College of American Pathologists
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  For nucleic acid extraction, choices galore


CAP Today




October 2008
Feature Story

William Check, PhD

Thomas J. Monroe PhD, director of molecular diagnostics at Spectrum Health in Grand Rapids, Mich., is looking for an instrument to do automated nucleic acid extraction. In fact, Dr. Monroe is looking for two such instruments: a smaller one with a fast turnaround time and a high-throughput instrument that integrates front-end nucleic acid extraction and back-end amplification/detection by real-time PCR.

While Dr. Monroe might appear to be in an enviable position, being able to purchase two pieces of advanced equipment, his experience shows that the process is not a simple one. Today’s market offers laboratorians an embarrass­ment of riches. “We have evaluated several instruments in the lab over the last couple of years,” Dr. Monroe says. To replace their current MagNA Pure LC, Dr. Monroe has looked at the smaller, fast-turnaround-time instruments, including the Qiagen QIAcube, Pro­mega Max­well, and Fujifilm AutoGen QuickGene-810. He now has a Qiagen BioRobot EZ1 in the laboratory for evaluation and plans to look at the Qiagen QIA­symphony, which he finds attractive because of its ability to handle large numbers of specimens. He hasn’t looked at any of the BioMérieux products, such as the NucliSens EasyMag, because, he says, “they appear to be going after the infectious disease market. We process some ID samples, but most of our testing is on blood, bone marrow, and tissue.”

For a high-throughput integrated system, Dr. Monroe looked at the Roche AmpliPrep/TaqMan system in a nearby institution. “That would be more attractive if we were running HIV and HCV viral loads, which we are sending out,” he says. A separate laboratory in Dr. Monroe’s hospital that tests for Chlamydia ­trachomatis and Neisseria gonorrhoeae (CT/NG) and is considering offering hepatitis C viral loads is currently evaluating the Abbott Molecular m2000, which consists of an integrated m2000sp instrument for sample preparation and an m2000rt based on an ABI thermal cycler for real-time PCR amplification and detection.

“Ten years ago there was not that much to choose from,” Dr. Monroe says. With greater choice has come more rigorous evaluation and comparison. Greater cost too. “We have to live with these decisions for years,” Dr. Monroe says. “Capital budgets are very tight. It will take us a year just to get approval for this expenditure.”

Richard L. Hodinka, PhD, director of the clinical virology laboratory at Children’s Hospital of Philadelphia and associate professor of pediatrics, University of Pennsylvania School of Medicine, has witnessed major changes in this field. “The first automated extraction instruments were large and expensive and not totally appropriate for laboratories with low to moderate sample volumes,” Dr. Hodinka says. He estimates that 85 percent of clinical laboratories that want to do molecular testing may be in this category. In the second wave, vendors brought out smaller instruments, such as the Roche MagNA Pure Compact and the EZ1. “Now there are even more options available,” Dr. Hodinka says. Another example is the Beckman Coulter Sprite, which is due out by year’s end. All of these smaller instruments have prepackaged, ready-to-use, foil-sealed reagent cartridges and can handle one sample or as many as six to 10 samples at a time, depending on the system. “Not much expertise is needed to run these systems,” Dr. Hodinka says. “They are fully automated and can extract nucleic acid from a variety of specimen types in a short period of time.”

There are good reasons for this proliferation of large and small instruments that do automated nucleic acid extraction. Ease of use is the first. “Some are truly walkaway,” Dr. Hodinka says. “All offer limited sample manipulation.” Some can be programmed to do post-elution dilution, concentration, or dispensing. “One of the biggest problems with manual extraction is that it requires lots of time and labor,” Dr. Hodinka says. “We were finding that 50 to 60 percent of our total molecular testing time was spent just handling samples and getting nucleic acid out.” Not only are multiple manipulations costly, but also they create many steps where things can go wrong and they introduce run-to-run variability. With manual extraction, yield is often low and samples are partially degraded, so they may not amplify well, and substances that can inhibit the subsequent PCR amplification reaction often co-purify with the nucleic acid. Automation simplifies specimen processing and adds consistency and purity. “Robots do it the same way every day as long as you program them correctly,” Dr. Hodinka says.

