Skip to main content

Affymetrix Unveils its Streamlined GeneChip Array Production Process


When Affymetrix began making microarrays in the early 1990s, founder Steve Fodor and his early collaborators cobbled together their manufacturing machinery from chemistry lab instruments and used semiconductor fabrication equipment they bought at auctions.

But today, the process of manufacturing GeneChips is as painstakingly streamlined and standardized as any ultra high-tech assembly line in the world.

In a recent tour of its Sacramento manufacturing facility, Affymetrix gave BioArray News an exclusive glimpse into the multiple stages of this process.

The facility, which makes GeneChips 24 hours a day, seven days a week, has been fully operational since January 1999, and produced its hundred thousandth GeneChip last August. Now, the facility is well on its way toward the one million chip mark, said Steve Karas, the general manager of the plant.

In unveiling these production methods, Karas described how each stage of the manufacturing process is carefully quality-controlled using cameras and computers that record every manipulation of the wafer that will be divided into GeneChips. The wafers themselves are tracked using batch records and serial numbers.

“A level of discipline and rigor is built into the process,” said Karas, who came to Affymetrix in 1998 from pharmaceutical giant Hoechst.

In April, US Food and Drug Administration officials visited the manufacturing plant and determined that the GeneChips were being reproducibly manufactured in accordance with their standards. This preliminary mark of approval signals the direction in which Affymetrix is heading, a path toward use of GeneChips as FDA-approved diagnostic tools. Karas, who has 23 years of experience manufacturing pharmaceutical products and reagents, has worked toward building the company’s manufacturing process into one that can withstand an FDA audit.

A key part of this process is a strictly enforced cleanroom standard. The chips are manufactured in a temperature- and humidity-controlled class 1000 cleanroom, which means that there is a limit of 1,000 particles greater than or equal to 0.5 micrometers per cubic feet of air, according to the federal standard that classifies cleanrooms.

The 175 operators and process engineers who work at the plant must don cleanroom garb, including hair caps, hoods, white jumpsuits, boots or cleanroom shoes, facemasks, and plastic gloves, and pass through a sealed corridor where air jets blow off any remaining particles, before they begin their 12-hour shifts at the plant.

The Affymetrix cleanroom standard is not quite as stringent as those now applied to semiconductors, which now typically are synthesized in a class 10 facility and can be tested throughout the process, unlike microarrays. Still, Affymetrix applies its standard rigorously ó a fact the company considers as a point of pride.

“Some of our competitors don’t even do [chip production] in a cleanroom,” said Karas. But “if we see a particle in any array, we don’t ship it.”

In the first stage of the manufacturing process, operators prepare the wafers for photolithography, the light-based method that Affymetrix uses to synthesize its oligos in situ on the array. The wafers are first coated on one side with a yellow polyimide coating, which serves as the basic filter for the light that will beam down onto the wafers.

Next, wafers are transferred to the room where the nucleic acids are applied and the photolithography takes place. On either side of this room, a row of ten photolithography stations is coupled with 20 chemistry stations. Operators stand between a photolithography station and two chemistry stations, intervening where needed and watching the process unfold line by line on the monitors of computers controlling it.

First the wafer is inserted into the chemistry station, and sits in a translucent vertical diamond-shaped window while being bathed in a liquid containing purified quantities of a single nucleotide. The liquid is pumped through the station, from a separate adjoining room (where the bases are held to prevent any spillage from damaging the machines), through color-coded capillaries to the chamber where the wafer is held.

Next, the wafer moves to a photolithography station, where it is covered by a selected mask with a tiny grid pattern in which certain squares on the grid block the light and others allow it to shine through. The computer cross-checks each mask to ensure that it is the proper one in the sequence.

In currently used equipment, video monitors allow operators to see whether the masks are aligned with the wafers, and synchronized levers allow them to manually align the two.

But a new generation of automated photolithography stations, which is just being installed and pilot-tested at the plant, will eliminate the operator-intervention stage of this process, saving time and reducing the variability that comes with manual alignment.

While the wafer-mask complex is held in the photolithography station, it is exposed to light from above, which fixes nucleotides on the GeneChips in the exposed areas.

The process is then repeated, with another base being added and another mask being inserted into the photolithographic station. The company has compared this process of synthesizing oligos on the wafer, one layer of bases at a time, to the construction of a building one floor at a time.

After the oligos are built in this manner, the wafers are then sent to a third room, where an operator first logs in each wafer, then slices up the wafer with a waffle-shaped instrument, into smaller chips. The wafers can be divided into matrices of 49, or 169, or 400 chips, depending on the specific features of the array.

Next, an operator at a second station uses machine-guided gluing devices to glue each genechip along the edges into the signature trapezoidal plastic cartidge that holds it. A vacuum device sucks any fumes from the glue away from the chip.

After the chips dry and final quality control steps are taken, they are packaged, catalogued, and sent to the distribution part of the facility.

In manufacturing GeneChips that follow the 49 chip-per-wafer model, the company saves four chips per wafer “We test two and we hold two,” said Karas.

“The beauty of our process is that if a customer says something is wrong, they can give us a sample, and we can take the chip off line and run it,” added Anne Bowdidge, director of investor relations for Affymetrix.

Currently, four different shifts of workers keep this manufacturing process going around the clock, rotating from station to station to avoid boredom and a consequent decline in product quality. The facility is poised for growth, with an entire room of unused photolithography and chemistry machines. The plant also has room to expand, as it occupies only three of the ten acres the company owns in the area. And it lies on land that is far from the fault lines that run through the Bay Area, including Affymetrix’s headquarters. If the market for Affymetrix’s arrays continues to expand as predicted by many analysts, the company appears ready to meet the demand.


Stages of Affymetrix Manufacturing Process:

1. Workers suit up in cleanroom garb and go through corridor to class 1000 cleanrooms where chips are fabricated.

2. In the first room, silica wafers in coded boxes are catalogued and coated with polyimide light-sensitive coating.

3. Wafers go to photolithography and chemistry station room.

4. Wafers are inserted in chemistry station and are coated with a liquid containing a single base.

5. A camera confirms the serial number of the wafer and the wafer goes to the photolithography station.

6. An operator inserts a mask in the photolithography station above the wafer. A computer checks the mask to ensure that it is the correct one for that stage.

7. The operator manually aligns the wafer and mask, or in new machines, a computer-controlled process aligns the wafer and mask.

8. The wafer is exposed to light.

9. The wafer is transferred to the chemistry station, where it is prepared for the addition of the next base.

10. The process is repeated until all of the bases in the 16- to 25- mer oligos are synthesized on the wafer.

11. The wafers are transferred to a new room, catalogued, and divided into chips.

12. The chips are glued onto cartridges using a patented machine process.

13. Chips are checked using quality control standards.

14. The chips are packaged and readied for shipment.

The Scan

Gap in COVAX Doses

BBC News reports that COVAX is experiencing a vaccine shortfall, as the Serum Institute of India has paused exports.

Sanofi, GSK Report Promising Results

The Wall Street Journal reports that the candidate SARS-CoV-2 vaccine from Sanofi and GlaxoSmithKline has had encouraging early results.

Influence of Luck

The New York Times examines how the US avoided variant-fueled increases in COVID-19 cases.

PLOS Papers on Retina GWAS, Hantaan Virus, COVID-19 Phenome-Wide Association Study

In PLOS this week: genome-wide association study of retinal morphology, analysis of hantaan virus found in a mouse, and more.