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Cheap PCR: new low cost machines challenge traditional designs

08/24/2010
Andrew S. Wiecek

Despite price drops, thermal cyclers still remain in the exclusive domain of the research laboratory. Andrew Wiecek talks with three groups working to change this by lowering PCR costs in an attempt to bring this key technology to everyone.   

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Although PCR is a fundamental tool for many biologists, thermal cyclers—essential to driving PCR reactions—have not yet become easily affordable or widely accessible. An instrument’s expense, which is between $4000 and $10,000, has essentially confined its usage to university laboratories, and excluded entities like public schools or field-based health initiatives, which could benefit from easy access to DNA amplification technologies.

Cheaper thermal cyclers can be found through online auction sites such as eBay for as little as $300, but these machines are often sold “as-is,” and lack the conveniences of newer devices. “Half the time it doesn’t work right,” says Josh Perfetto of OpenPCR, a group currently developing low-cost PCR machines. “If you do get a working one, it’s typically an older unit. It doesn’t have fast ramp time rates. It doesn’t have a heated lid.”

While researchers experienced in PCR can work without these features, it creates another barrier for less-skilled users. “Anything we could do with the hardware to make it more robust, I think that’s good,” says Perfetto. “For example, I think it’s important for people to have a heated lid rather than putting oil on the PCR reaction. It creates another step that they can screw up or contaminate.”

But a change might be on the horizon. Three companies have been trying to develop affordable, robust open-source PCR machines. Working out of bedrooms and borrowed lab space, each group’s design choice reflects its particular aspirations, but they all have the same ultimate goal in mind—to lower the financial and knowledge barriers and bring PCR to the world at large.

Polymerase education

Otyp's prototype for their thermal cycler, which they plan to lease to schools for educational purposes. Source: James Peyer, Otyp

James Peyer knew he had to develop an open-source PCR machine. A first-year doctoral student at the University of Michigan studying stem cell biology, the 23-year-old is interested in advancing high school science education. His idea is to develop laboratory exercises in which students perform advanced experiments such as genetically engineering Escherichia coli to fluoresce green. But such experiments require PCR machines and pipets, which most schools cannot afford.

With the help of his younger brother David, a 20-year-old biomedical engineering undergraduate at the Miami University of Ohio, Peyer founded Otyp, a company that leases PCR machines and pipets to schools. Their goal is to provide kits containing leased equipment and necessary reagents for $400, which would fit most schools’ budgets. But Peyer quickly found he could not find reliable PCR machines at this price.

“Even with bulk discounts, I was still paying about $2000 for a PCR machine, which meant that even when I boiled down the cost as much as possible … it still cost a school about $600,” says Peyer. To avoid an unsustainable business model; Otyp trimmed its margins and currently offers the educational kit to schools for that price.

Peyer, a 23-year-old first year doctoral student at the University of Michigan studying stem cell biology, is interested in advancing high school science education. Source: James Peyer, Otyp

“Schools don’t have the money to spend $600 on a 2-week laboratory course, even though it’s important,” says Peyer. He needed to come up with a cheaper way of acquiring working PCR machines, or Otyp’s educational leasing kits would only be affordable to a limited number of schools. With no other option, Peyer and his colleagues decided to build their own instrument.

Considering the current PCR marketplace, such a reinvention seems bold for a group of twentysomethings. But Peyer keeps his mind on the basics. “A PCR machine is pretty simple; it’s just an aluminum block that heats and cools on a schedule,” he notes.

With the help of the newest member of their team, Kyle Lawson, a 23-year-old industrial design graduate from Savannah College of Art and Design, the Peyer brothers spent the last four months working in a makeshift laboratory set-up in Peyer’s apartment bedroom.

“Keep it simple and straightforward” is the design principle for Otyp’s PCR machine prototype, and the team has used open-source protocols to cut costs and increase accessibility.

Otyp's first laboratory was located in James Peyer's Ann Arbor apartment. Source: James Peyer, Otyp

“Our main goal was to cut out the fat of existing PCR machines,” says Peyer. Instead of using an injection-molded plastic case requiring expensive custom models and special plastic to withstand high heat , Peyer’s group went with a simple steel computer case. And rather than using an integrated computer with touch-screen controls and custom circuitry controlled by a proprietary operating system, the Otyp PCR machine will be controlled by the Arduino open source microcontroller and a standard PC through a USB port.

“Trying to figure out what circuitry we want to use and how to write the program to control the machine was a pretty long and uphill process that we’re still grappling with,” says Peyer, who has no programming or electrical engineering background.

The prototype costs $300, not including labor, and the group hopes to refine its design during next year in order to decide whether to go into large-scale production in early 2012.

“It will help us reduce the costs from $600 per school to $400, and if we can do that, that’s only a hair over what they are already spending for gene transfer kits [from other science education suppliers],” says Peyer. These kits eliminate the amplification step and bypass the need for a PCR machine. “If we can get the costs down to that level, then we’ll be able to go viral as far as the education market is concerned.”

Groovy amplification

The first LavaAmp prototype weighs only 180 grams, fits in the palm of a hand, and is powered by a USB cable or 4 AA batteries. Source: Jim Hardy, LavaAmp

Outbreaks of Chagas disease are on the rise, affecting about 10 million people living in endemic Latin American countries. The disease is caused by a parasite, and leads to swelling and potentially fatal heart and digestive system disorders in chronic cases.

“There are people that suffer but have no way to know if they are affected,” says Guido Núñez-Mujica, a Venzuelan computational biologist. Chagas outbreaks in his home country inspired Núñez-Mujica to find a cheap, portable PCR machine to help diagnose those infected with Chagas and other neglected diseases in developing countries.