One downside is having to choose, as Dr. Monroe is, from all that is available. “People often call and ask me what do I use and how did I decide on that instrument. It’s difficult,” Dr. Hodinka says. “Companies are reluctant to simply drop an expensive instrument into your lab to evaluate its performance for several months or more and then have it removed. They want you to commit to their product first.” And the instruments are expensive. Dr. Hodinka provides a few list prices: Roche MagNA Pure LC, ~$85,000; BioMérieux NucliSens EasyMag, ~$80,000; Roche MagNA Pure Compact or Qiagen BioRobot EZ1, ~$30,000; Roche AmpliPrep/TaqMan, ~$130,000; Abbott Molecular m2000sp, ~$140,000. “Most people don’t pay list price,” Dr. Hodinka notes, “but they are still expensive.” Because many clinical laboratories may not be able to buy the equipment outright under a capital purchase agreement, the availability of leasing and reagent-rental options can be important.

Size and weight considerations may be overlooked. A MagNA Pure LC weighs more than 400 pounds. The AmpliPrep/TaqMan and m2000sp platforms are “huge,” Dr. Hodinka says. Neither sits on a bench. “Do you have that kind of space?” he asks. “You may have to go to administration to have your lab reconfigured.

“The bottom line for me,” he says, “is that automated extraction instruments are practical and easy to use.” They offer rapid protocols and a high yield of intact and pure nucleic acid, usually free from inhibitors. And they replace error due to human variability with consistency. “Typically there ends up being a direct cost savings due to decreased labor,” Dr. Hodinka says. “The downside is the upfront financial outlay. But if you figure how much you’re spending without automation, it makes financial sense to bring one in because it pays for itself quickly and it clearly helps the technologists do their work more efficiently and in a less stressful environment.”

Ray Widen, PhD, scientific director of the esoteric testing laboratory at Tampa General Hospital and clinical assistant professor of molecular medicine at the University of South Florida College of Medicine, underscores Dr. Hodinka’s point about reproducibility. When he was validating an Abbott m2000 for HIV viral load testing, he found inter-run CVs of 1.5 percent for a target value of about 1,000 copies/mL and less than one percent for a target value of 120,000 copies/mL. Dr. Widen calls these numbers “really excellent,” and adds: “They apply to any automated system. It is very difficult for a human to accomplish that degree of precision when pipetting small volumes.”

Karen Kaul, MD, PhD, is another molecular pathologist who stresses the difficulty of making decisions about automated extraction instruments. “It is complicated trying to figure out how fast you need the DNA, how much flexibility you need in terms of input samples and output volumes, as well as cost and performance,” says Dr. Kaul, who is Board of Directors chair of molecular pathology and director of the molecular diagnostics laboratory at NorthShore University HealthSystem, Evanston, Ill., and professor of pathology and urology, Northwestern University Medical School. “The field is moving so quickly. It takes a lot of time to evaluate all the available instruments,” she says.

Of the Ampli­Prep/ TaqMan and m2000 systems, she says, “The options are becoming more complex, larger, and more expensive.” Dr. Kaul is acutely aware of cost and space considerations, describing the new integrated systems just as Dr. Hodinka did—“huge.”

“I can’t get them into my lab to evaluate without taking out benches,” she says. “And it costs money to take out benches. My hospital won’t do it on a trial basis. Not that I have benches that I can spare in the first place.”

Dr. Kaul has a MagNA Pure LC. “It has served its purpose well, although it is a bit unwieldy and slower than some of the newer instruments,” she says. Then she added two EZ1s to the lab. “They are rapid and straightforward and work well,” she says. “Essentially, you push a button and 30 minutes later you have nucleic acid. Our techs love them, but they don’t have so much flexibility in tailoring protocols.” Her lab began to outgrow them in the past couple of years—they process only six samples at a time—and she and her colleagues began to look at higher-throughput instruments that would allow them to do 24 to 48 samples more quickly and with less hands-on time. They settled on the EasyMag, which she says is also working well.

Though Dr. Kaul does not yet have one of the “huge” integrated systems, she endorses Dr. Monroe’s two-instrument approach. “Maybe,” she says, “a molecular lab needs both a more nimble, lower-throughput instrument that provides flexibility and a less flexible instrument committed to specific protocols for very high-volume tests like quantitative viral load and Chlamydia/Neisseria.”

Interviews with almost a score of molecular pathology laboratory directors revealed adherents of Qiagen, BioMérieux, and Roche instruments. About half of those interviewed have gone the two-tier route, typically combining either a BioMérieux or Roche medium-throughput instrument with the Roche AmpliPrep/TaqMan or the Abbott m2000. Only one of the Qiagen users has a large integrated system as well.

