So you need some DNA sequencing? (pt 2.)

Following up Sunday's post based on the most-excellent Next Generation Genomics: World Map of High-throughput Sequencers, let's try the same experiment on an international basis.

(But first, a caveat: after spending more time with the map, it is pretty clear that the census is really of non-profit academic institutions & service providers. There's really no incentive for a for-profit R&D to report their sequencing capacity.That said, shouldn't commercial DNA sequencing activity track academic efforts, or are some countries biased towards (or against) for-profit R&D?)

DNA sequencers by country:

USA: 827
China: 216
UK: 140
Germany: 112
Canada: 73
Spain: 56
France: 36 (and very well dispersed geographically)
Japan: 35 (there's much consternation that Japan is falling behind in sequencing.)

Italy: 31

South Korea: 29

Taiwan: 28

Switzerland: 27

Sweden: 25 (rest of Scandinavia (DEN, SWE, FIN, NOR: 30))

India: 23

Singapore: 16
all of South America: 18
all of Africa: 12 


Undeniably in LAST place: Indonesia. Human population: 237M (4th most populous country) DNA sequencer population: 0

Observations:

-Even I'm surprised at how dominant the USA is in sequencing. A quick glance suggests that half of all sequencers are located in the USA. As a policy point, this is worth exploring in another post of its' own (US healthcare model vs. socialized medicine, anyone?), but for now, let's just debate the drug discovery implications. Is there any reason to believe that at least half of the RX & DX innovations won't come from the USA? And if so, is there any reason to believe that countries with socialized health systems aren't free riding on innovation funded by the US system? (Oops. Sorry. That last question just slipped out.)

-As nice as it is to have a large lead in hardware, keep in mind this also means that the USA will led the world in stranded assets and hardware depreciation. Just to illustrate, if the average American sequencer represents a $300k investment, there's a quarter billion dollars of value depreciating quickly.

-wouldn't it be great if LIFE or ILMN donated a few sequencers - even used/last generation - and a supply of reagents to a few universities in Africa? Maybe LIFE could use the US tax code to sell more Ion Torrent machines to existing sequencing centers by facilitating tax write-offs of SOLID equipment donated to universities in Africa or South America? (Company X donates $150k in SOLID equipment to the University of Witwatersrand (Nobel Laureate Sydney Brenner's alma mater). Company X then uses their $50,000 in tax savings to buy a new PGM.) (Does such a program already exist?)

-I'm kind of surprised at the modest presence of the Gulf States. 4 sequencers in Qatar, zero in Bahrain/Dubai/the Emirates.

-I stated that the map listed BGI as having only 15 sequencers in my Sunday post. Turns out that the bulk of BGI's sequencers (166) are in Shenzhen. Apparently even the Beijingers outsource to lower-cost parts of China.



Next up: a look at what this all means.

So you need some DNA sequencing? (pt 1.)

There's an absolutely brilliant map and website devoted to taking a census of DNA sequencers around the world, and through it, you can monitor the tug of war between the placement of instruments in large DNA sequencing centers, and in individual labs (or core labs) on a onesie-twosie basis.

(The map may be a little dated - it shows only 15 sequencers @ BGI, for example - but the brilliance of the map is in how the data was generated. Do a little web surfing for the WWII spy technique that spawned the map.)

Anyway, a VERY interesting story is told when looking at the USA map (select USA under the country pull-down. Unfortunately, I can't link to this specific page.) The sequencer census really indicates who and what are on the edge of the genomic revolution.

A rough read of who's ahead by sequencer placement:

Boston: 129 (Broad Institute = 104)
St. Louis: 85 (includes 11 at Monsanto)
San Francisco Bay Area: 58
Washington, DC area: 51 (with an additional 23 in nearby Baltimore and Frederick, MD.)
NYC area: 47 (includes 18 @ CSHL on Long Island.)
RTP, NC: 37
Houston: 35 (driven by MD Anderson.)
Toronto: 33
Southern California (LA + SD): 27
New Haven, CT: 23 (birthplace of 454 and IonTorrent.)
Philadelphia: 22
Albuquerque, NM: 19 (Sandia)
Montreal: 18
Memphis: 12
Seattle: 5

most other US metropolitan areas and universities had 1-5 DNA sequencers listed.

(Note: some of the math above is fuzzy, as figures change slightly depending on how far you drill down on the map. Plus, the math is skewed by self-reporting and non-reporting. For example, there is a paucity of hardware listed in 'PharmCountry' (NJ & eastern PA) and there's virtually no privately owned sequencers in the Bay Area, but you can be sure that both Big Pharma and Genentech have some sequencing hardware on campus.

What does this all mean:

-you can see which cities are in position to lead the genomic revolution, and which are likely to be laggards. For example, according to the map, there is only 2 DNA sequencers in the city of Chicago. There's roughly 25X more genomic activity on the i-270 corridor outside DC.

• I was surprised by the strong figures in St. Louis and RTP. Both locations have strong ag-bio efforts, so you might be able to extrapolate that the earliest exciting NGS uses will come from ag-bio, and not cancer genomics.
• Anyone else as surprised as I am that NYC was in the top 5? Certainly there is great science at places like Rockefeller, MSKCC, and such, but I wouldn't have guessed top 5. With some announced initiatives, NYC should stay near the front.

-you can see funding philosophies in action (if you squint). There is a tremendous amount of hardware in Canada relative to population, representing governmental support skewed towards hard assets rather than funding annual research. (And the good work of bodies like Genome Canada.) However, with the rate of technological innovation in sequencing, hardware represents a quickly depreciating asset. Maybe the better use of the funds was to pay for outsourced sequencing. (Perhaps this was the case in California, where the inverse was present - less hardware than you might expect.)

-if I had to bet which institution will lead in the adoption of DNA sequencing in patients, MD Anderson would be my first bet. My quick survey suggests that they're the practicing center with the most NGS hardware. Yale isn't far behind.

-on the other hand, some NCI comprehensive cancer centers were extremely lame, including my hometown University of Virginia, Northwestern U, and OHSU. 1 sequencer each? Lame!


Tomorrow I'll do some analysis based on the type of hardware, and take a guess at what this means for adoption. I'm especially interested in analyzing the question of what the distribution in sequencing is likely to be between CRO/service providers and sequencing with internal assets.