Portable detection devices are necessary in third-world countries because those infected often live in rural areas. Chagas, for example, is transmitted by triatomine bugs, which live in the cracks of homes in rural or suburban communities. Treating these individuals can be a multiple-day journey: a doctor must travel to the patient to take a sample, return to a laboratory in an urban area, and then return to the patient to present the results and begin treatment. However, with a portable PCR device, diagnosis and care can begin immediately.

Jim Hardy works on another project in his lab where the LavaAmp prototype was developed. Source: Jim Hardy, LavaAmp

At the 2008 SciFoo camp—a weekend retreat for scientists, technologists, and writers, and organized by Google and Nature—Núñez-Mujica found four kindred spirits: open science philosopher Joseph Jackson, former Life Technologies researcher and biotechnology entrepreneur Jim Hardy, and engineers Rik Wehbring and Rob Carlson of Biodesic LLC (Seattle, WA). After the conference, they founded LavaAmp to develop a new breed of portable, cheap PCR machines.

“Make the device rather inexpensive, make it portable, make it run on batteries if you need to, and make it lightweight. That’s the device that we’re working on now,” says Hardy. Their first prototype weighs only 180 grams, fits in the palm of a hand, and is powered by a USB cable or 4 AA batteries.

The LavaAmp team reduced the overall size by eliminating a standard part of typical PCR machines: the aluminum block, which is used to heat and cool the reactions ”It’s a buoyancy-driven convection current of different thermal zones created by different heating elements,” says Hardy. “And the liquid circulates through different zones. That’s how we get the PCR.”

While most PCR machines are designed for high-throughput, the LavaAmp instrument takes the opposite approach. “You don’t have the need to run 96 samples at once,” says Hardy. “For most applications, that’s not necessary.” While the industry-standard 96- and 384-well formats are really good for screening, says Hardy, it’s not practical for diagnostics purposes. Rather than this high-throughput approach, the LavaAmp PCR device can run 20–25 samples at once.

The LavaAmp’s thermal-gradient convection currents provide three different temperature zones that perform denaturation, annealing, and extension. “The platform itself made it much simpler,” says Hardy. “There’s not a need for a lot of sophisticated electronics.”

The biggest technical issue that remains is a convenient way of loading and unloading the samples into the system’s loops. “The loops have a very small volume,” says Hardy. “Trying to keep air bubbles out is a problem because air bubbles disrupt the current.”

While the initial price will be about $300 to $500, the group’s ultimate goal is to design an instrument that will cost less than $100. “The device is just going to be more or less disposable. You can use it two or three times and just get another one if you leave it behind somewhere,” says Hardy. The first commercial versions are expected to be available in early 2011.

Hack this PCR!

Although the OpenPCR machine will have a rather traditional design with an aluminum block, it will have an untraditional case made from birch wood. Source: Josh Perfetto, OpenPCR

At the January 2010 Outlaw Biology conference, Perfetto and software developer Tito Jankowski heard first-hand from several individuals about how the DIY Bio community could benefit from a cheap, open-source thermal cycler that could be adapted for different applications. Driving back from the conference, the pair agreed that they could fill this void.

Thus, the OpenPCR project began. According to Perfetto, OpenPCR started more as an open hardware project, not so much as a big company start-up. “But as we’ve gone forward, new ideas have emerged and we think we could meet some potentially bigger things coming out of this,” he adds.

Neither Perfetto nor Jankowski has formal training in biology, but they have been involved in the California DIY Bio community. Jankowski was part of the Brown University iGEM team that designed an open source gel electrophoresis box, which is now being sold by Pearl Biotech for $499. Perfetto is excited about the potential of the DIY Bio community. “I’ve worked on a lot of mobile phone software and rep software,” says Perfetto. “There’s still innovation, but the field is relatively mature. Biotech is where we’re going to see a lot more innovation and excitement for the next coming years.”

Computer scientist Josh Perfetto and software developer Tito Jankowski heard first-hand from several individuals about how the DIY Bio community could benefit from a cheap, open source thermal cycler and agreed that they could fill this void. Source: Josh Perfetto, OpenPCR

Although the OpenPCR machine will have a rather traditional design with an aluminum block, Perfetto and Jankowski have experimented with different parts and materials to create the fastest, cheapest machine for the unskilled biology enthusiast. The machine’s design features a heated lid, which is essential, according to Perfetto, because untrained users struggle with the mineral oil addition step to reduce condensation. The group considered different heating and cooling options—including convection and radiation to cool the heat block—but they ultimately decided on a complex Peltier cooling solution to quicken experiments and enable the use of cheaper reagents. And, instead of permanently gluing the case shut, the case will be shut with bolts for easy removal for their bio-hacker clients.

In two months, OpenPCR kits will be available for biology hobbyists for $300–400, and will include all the necessary parts and schematics. Pre-assembled machines will also be offered as well.

While OpenPCR is initially targeting the hobby and educational markets, Perfetto and Jankowski do have some next-generation ideas, including developing a line of customized detection devices that could be used by anyone, even those without an understanding of PCR. “We’re focusing on the user interface and making it easier,” says Perfetto. “We want enable people that don’t have a strong biotech background and don’t know the details of PCR to use this device to answer questions that interest them.”

PCR for all
Cheaper PCR machines are well on their on their way in their promise of educating the next generation of scientists, diagnosing diseases more quickly in third-world countries, and changing PCR applications around the globe.

Although each effort is separate, Jackson from LavaAmp explains that it all stems from a small but growing community attempting to push open-source biotechnology innovation. They all know each other, he says. “So it looks like there is this demand, and at least we’re converging.” He says the next year, when these cheap machines begin stocking shelves, will indicate how people want to use them.

“So how many people are going to be running PCR in their kitchen? We’re all interested in seeing the applications of the machines.”