Alexandra Valsa­makis, MD, PhD, is a Qiagen user. “We use the M48 mid-size extractor,” says Dr. Valsamakis, who is director of clinical virology and molecular microbiology and associate professor of pathology at the Johns Hopkins Medical Institutions. “We started using it when it was Genovision,” Dr. Valsamakis says. Her laboratory uses the M48 to extract nucleic acid for all assays, including hepatitis C and B viral load. “We have two M48s and they are very busy,” she says.

Before putting the extractor into clinical service, the laboratory validated every assay with every specimen type used. They also had to re-test all banked samples used for in-house proficiency testing, QA, or training panels. “It’s a lot of work to make a switch,” she says, “but once you do, the techs will never want to go back. Your productivity will skyrocket as techs are liberated to do other work.”

Though Dr. Valsamakis’ laboratory does not have a large integrated instrument, she did trial work with the AmpliPrep/TaqMan and liked it, especially in the configuration with the TaqMan 96 linked to the extractor through a docking system, which provides “sample in–answer out” performance. “It was a thing of beauty to watch,” she says. “Unfortunately, it is not approved for clinical use in the U.S.” She notes one unique feature of this system: It extracts each sample individually, which reduces the risk of contamination. “The tradeoff is fairly slow throughput,” she says. “Its other disadvantage is that in its current format it is designed almost exclusively for plasma and serum.”

Daniel H. Farkas, PhD, HCLD, executive director of the Center for Molecular Medicine, Grand Rapids, Mich., has a full range of ­Qiagen instruments. “We have low-, medium-, and high-throughput systems,” he says—the EZ1, ­QIAcube, and 96-well BioRobot Universal System, respectively. He has been a Qiagen customer since 1987. “I chose to go with the company that I’ve known for so long and that has been doing this the longest,” Dr. Farkas says.

Several others have also selected the QIAcube. Qiulu Pan, MD, PhD, director of the molecular pathology laboratory at Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, used a preexisting MagNA Pure for factor V Leiden, HCV genotyping, and herpes simplex virus.

When Dr. Pan started doing real-time PCR, however, he found that DNA and RNA concentrations from the MagNA Pure were not so high and that the yield varied for separate extractions of the same specimen—there was sometimes a difference of 10 in Ct value between separate extractions of the same sample, which translates to almost a 1,000-fold difference in concentration. Subsequently, he used it only for FVL mutation analysis where the DNA concentration is not critical, since every cell should have the mutation. “It was not even good for HCV genotyping, because you need enough template to do the determination accurately,” Dr. Pan says. (In his experience, the yield problem is peculiar to magnetic bead instruments; he observed it with the EZ1 also.)

Dr. Pan then purchased a QIAcube, which he says gives higher DNA yield and smaller variance. Because it processes only 12 samples at a time (compared with 32 for the MagNA Pure LC), he plans to purchase a second QIAcube. At less than $20,000 list price, it is not a major expenditure. When Dr. Pan first got the QIAcube, he experienced difficulties and was calling technical support daily. It turned out he had received an early model. After the company sent a recently manufactured one, “the problems nearly disappeared,” he says. Dr. Pan remains what he calls “a diehard Qiagen fan,” and says he used their manual columns for 10 years.

Robyn Temple-Smolkin, PhD, director of laboratory operations at Big Sky Diagnostic Labs in Helena, Mont., tells a similar story. “I kind of grew up on Qiagen manual spin columns,” she says. In her previous position she converted the laboratory from manual extraction to a QIA­cube for certain applications. “We saw really clean results with less technologist hands-on time,” Dr. Temple says. One advantage of the QIAcube is its flexibility—many of Qiagen’s spin columns can be run on it. “QIAcube is not for all labs,” Dr. Temple says. “But for small to medium labs that need to do a range of applications, it is a nice fit.”

In her current position in a startup clinical laboratory, Dr. Temple says, “A QIAcube was one of the first things we considered buying. It starts at an affordable price and is a nice entry into automated protocols.” They have since purchased one as part of their new laboratory.

Some laboratorians have said that, because tubes are open during extraction on the QIAcube, there is potential for contamination. Dr. Temple acknowledges this possibility. “But,” she says, “that is true of almost any more-open system.” When she first validated the QIA­cube, she put samples with extremely high cell numbers onto the platform in a checkerboard pattern, then repeated the test in reverse order multiple times. She was asking, do you get aerosolization that compromises product integrity? “I never observed contamination in various downstream applications,” she reports, either during validation or during routine use.

