Why Shouldn't You Buy Your Own Sequencer?

This page is written for the PI who is considering the purchase of their own DNA sequencer. Perhaps you think you can save money. I may be biased, but it seems to me that it is FAR more economically advantageous to send samples to the UM DNA Sequencing Core than it could ever be to buy your own sequencer and do them yourself. Consider the following points:

We have the best purchasing power. When you process hundreds of thousands of samples per year, you get some great bulk purchasing deals.
We have the latest expertise. Do you have any idea how many artifacts crop up in DNA sequencing? Or even how many new ones crop up each year? I'm in frequent contact with other Core facility operators around the globe. When new artifacts are encountered here - or elsewhere - we have the resources of dozens of sequencing experts at our fingertips. Do you really want to spend time troubleshooting artifacts?
Our level of experience really counts. Your techs will need years of experience to match ours. This makes a huge difference in the failure rate of samples, the incidence of pipetting mistakes, their ability to spot instrument problems and their ability to maximize cost effectiveness.
You don't really want to train sequencing techs, do you? Sure, the PI may really know his/her stuff. Is s/he actually going to run a sequencer? Calculate the hourly wages before you answer.

OK, so the PI is NOT going to run the sequencer. Who is, then? and who's going to train that person to sequence? Again, not the PI, I hope. What happens when the expert sequencing tech leaves? Will there always be overlaps so each sequencing tech trains the next before they depart?

We have a pool of the most highly-trained and highly-experienced sequencing technicians in the business. Continuity of expertise is easy for us.

What will you do when your sequencer breaks down? We have two high-throughput sequencers and a third as an emergency backup, plus agreements with other Core labs for emergency help. We have service contracts on all sequencers, and excellent rapport with the Field Service Technicians. We also have outstanding expertise in handling many problems without ever calling in outside repair specialists. How are you at troubleshooting complex instruments? I am very good.
How often do you want to upgrade your sequencer? We constantly upgrade our systems to the latest and greatest possible. When new technology provides a cut in price or improved read lengths or better quality, we'll know about it and we'll have it. That's our job.

We upgraded sequencers in 1997 (improved read length), 1999 (faster runs), 2001 (much faster, much cheaper) and 2003 (faster, cheaper, longer reads). Do you want to buy new sequencers every two years? If not, you'll automatically take a hit in cost efficiency and data quality.

Ease of use:
We've got it.
What could be easier than just sending samples our way and letting us do it all?

What will you do when your sequencer blows a sample? Will you notice it? Re-run it? We do.

Do you want to bother with all the routine instrument maintenance? Stock reagent preparation? Ordering? Data archiving? Quality control checks?

Support: We've got it. Need help figuring out why your samples failed? I've seen it all, and am glad to talk you through the possibilities. Lose a sequence file? No problem. We've got all results archived back to the Dawn of Time. Gotta run BLASTs on 10,000 clones? It can be tedious - unless the Core did the sequencing. I can get that BLAST analysis done with just a few keystrokes and a few hours of hands-off compute time. Need to spot heterozygotes in your PCR products? We run polyphred. A BIG sequence assembly? Phred/phrap. Got other informatics needs? Talk to me.
Latest techniques: We've got 'em. When all the Core Directors discuss the advantages of various new reagents and techniques, I'm in there. We compare notes on protocols, instruments, reaction additives, bioinformatics techniques, etc etc. If people are pushing their read lengths out another 50 nt, I'll hear about it.
Big Throughput: How can you compete? If you have a BIG project, we'll help you get it done faster. Unless you, too, are planning to sequence hundreds of thousands of samples, our sequencers are bigger and faster than yours.

If you ARE planning on running hundreds of thousands of sequences, though, see the next section.

Support Your Peers! If you have a REALLY BIG project, you might think you could get as efficient as the Core, but think about this. Add your size with that of the Core, and we grow even bigger. That translates to yet more savings - for everyone at U-M. You'll get all the benefit, and so will all your colleagues.

That's the whole point of the Core Lab system - combine your needs and efforts for bigger savings. Please don't go it alone and leave your colleagues at a disadvantage.

Discounts: Get more research funding! When you get a discount to use the Sequencing Core, it's like being handed a mini-grant. Several research centers offer these discounts for using the UM DNA Sequencing Core. Why not take advantage of it?
You think you can run cheaper than we can? Consider the following:

  • Are you including ALL the costs? It's not just the dye costs, I assure you. Don't ignore personnel/time costs (huge!), service contracts, software and hardware, replacement arrays, all the disposable plasticware (it adds up!), ancillary reagents, calibration standards.
  • For personnel costs, don't forget to include all the ancillary time spent on troubleshooting, preparing reagents, sequencer upkeep, etc.
  • Don't forget to divide the cost of your sequencer by 2-3 years' worth of samples and add that into your per-sample costs.
  • Are you including the cost of repeated samples, standards, blanks, test samples, calibration runs and procedure development? We are.
  • We are, to our knowledge, the most cost-effective sequencing core in the world. Only the big genome centers run cheaper. Oh, and if you've got a genome-center-sized project, you should be sending your samples to one.
  • Got a gel-based sequencer? Found one for sale cheap? Forget about it - you'll immediately incur at least 100% more in operating expenses than we do. Probably closer to 200%, unless you are very, very good at this.

If you still think you are including everything in your cost calculations, and if you still think you can run more cheaply than we can, I'd like to sit down with you and talk. In fact, I want to sit at your feet and learn - as do most of the other SeqCore Directors in the world!

What's the best way to spend yourtime? Research, not Sequencing! Here's perhaps the most important point. You and your students have better things to do than sequence ... RESEARCH. Your time and theirs is better used on performing real experiments, not slogging away at the sequencing bench. Using the Sequencing Core is like hiring extra technicians to do your work - the best ones in the business, in fact!