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A couple of years ago, I answered a reader’s question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and the reported coverage to estimate the cost of sequencing Craig Venter’s genome. As you can imagine, the cost of sequencing has dropped quite a bit since then.

In 2007, Genome Technology reported the cost of sequencing Venter’s genome was $70 million. Watson’s genome at only $2 million, was a bargain.

Why was Watson’s genome so cheap?

Even though the Venter and Watson genomes were both published in 2007, the price of the two genomes was substantially different. The biggest reason for the difference was the technology. Where Venter’s genome was sequenced with Sanger dideoxy sequencing, the gold standard technology of the day; Watson’s genome was sequenced with the first of the Next Generation Sequencing instruments, the 454 (now owned by Roche).

Where are we now?

Today, the price has dropped still further. CoFactor Genomics will sequence a human genome (at 1.6X coverage) for $22,900. Knome is putting a human genome on EBay with bids starting at $68,000. As my Scibling from Genetic Future writes, it’s not clear what a purchaser gets for these prices beyond a hard drive full of A’s, T’s, G’s and C’s; but the idea of having your own genome sequence is still fun to think about.

Comparing the prices for Next Gen with the previous gen

Today, if we look at the prices we can find on the web and do a little math, we come up with these kinds of results for sequencing costs:

For Sanger, we find costs for sequencing samples in 96 well plates average about $5 a read, or about $10 per kb (1000 bases of DNA).

For 454 sequencing, laboratories charge about 20 cents per kb.

If I use the prices from CoFactor Genomics, sequencing with the Illumina GA II is the cheapest at 4 cents per kb.

(I couldn’t find any prices advertised for the ABI SOLiD instrument, but given the amount of data produced, the cost is probably similar.)

What does this mean?

It’s pretty clear from the cost comparisons and this year’s publications, that Next Gen technologies are going to be used more and more and Sanger sequencing will be used less and less.

People will probably use Sanger for some time when they have small numbers of samples, a gap to fill, or repetitive sequences to untangle. Small colleges and community colleges will probably continue using Sanger, too, since they tend to use smaller numbers of samples.

There is one community college that I know of, that’s sequencing a bacterial genome with Sanger sequencing. I don’t know how many schools will want to do that in the future though, when Sanger sequencing costs about a thousand times more and takes much longer. It could be kind of depressing to spend a year sequencing a bacterial genome, when another group can get a genome sequenced in a day.

On other hand, if the science instructors aren’t too attached to the wet lab and science classes want hands on practice with bioinformatics, they can get a bacterial genome sequence for under $5000 (or free if they win CoFactor Genomics’ competition), and change their focus to digital biology. Maybe college biology students will put down their pipettes a little more often and work more with the data.

Comments

  1. #1 Jeffrey Boore
    April 24, 2009

    These estimated costs could be easily refuted by even casual investigation. It is outrageous to suggest that Sanger sequencing costs $5 per lane. Maybe that is the cost if you want exactly one sequence from a commercial provider, but genome centers went below 50 cents per lane three years ago, and that cost includes making the libraries, all of the QC, amortizing the equipment, all of the informatics for whole genomes, and even the overhead such as having Human Resources and Safety departments. I am disturbed by the casual spreading of such disinformation in the guise of scientific education.

  2. #2 Sandra Porter
    April 24, 2009

    Jeffrey,

    My impression, which could be wrong, is that many genome centers are using the Next Gen platforms for doing most of the genome sequencing and then using Sanger to fill in gaps, resolve repeats, or help with tricky parts. When they do use Sanger, they don’t use lanes in gels. They use capillary electrophoresis.

    Certainly, genome centers can sequence DNA more cheaply than others, but since they don’t do contract sequencing (at least in the US), their costs don’t really apply to the rest of the world. Genome centers also don’t put price lists on the web.

    Further, my information is not disinformation. It’s all readily available on the web. I got my Sanger and 454 pricing data from University core lab web sites (you can also click the link in the post, under the 20 cents per kb, and confirm this) and the Illumina data from a commercial company that spun out of the Wash U genome center.

  3. #3 Sandra Porter
    April 24, 2009

    And Jeffrey, what does your sequencing company charge for Sanger sequencing vs. Next Gen?

    You didn’t mention your prices in your comment.

  4. #4 Jeffrey Boore
    April 29, 2009

    Agreed that genome centers don’t put prices on the web, because they don’t offer these services to the public. Anyone interested in the real numbers regarding costs of the various forms of DNA sequencing can feel free to contact me at JLBoore@berkeley.edu.

  5. #5 RM
    May 1, 2009

    Commercial offerings of $5 per sample for Sanger sequencing sound relatively reasonable to me, depending on what you’re getting. The on-campus sequencing facility (run pretty much at-cost) charges us about $3.50-$4.00/sample for 100+ samples taken from the primer+template stage onwards. From this you’ll get ~500-1000 nt, single direction. In comparison, if our lab wants to do a 454 run, it’ll cost us ~$0.20-0.30 per kb through the same facility.

    Now granted, they’re doing most of the pipetting and plate transfers manually, so there’s a significant labor cost involved. If you’re going with a large sequencing center they’ll probably have robots to do all that. Although, while the labor costs will go down, they’ll still need to recoup the price of the robots, so I don’t know how that would affect prices.

    Finally, I’ll note that, from a researcher’s perspective, it doesn’t matter how cheap some third party can do something if that researcher has no realistic way of obtaining that service.

  6. #6 Shahid
    November 25, 2011

    Hello
    I required identification of my chromate resistance strains through sequencing. So please guide me how and whom i can send my strains for identification and what will be price for complete sequencing.

    Shahid Mahmood
    Ph.D Student
    Department of Environmental Sciences
    PMAS-Arid Agriculture University, Rawalpindi

  7. #7 Sandra Porter
    November 25, 2011

    I’m not very knowledgable about commercial DNA sequencing companies in India, but I’m sure they exist. If you want to have your bacteria sequenced in the U.S., there are several companies that do whole genome sequencing. I would just search for “whole bacterial genome sequencing services” with Google.

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