Hui Jia Dong, PhD, technical director of molecular pathology at the University of Florida Gainesville Medical Center, ordered a QIAcube earlier this year. She uses it for HCV RNA extraction but is still using manual columns for blood and genetic tests. “It is definitely my goal to switch some of that to the QIA­cube,” she says. In a comparison of the QIAcube to manual extraction, Dr. Dong found that the automated instrument saves time and “consistency [of RNA extraction] from run to run is so much better than manual.” Setup time is 10 minutes and, depending on sample load, run time is 40 to 70 minutes.

One of the few Qiagen laboratories where the two-tier approach prevails is the molecular diagnostics laboratory at Case Western Reserve University, where Lan Zhou, MD, PhD, assistant professor of pathology, is the director. They have a QIAcube, which they use for cytomegalovirus and herpes simplex virus DNA extraction from whole blood, plasma, and cerebrospinal fluid and for JAK2 mutation analysis; and an AmpliPrep/TaqMan 48, which they plan to use for HIV, and possibly HCV, viral load.

According to Dr. Zhou, one attraction of the QIAcube was that it was easy to make the transition from Qiagen manual spin columns, which they had been using for HSV and JAK2 assays. Technologists like the fact that, after about 20 minutes of prep time, the QIAcube is total walkaway. Dr. Zhou likes the fact that HSV DNA extraction with the automated instrument is actually a little better than the manual method. “The Ct value looks a little lower,” she says, “which suggests more efficient extraction.”

In-house validation of the AmpliPrep/TaqMan for HIV viral load measurement, which is an FDA-cleared assay, is about half done, Dr. Zhou says. “We have pretty comparable results to Amplicor with manual extraction,” she reports. The laboratory performs about 300 HIV viral load assays per month. The technologists were trained on the instrument recently, Dr. Zhou says. “They need some time to get used to the system. It requires a lot of daily maintenance. But it saves a lot of time on extraction and PCR setup.” Roche is applying for approval of the HCV viral load assay also.

Christine C. Ginocchio, PhD, director of microbiology, virology, and molecular diagnostics at North Shore-LIJ Health System Laboratories, Lake Success, NY, has also adopted a two-tier approach. They have been using a BioMérieux EasyMag for three years as their basic instrument and bought a second unit last year. It is used for extracting bacterial and viral DNA and RNA from a broad range of specimen types, including serum, plasma, cerebrospinal fluid, tissue, and respiratory samples. It has flexible input volume, from 10 µL to 1 mL, and variable elution volumes, which is good for concentrating samples or increasing the volume for multiple tests. “It gives extremely low levels of inhibition,” Dr. Ginocchio says. It isolates total nucleic acid, which is convenient for doing multiple tests on small samples, such as looking for DNA and RNA viruses in CSF. In addition, the EasyMag offers flexibility: Since it uses the same reagents for RNA and DNA and for different sample types, one can put different sample types in adjacent wells and set different parameters for input and elution volumes for each chamber. Contamination has not been a problem. “We do wipe tests and clean the instrument well,” Dr. Ginocchio says.

As its high-throughput instrument, Dr. Ginocchio’s laboratory has an Abbott m2000 with an ABI 7500 real-time PCR backend. This integrated system does automated extraction, PCR setup in a 96-well tray, and PCR amplification and detection; turnaround time for 96 samples is about six hours. Dr. Ginocchio notes that the m2000 is not true sample in–result out. “You have to take the plate out [of the extractor] and put it into the real-time PCR machine,” she says. However, this is also true of the integrated Roche instrument that is available in the U.S., the Ampli­Prep/ TaqMan 48.

Dr. Ginocchio uses the m2000 for HIV viral load, for which it is FDA cleared. She plans to convert hepatitis C viral load to the m2000 when that assay is cleared. “First we will have to validate it [against our current method],” she says. “If it performs well, we will switch that also.” The same applies to hepatitis B viral load.

When choosing a high-throughput integrated system, Dr. Ginocchio was impressed with the Abbott data on recombinant viruses and non-B HIV strains. “In the New York area we have seen many patients with recombinant viruses and non-B viruses,” she says, “so for us that is important.” In addition, Dr. Ginocchio did a very large validation study with the m2000. “I was pleased with its linear range, precision, reproducibility, sensitivity, and reactivity with cases that had non-B subtypes,” she says.

Three other laboratories combine an EasyMag with an m2000. A combination of MiniMag, EasyMag, and MagNA Pure Compact fills the low- and medium-volume testing needs in the laboratory of Kathleen Stellrecht, PhD, D(ABMM), HCLD (ABB), director of microbiology and associate professor of pathology and laboratory medicine, Albany (NY) Medical Center. Several years ago Dr. Stellrecht found that the BioMérieux instruments recovered higher levels of DNA from CMV and, to a lesser extent, Bordetella than did MagNA Pure or their manual phenol-chloroform method.

