Skip to main content
Premium Trial:

Request an Annual Quote

NxGen MDx Mixes Synthetic DNA into NGS Samples to Prevent Lost Specimen


NEW YORK (GenomeWeb) – Many labs have invested in automation to reduce lost lab specimens, but those investments usually involve improved tracking of the containers in which specimens are transported around the lab.

NxGen MDx, a lab focused on genetic carrier screening, decided to take a different approach. It was looking for a way to track the actual specimen, rather than the vessels that contain them.

"We were thinking how could we have a foolproof way to always know that a patient's specimen remains identified correctly throughout the process," said Jonathan Karnes, vice president of scientific operations at NxGen MDx. "The idea that came to me was a [synthetic] DNA sequence molecule that is added to the patient sample early in the testing process and is carried throughout the process."

The result was active molecular identification or AMI tagging, a synthetic DNA tag that is uniquely identifiable by the lab's next-generation sequencing process.

"It's a unique tag that is kind of just floating through the blood sample, and when we go to isolate the patient's genomic DNA, we end up isolating that tag out of the blood sample along with the genomic DNA," Karnes said.

For NxGen MDx, AMI (pronounced Amy), complements a traditional bar code scanning system for tracking specimen. When a specimen arrives at the lab, a bar code is added to the specimen container along with the patient's name and date of birth. Accompanying paperwork is entered into the system and assigned a case number that matches the specimen bar code.

"We would identify the patient's specimen by location, so row H in well 12 would be the way you're tracking that in the computer system as it moves throughout the testing process," he said.

The AMI system is used in conjunction with the bar code system, but the reason that Karnes felt the need to create AMI was a concern that bar code scanning tracks a specimen container and location rather than the specimen itself.

"This AMI tagging is redundant to [bar code scanning] but it's also foolproof," Karnes said. "In other words, a laboratory error can occur when someone is transferring a specimen from one vessel to another. When it's going from one place to the next, there is the possibility at that point that the well that the patient specimen should be going to is not the well that the patient specimen ends up in."

If a specimen was placed in the wrong location, it would be misidentified by a location-based tracking system and the test results could be attributed to the wrong patient, he noted.

In next-generation sequencing testing, a specimen could be transferred from three to five different vessels, depending on the workflow, Karnes estimated.

"That happens on an automated system, but if something goes wrong with the instrument, or something happens to be done manually, that's where an error can occur," he said.

Karnes noted the error rate related to lost specimens in laboratories, particularly with next-generation sequencing pipelines that are highly automated, is low. He estimated the rate to be less than 1 in 5,000. But given the cost and the significance of the medical decisions that patients make based on next-generation sequencing results, even a rare error is concerning, he said.

With AMI tagging, approximately 250,000 copies of a synthetic DNA molecule are added to a blood sample. The lab has 400 AMI tags currently stocked in a freezer and is working to increase that number, Karnes said. A unique tag can be reused in another sample, he said, but the lab would not use a tag currently in use in another sample in the lab.

The AMI tag system has been primarily designed in house at NxGen MDx. An outside supplier created the synthetic DNA tags, but NxGen MDx designed them and customized them to work with an in-house developed analysis system that compares the tag in the blood at the end of the testing process with the original tag that was assigned to the specimen, according to Karnes.

AMI tags can be added to blood saliva or any type of specimen that arrives in the lab, he said. While the tags are currently only being used with next-generation sequencing, Karnes anticipates the system could eventually be transferred to other types of testing.

"Every single panel we offer involves next-generation sequencing, so that means every patient sample is getting the tag identified on the back end, but you could imagine using this with quantitative PCRs and tests we do in addition to NGS. Today, we haven't yet tacked the idea of how to make those tags detectible," Karnes said.

NxGen Mdx began implementing AMI tags within its lab three to four months ago and has found the system to work well. It was relatively seamless to implement and required little training for employees, Karnes said. The company does not yet have specific results from its use of the system, but plans to conduct a study and eventually publish a paper on the results of using AMI tagging, he said.

While AMI tags were originally developed as an in-house solution, NxGen MDx has begun to explore the possibility of outsourcing the technology to other labs.

"The way we implement AMI tagging in our laboratory is actually custom fit to us, but we have had at least some initial discussions in terms of how this would look or how we would need to make some changes to this in order to make it more universal to any laboratory," Karnes said. "It is definitely an outcome that we are exploring."

However, Karnes stressed that NxGen Mdx's core area of expertise is lab testing, so if AMI tags were to be offered externally, the company would likely need to partner with a company to package the service as a kit and manufacture and market it.