Alan-Philippe Blanchard, Ph.D.

BS Mathematics, 1980 Caltech
Ph.D. Computation and Neural Systems, 1993 Caltech
Thesis: Sequence Specific Effects on the Incorporation of Dideoxynucleotides by a Modified T7 Polymerase

Since the July, 2006 aquisition of APG, I have worked for Applied Biosystems where I am a Scientific Fellow working on improving our next-generation DNA sequencing platform.
From September 2004 to July 2006 I worked for what was called Agencourt Personal Genomics (APG) in Beverly, MA. APG had developed a very high throughput DNA sequencing instrument based on a chemistry using DNA ligase instead of the customary polymerase-based Sanger sequencing. Using our ligase-based approach allows us to sequence homopolymer stretches that are problematic with polymerase-based sequencing-by-synthesis schemes. Our instrument sequences many millions of short DNA fragments in parallel giving it a potential throughput orders of magnitude greater than existing Sanger sequencers.
Part of my contribution was inventing a scheme that produces partial sequence information from two (or more) bases at each cycle. This allows for the detection of certain classes of error beyond what is possible with traditional single-base encodings.
A degree in math does come in handy at times.
On May 30, 2006 it was announced that Applied Biosystems of Foster City, CA had agreed to buy APG for $120M. They have announced plans to start placing instruments based on our chemistry at customer sites in 2007.

From March to November of 2003 I was VP of Research and Development at Manteia SA, based in Coinsins, Switzerland. Manteia went bankrupt and the assets were sold to Lynx (Hayward, CA) and Solexa (near Cambridge, UK).
Lynx and Solexa subsequently merged to become the present-day Solexa which has announced a sequencing instrument using the Manteia DNA amplification technology (clusters).
Solxa was subsequently bought by Illumina of San Diego, CA.
I never made a dime off the Manteia gig, but the experience was invaluable at APG, starting day 1.
If anyone from Manteia is reading this, please send me a note. I'd love to know where everyone went.

My previous project was developing an instrument to make arrays of DNA molecules using ink-jet printer technology. I started this project while I was finishing up my Ph.D. at Caltech. It took another 4 years, while I was a post-doc at the University of Washington, to bring the technology to the point where venture capitalists get interested. Rosetta Inpharmatics was founded in 1997 on the basis of this and related technologies.
The ink-jet technology was licensed and transfered to Agilent, who now sell custom in situ synthesized DNA arrays using machines based on my designs.

Machines I designed at Agilent's production facilities.

Merck bought Rosetta in 2001 for $600M and I left shortly thereafter.

Ed Southern did much of the pioneering work on synthetic DNA arrays at Oxford, and was the first person to suggest using ink-jet technology for their manufacture. Ed founded Oxford Gene Technology to commercialise some of his inventions. For a while, OGT was using array makers that I designed.
Two of these machines found their way to London when part of OGT was aquired by Arrow Therapeutics

Here is a review I wrote on the subject of Synthetic DNA Arrays.

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