Stat tests, such as herpes simplex virus and enterovirus in CSF, are done with the MiniMag and a Cepheid SmartCycler. For higher-volume tests, the EasyMag comes into play. Finally, the MagNA Pure Compact is used for some bacterial targets, particularly Staphylococcus aureus and genetic testing—FVL and prothrombin mutations—on whole blood.

Dr. Stellrecht had been satisfied doing HIV viral load testing with the EasyMag and a BioMérieux assay, but higher volume, combined with BioMérieux’s discontinuing its HIV assay, forced a switch. “I evaluated the literature and talked to colleagues,” she says. “I chose the m2000 because the assay itself looks more robust in terms of less variation in viral load from different individuals, and it is more robust in detecting virus strains that might have some sequence divergence.”

Dr. Widen’s laboratory performs a wide range of molecular tests: infectious disease, genetics, oncology, and hematology. For lower-volume tests, an EasyMag and Qiagen columns are used. For high-volume tests, like HIV viral load testing, Dr. Widen purchased an m2000 with an ABI 7500 thermal cycler. He has also switched hepatitis C viral load testing to the m2000 using the Abbott analyte-specific reagent kit, which he says is allowed because Abbott has declared its intent to seek FDA clearance. Volume for each assay is about 150 per month, which Dr. Widen calls “high enough to justify the instrument.” He chose the m2000 because it was the first cleared for HIV, because he had been using the Abbott HCV kit, and because Abbott is working on putting CT/NG on this platform, as well as HBV. He was also influenced by the data showing that the m2000 does a better job of picking up unusual subtypes of HIV. Otherwise, he says, “I see them as equivalent systems.”

Linda Sabatini, PhD, HCLD, technical director of molecular pathology at ACL Laboratories of Illinois Central Laboratory, also has an EasyMag and an m2000. ACL’s annual volume of 30,000 specimens is made up of a variety of analytes, but HIV and hepatitis C viral load testing makes up more than one-third. (Testing for CT/NG and HPV is done in other laboratories.) All of ACL’s nucleic acid extraction was done manually. “Our biggest motivation [for purchasing automated extractors] was increased volume,” Dr. Sabatini says. She brought in an EasyMag, on which they do viral assays. “It can handle viral transport media, CSF, and bronchoalveolar lavage,” she says—and genetic assays on whole blood. One downside is its 24-sample capacity. “We have another one on our capital equipment request list,” Dr. Sabatini says.

She also wanted to automate the viral load assays and update them to real-time PCR. “Our choice of the Abbott instrument was somewhat accidental,” Dr. Sabatini says. She was intending to evaluate both instruments, but “we could only get hands-on access in the lab for the Abbott.” She had it live in the laboratory for a year. Her technical supervisor, Lech Mazur, MT, MS (ASCP), oversaw a 500-specimen comparison with the lab’s manual method for HIV viral load. “I was very pleased with the performance of the whole system,” Dr. Sabatini says. “The m2000 has a much broader dynamic range than the Cobas” (which she notes is true for any real-time assay), eliminating the need for a second (quantitative or ultrasensitive) assay. Dr. Sabatini has also set up hepatitis C and B viral load on the m2000 as analyte-specific reagents. She validated linearity up to 200 million HBV copies.

Mazur says one FTE was saved per instrument by converting from all-manual to all-automated extraction. At the same time, the number of specimens that are inhibited has been reduced from about 10 percent to one to two percent for both instruments.

An EasyMag-Ampli­Prep/ TaqMan combination proved to be the solution to increased volume for Yi-Wei Tang, MD, PhD, director of the molecular infectious diseases laboratory and associate professor of pathology and medicine, Vanderbilt University Medical Center. His test volume has been growing by 50 percent per year for several years. In 2005 he compared the MiniMag, EasyMag, MagNA Pure Compact, and EZ1. He chose the EasyMag because of its high yield and precision. He likes the flexibility of specimen volume, from 25 µL to 2 mL, but has had problems trying to use the same protocol for specimens with different cellularity—whole blood and urine, for example.

For high-throughput tests—HIV, HCV, and HBV viral load—Dr. Tang acquired an Ampli­Prep/ TaqMan 96. “I think they did a good job with that,” he says. “It is fully automated. The bad thing,” he adds, “is if something goes wrong, you don’t know where the problem is because the nucleic acid extraction is automatically linked to the subsequent amplification and detection steps and cannot be separately investigated.”

