that can significantly increase their efficiency. For example, by using our algorithm and services they can spend the same time and resources but sequence 2-10x more samples, and with that they can reduce their operational costs and thus offer lower prices for clients (which in turn makes the facility more competitive) - in other words it's a win-win scenario for everyone.

We didn't convey that message in our original post, so thanks for noting and pardon for confusion.

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3 months ago
Juke34 ★ 6.0k

You may find interesting information from National Genomics Infrastructure - Stockholm here:
https://ngisweden.scilifelab.se/resources/ngi-stockholm-status/

That is pity National Genomics Infrastructure - Uppsala that use more diverse sequencing technologies do not provide similar information...

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