When Analyzing Cancer at the Molecular Level, Microliters Matter

This year, more than 1.4 million Americans will be diagnosed with cancer. An extremely complex disease family, cancer affects all types of people, from all nationalities and genetic make-ups. Yet a lack of knowledge and insight at the time of diagnosis often results in a one-size-fits-all approach to treatment. While improvements in disease detection, diagnosis, and therapies are continually increasing the survival rate, cancer is the second leading cause of death in the United States, killing more than 550,000 Americans each year.1

But Genomic Health is on the case. A life science company based in Redwood City, CA, Genomic Health is focused on the development and commercialization of genomic-based clinical laboratory services for cancer that allow physicians and patients to make individualized treatment decisions. In 2004, the company launched its first test, Oncotype DX, which has been shown to predict the likelihood of breast cancer recurrence and the likelihood of chemotherapy benefit in a large portion of early-stage breast cancer patients. This knowledge enables treatment options to be tailored to better fit patient needs and increase the chances of survival.

Figure 1 - ARTEL MVS.

Core to Genomic Health’s success are laboratory efficiency and quality, helping the company speed development, and delivery, of new technologies for cancer patients who simply do not have the luxury of time. Given that its automated liquid handlers are used in a large number of its critical processes and tasks, Genomic Health maintains a rigorous liquid handling quality assurance program using the MVS® (Multichannel Verification System) from ARTEL (Westbrook, ME) (Figure 1). The MVS employs a rapid, robust technology that can quickly measure the volume transfer performance of liquid handling devices. This system provides data on liquid handling accuracy as well as precision, even at very small volumes. And this has helped Genomic Health grow confidence in its liquid handling operations.

The impact of one microliter

As a company aiming to analyze cancer at the molecular level, it is essential that Genomic Health’s liquid handling devices perform accurately at the microliter level. This is true for both its commercial and R&D laboratories.

Genomic Health’s diagnostic innovations are born in its research and development laboratory. Here, scientists conduct research and clinical studies to develop new innovations and product features to further the company’s efforts to improve cancer treatment. The commercial laboratory is tasked with analyzing tumor samples using the company’s proprietary diagnostic kits, and providing detailed reports to oncologists to guide patient treatment.

“We do a substantial amount of pipetting using our automated liquid handlers and, due to the quantitative nature of our assays, accuracy is critical,” according to Keith Volk, Assay Development Engineer, Genomic Health. “Inaccuracies of one microliter can make a large difference in results, with errors resulting in inefficiency and loss of productivity.”

To illustrate the prevalence and importance of liquid handling at Genomic Health, consider the company’s first commercial diagnostic assay, the Oncotype DX. The development of this product, which quantifies the likelihood of distant breast cancer recurrence and allows for better treatment selection, relied heavily on liquid handling, as do current analyses performed with it.

The analysis process starts once a mass in a patient’s breast is identified by a physician as malignant, at which point the tumor is sent to a pathology laboratory. This laboratory preserves the tumor, embeds it in paraffin, and sends it to Genomic Health for further analysis using the Oncotype DX specimen kit. Genomic Health’s commercial laboratory extracts tiny amounts of RNA from the paraffin-embedded tumor specimen and the diagnostic process begins.

Automated liquid handlers are used in almost every step needed for sample analysis, from quantifying the RNA and checking for DNA contamination to reverse transcription and qPCR testing. The objective of the process is to measure the expression levels of the RNA in the given panel of genes, and this measurement is used to determine the percent chance of disease recurrence in a given period of time. An accurate measurement of expression levels is contingent upon accurately quantifying the amount of starting material. If only half of the desired sample material is initially dispensed, the measured expression level could quite possibly be affected.

The R&D laboratory uses many of the same processes as the commercial laboratory. Here, automated liquid handlers are used to continually run patient samples to develop new products and conduct validation studies. Although results from the R&D laboratory are not used for patient treatment, accurate and precise volume deliveries are critical to correctly steer development efforts and eliminate inefficiency.

Quality assured

To strengthen confidence in results and quickly verify the performance of its automated liquid handlers, Genomic Health relies on the ARTEL MVS. The MVS is a standardized platform that produces traceable accuracy and precision measurements in minutes, providing the ability to quickly rule out errors in liquid handling processes. Additionally, due to the standardized, traceable data provided by the MVS, Genomic Health’s liquid handlers all can be directly compared for dispensing the same critical volumes in their assays, which is especially important when different liquid handlers are performing identical tasks. “We have extensive quality control processes in place to ensure accurate and precise diagnostic test results,” said Volk. “And the MVS is an important part of that process. The system gives us confidence that our robots are pipetting what we asked them to pipet across all volume ranges.”

The MVS is based on ratiometric photometry, ARTEL’s proprietary technology that measures the absorbance of light by two specially formulated dyes to verify volume. Bar codes on the MVS’s microtiter plates, reagents, and calibrator plate contain metrological information that is passed to the system’s software through scanning. The software also automatically records the photometric measurements taken by the MVS and rapidly determines both the accuracy and precision of the volume delivered from each individual tip of the device being tested.

In addition to automated documentation, the system provides results traceable to the NIST. As well as instilling an additional level of confidence in data integrity, traceability also allows Genomic Health to meet regulatory requirements, including those set forth in the Clinical Laboratory Improvement Amendments (CLIA), which the company is required to follow.

The importance of accuracy

Laboratory life before the MVS was not so easy. While Genomic Health always took care to ensure quality in its liquid handling operations, its previous verification process was more painstaking.

One method involved photometric measurement using tartrazine dyes. This process was time consuming due to lengthy reagent preparation. A more critical drawback of the tartrazine method was its inability to provide accuracy information. While the method measured how close the dispensed volumes—from each channel of the liquid handler—were to each other, it was not able to determine how close the dispensed volumes were to the required target volumes. “A huge advantage of the MVS is its provision of both accuracy and precision information in one rapid run,” explained Volk.

To derive accuracy and precision information before it implemented the MVS, Genomic Health employed gravimetric calibration, which uses a balance to weigh dispensed liquid quantities to determine volume. This process was time-consuming, requiring multiple dispenses to verify each individual channel in an automated liquid handler. Gravimetric calibration also has limitations at low volumes, and is affected by vibration, evaporation, and other environmental conditions.

Streamlined process

With the MVS in place, Genomic Health is able to streamline its liquid handling quality assurance program and strengthen confidence in results. The company verifies the performance of its automated liquid handlers on a quarterly basis. This frequent monitoring schedule, permitted by the MVS’s speed and ease of use, ensures that Genomic Health has ongoing performance data on its robots and reduces risk of error. “The MVS is easy to use, facilitating a frequent performance monitoring schedule,” said Volk. “Training new employees is a painless process.”

The rapid performance of the MVS also allows Genomic Health to calibrate new liquid handlers with a range of volumes and specific tip types. If a tip vendor goes out of business or runs out of stock, the company will be able to easily and rapidly switch to a previously qualified tip to avoid a lag in productivity.

The MVS is also used after instrument maintenance to ensure that newly installed parts are functioning properly. Multiple calibrations are run until all parts are properly installed. “The MVS has made a big difference in our laboratories, both from an efficiency point of view, as well as from a confidence standpoint,” summarized Volk.

With a stringent liquid handling quality assurance program in place, Genomic Health scientists can focus their efforts on more important issues, like analyzing cancer.

Reference

  1. Cancer Facts and Figures 2007. American Cancer Society, www. cancer.org.