Read on Twitter
As a part of the discussion of sequencing of different #Covid19 strains, I've been asked by many, what the sequencing capacity of Finnish universities would be (and if they should be doing large-scale sequencing of Finnish covid samples). 1/17
This thread speculates a bit on this topic (Disclaimer, yes pure speculation).
I don't think that for Finnish universities, sequencing capacity is the bottleneck, but rather the logistics and processes (and perhaps supplies). 2/17
I don't think that for Finnish universities, sequencing capacity is the bottleneck, but rather the logistics and processes (and perhaps supplies). 2/17
Based on my knowledge of the sequencing capacity of Finnish universities and the published #Covid19 protocols, I guesstimate that the theoretical capacity of the sequencing instruments in Finnish universities, would be around 5000 covid genomes per day (150k/month). 3/17
Acquiring new sequencing instruments is quite easy, and ramping up the sequencing capacity could be done rapidly by throwing in some money, e.g. 10x capacity within a month or so (=> 50k samples per day). 4/17
People working in the academia often complain about the high cost of the sequencing instruments, but at the end of the day, the instruments them selves are actually relatively cheap, running them (consumables & work) are the expensive part. 5/17
Just as a ballpark example (haven't checked actual list prices in ages, so again, just guesstimating), high-end sequencing instrument could cost you something like 700 k€, and cost 30 k€/day to run (11 m€ per year if run full time). 6/17
So, right now from the sequencing capacity point-of-view, we could run 5k samples per day, and with some new hardware, 50k samples per day. 7/17
So, sequencing capacity is not the problem, the problem is how do you handle logistics & processes for high clinical quality stable sequencing operation within a university setting (5-50k patient samples coming in and processed each day). 8/17
This is really hard in universities in Finland (and in many other countries as well), because the sequencing facilities are not set up for this. 9/17
Because of the funding models, sequencing facilities have small staffs, and in many cases, many of those people are not working full time on operations (but e.g. work as a researchers). 10/17
This makes it really hard to run a stable high-throughput operation, where you need dozens of trained people working in a "factory like setting", working with a single standard operating procedures day and night. 11/17
The whole workflow (from sample accessioning, handling, sequencing, data management, data analysis and reporting) needs to be well developed, documented, tested and validated, preferably by external accreditation services looking in to this specific workflow. 12/17
All this is in many ways against the basic operation model of academic institutions, where people work part time (and often with 1-3 month job contracts, or grants), where most projects are research projects where the process, quality and goals change by project etc. 13/17
All this being said, we do have great talented people working on different sequencing facilities within universities in Finland, and the people would have the skills to setup the required large-scale industrial sequencing platforms. 14/17
The challenge is that the environment (from infrastructure, politics and ways of working viewpoints) hardly supports them in that task. 15/17
Also it is important to note that Finnish university researchers have already done a great job sequencing & analyzing covid samples, and there certainly is more to come! 16/17
P.S. Those of you who are more familiar with the topic, would love your thoughts about the current sequencing capacity and bottle-necks! 
17/17
17/17
