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Alternative Sequencing Technologies

Following is a handful of the higher-profile companies and labs developing alternative sequencing technology.

 

Perlegen

Founded: 2000

Home: Mountain View, Calif.

Fast facts: This Affymetrix subsidiary is focused on using chip technology for resequencing

Boast: Already doing one genome every 10 days.

 

Mobious Genomics

Founded: 2000

Home: Exeter, UK

Fast facts: Launched by 27-year-old Daniel Densham, this startup is developing "molecular resonance sequencing"--a process that detects bases as they are added to a strand during replication.

Boast: 300-500 base pairs per second this year; read length of 150 Kb

 

Solexa

Founded: 1998

Home: Essex, UK

Fast facts: This Cambridge University spinoff is working with re-usable fluorescence and microarrays to develop a highly parallel base-by-base resequencing method that does not require amplification.

Boast: Five orders of magnitude faster sequencing; product launch in 2004.

 

Callida Genomics

Founded: 2001

Home: Sunnyvale, Calif.

Fast facts: A surprise joint-venture denouement to a lawsuit between Hyseq and Affymetrix, Callida is developing a method that creates high-density microarrays with all possible four-base sequences. This allows sample DNA to hybridize to these probes, and reassembles the results. Husband-and-wife team Rade and Snezana Drmanac plan to use the platform for both de novo and resequencing.

Boast: read lengths three times the current maximum at a comparable cost.

 

US Genomics

Founded: 1997

Home: Woburn, Mass.

Fast facts: US Genomics' GeneEngine platform promises to eliminate assembly through direct linear analysis of DNA. It has the backing of Craig Venter, who joined the company's board and plans to bring its technology (among others) to his new sequencing R&D lab.

Boast: Eventually, "up to millions of base pairs per second."

 

Visigen

Founded: 2000

Home: Houston, Texas

Fast facts: This University of Houston spinoff is developing a polymerase-based sequencing method that transiently adds fluorochrome to a growing DNA molecule; the signal is read through fluorescence-energy resonance transfer.

Boast: Ultimately, one genome in 24 hours

 

Daniel Branton, Harvard Department of Molecular and Cellular Biology. Avoiding enzymology altogether, Branton's group is working on a nanopore-based system that will draw a single strand of DNA through a machined pore. A detector at the pore will identify bases as they pass.

 

David Burke, University of Michigan Department of Human Genetics. Burke, working with Michigan's Mark Burns, wants to bring sequencing equipment down to the computer-chip scale, ultimately allowing sequencing machines to be produced cheaply and quickly by the same machining technology that the computer industry uses.

 

Dan Ehrlich, director of the BioMEMS lab at Whitehead/MIT. Ehrlich's group is developing an electrophoresis system that uses miniaturized

chips; the machine is being commercialized by GenoMEMS and Shimadzu

Biotech and scheduled for launch in 2003.

 

Elaine Mardis, co-director of the Washington University Genome Sequencing Center. Her team is now trying to figure out how to add robotics to other steps of the capillary process, and integrate sample prep into sequencing.

 

David Schwartz, University of Wisconsin at Madison. Schwartz is adapting to sequencing his optical mapping technique, which use polymerases to incorporate labeling fluorochromes into DNA.

 

Watt Webb, Professor of Applied Physics, Cornell. Webb is developing a method of briefly incorporating fluorescently labeled trinucleotide into the growing DNA chain to generate a signal.

 

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