Courtesy of Agilent Technologies
With last year's complete sequencing of the human genome, a number of manufacturers raced to produce the first series of human genome microarrays, which were actually sets of two or more chips or slides. The next generation of human whole-genome arrays places the entire genome on a single chip, allowing scientists to observe gene expression profiles on one surface and under uniform experimental conditions, minimizing sample use and labor. "Now that the human genome is sequenced, putting it on a single chip is like conquering Mt. Everest. You do it because it's there," notes Todd Martinsky, vice president of microarray maker TeleChem International of Sunnyvale, Calif.
Three intrepid microarray manufacturers are now racing to the proverbial summit. Applied Biosystems of Foster City, Calif., started first, announcing on July 22 plans to release an array before year's end 2003. Then, on July 28, NimbleGen Systems of Madison, Wis., announced availability of its human whole-genome oligoarray, while Agilent Technologies of Palo Alto, Calif., declared its intention to release a competing product by year's end. All three companies will employ 60-nucleotide-long oligonucleotide probes; these longer sequences should enable tighter binding to targets with greater selectivity and specificity.
NimbleGen has actually won the race; its human whole-genome array contains 190,540 probes, with average coverage of five probes per gene. NimbleGen's in situ manufacturing process employs photolithography using "virtual masks" that are dynamically created using a solid-state array of miniature aluminum mirrors to pattern up to 786,000 individual light pixels.
Applied Biosystems' Expression Array System will use chemiluminescent technology to detect more than 30,000 human genes, while Agilent's microarray, says PR manager Christina Maehr, will sport 44,000 features covering at least 36,000 genes and transcripts on a 1 x 3" slide. Probes will be synthesized in situ using an ink-jet-based technology.
With all these choices, how do microarray researchers decide which system to use? Ezra Abrams, director of new technologies at Matrix Technologies, Hudson, NH, offers these tips: "Data reliability and reproducibility will be the most important features of these microarrays," he says. "Chip price is a big factor. Competition is driving down prices, but chips are still a significant cost component of an experiment."