Nicholas T. Potter, PhD, recently converted his laboratory’s HIV viral load testing from Amplicor to AmpliPrep/TaqMan 48. “It is a very reliable piece of robotic equipment,” says Dr. Potter, who is chief scientific officer and director of molecular diagnostics at Molecular Pathology Laboratory Network Inc., Mary­ville, Tenn. With 2,000 tests annually, Dr. Potter aims for three-day turnaround.

Two years ago Yury Monczak, PhD, bought two MagNA Pure Compacts and has been happy with their performance. “We had a couple of issues at the beginning, but they were well dealt with by Roche technical support,” says Dr. Monczak, laboratory director of molecular pathology at Jewish General Hospital and assistant professor of medicine at McGill University, Montreal. It turned out that technologists were not adequately performing preventive maintenance. The Compacts are used about 18 hours a day seven days a week for VRE screening (“VRE is quite a problem in some hospitals in Quebec,” Dr. Monczak says) and for several genetic tests. “What would interest me would be slightly higher throughput,” Dr. Monczak says. He saw a demo of an Invitrogen instrument last year that might meet this need.

Safedin Sajo Beqaj, PhD, HCLD (ABB), technical laboratory director at DCL Medical Laboratory, a regional reference laboratory in Indianapolis, has experience with both medium- and high-throughput Roche instruments. He uses a MagNA Pure LC for all tests in his current laboratory’s repertoire, which includes cystic fibrosis, factor V Leiden, herpes simplex virus, and JAK2. In his previous position he validated the MagNA Pure for mycobacterial DNA from FFPE tissue. Also in his previous position, Dr. Beqaj used an Ampli­Prep/ TaqMan for HCV viral load. “It was sensitive down to 15 IU/mL,” he says. “We need more of those tests.”

After cutting his teeth on the original Organon Teknika extractor, subsequently acquired by BioMérieux and transformed into the EasyMag, Dr. Hodinka now has four MagNA Pure LCs. “We went the route of redundancy because of our high volume of specimens received and the desire to have a rapid turnaround to have the greatest impact on patient care and management,” he explains. “Also, we felt we needed a fallback in case a single instrument would go down for any reason on any given day.” When Dr. Hodinka was choosing an instrument, the Qiagen M48 and Roche MagNA Pure LC were both newly available and “essentially the same box from the same manufacturer,” he says. “There is not much difference. Both do a good job.” One factor in the selection, Dr. Hodinka says, was that the M48 had been designed more for research and the MagNA Pure more for clinical use. “Qiagen has subsequently developed a new instrument primarily with clinical laboratories in mind—the QIA­symphony SP,” he notes.

This year, after several months of validating the m2000sp and rt versus the Ampli­Prep/Taq­Man 48 instruments, Dr. Hodinka selected the m2000. “Both work well,” he says, “with very little difference in end results in the quantitative measure of HIV viral loads. We found the Abbott m2000 to be a little more user-friendly and simpler to use in our hands,” he says. “It doesn’t require a lot of effort to learn, it fits into our workflow better, and it has far fewer manipulations on the deck.” As far as moving the sample tray manually from the extractor to the analyzer, Dr. Hodinka says, “That ­doesn’t matter to us.” He also notes that a similar manual transfer step is required with the Ampli­Prep/ TaqMan 48. One additional advantage of the m2000 is that it requires less upfront daily maintenance than the Roche instrument. “A big advantage of the Roche system is that it uses preformed sealed, bar-coded, ready-to-use reagent cassettes,” Dr. Hodinka points out. He plans to add HBV and HCV quantitative assays to the m2000 as well as quantitative assays for CMV and EBV, when available.

As nucleic acid extraction and amplification/ detec­tion systems become more automated and simpler to operate, Dr. Hodinka foresees them migrating out of the dedicated molecular laboratory. “My lab started as clinical virology, not molecular pathology or molecular virology or molecular diagnostics,” he says. “People in my lab are virologists or microbiologists who learned to do molecular technology, including myself.” There is no reason, he says, why molecular testing cannot be integrated into any clinical laboratory, regardless of size, resources, or experience. “Eventually,” he predicts, “molecular will translate into point-of-care testing. Companies such as Cepheid are using microfluidic and microelectronic technologies to produce very compact systems that not only extract and purify nucleic acid but amplify and detect the target as well.”

William Check is a medical writer in Wilmette, Ill.