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Helix Lab, Built for Scale, Prepares for New Product Launches, Exome+ Assay Update


NEW YORK (GenomeWeb) – Consumer genomics firm Helix is getting ready to launch a number of health-related testing products from third-party developers in its online store in coming months. Meanwhile, the firm's high-throughput clinical sequencing laboratory is preparing for an update of its Exome+ assay, which will enable future health tests that require features not covered by the current version.

Earlier this year, PerkinElmer said it is developing a test for the Helix store that will look for disease risk variants in 59 genes assembled by the American College of Medical Genetics and Genomics, the so-called ACMG-59 genes, that are associated with certain types of cancer and other inherited health conditions, such as familial hypercholesterolemia. Also, NorthShore University Health System said it is developing a polygenic risk score for prostate cancer that it plans to sell on the Helix platform. Both tests are expected to launch "in the near future," according to James Lu, Helix's co-founder and senior vice president of applied genomics.

Helix also recently released the Mayo Clinic GeneGuide in its store, a test that provides selected genetic results for carrier risk, disease risk, drug response, and health-related traits.

While it remains to be seen how many new customers these and other new health-related testing products will attract, the company's CLIA-certified and CAP-accredited clinical laboratory is ready to scale, while working on improvements to its Exome+ assay.

Helix's Exome+ test combines exome sequencing with sequencing of important noncoding regions across the genome. According to a white paper published by the company, the test targets about 22,000 genes, mitochondrial DNA, and several hundred thousand noncoding regions. The latter include loci that have come out of genome-wide association studies, known ancestry markers, and common SNPs that improve the accuracy of imputation. In addition, the assay provides extra coverage for about 6,000 medically important genes and for select regulatory and intergenic regions.

Under the company's "sequence once, query often" model, customers submit a saliva sample for sequencing once and have their sequencing data stored by Helix for future purchases. They can then order specific tests, or applications, from third-party providers on the Helix marketplace that use the sequencing data for their interpretations.

However, in a blog post this summer, Helix said that for some new tests, it might need to collect a new saliva sample from existing customers, at no additional cost to them. The reason, Helix said, is that these tests would utilize "specific DNA data that was not previously used" by existing tests and "would require quality checks on specific regions of DNA that were not previously needed."

Lu said that neither the current tests in the Helix store nor the upcoming PerkinElmer or NorthShore tests will need version 2 of the Exome+ test, but that "some future health tests may require features that are only available on Exome+ v2." According to David Becker, vice president of lab operations at Helix, version 2 will cover additional regions of noncoding DNA.

The company's San Diego-based laboratory, which GenomeWeb recently visited, was built to be able to process millions of samples per year and is one of the largest clinical exome sequencing laboratories worldwide, Becker said. However, the firm does not disclose how many samples it has processed so far, or what its current sequencing capacity is.

The lab, located only a short distance from the corporate headquarters of Illumina, Helix's cofounder and investor, boasts 29 Illumina HiSeq sequencers of an unspecified type, as well as one NovaSeq sequencer. The plan is to transition to the newer NovaSeq instruments entirely over time, Becker said, once the lab is sure the data quality produced is the same as that from the HiSeqs.

The sequencers are organized in groups or "pods" that each follow a different naming scheme, such as mythological creatures, aliens and robots, and female scientists. The laboratory is currently licensed in all states except New York, though it hopes to obtain a license from the New York State Department of Health next year.

Helix uses a laboratory information management system that is based on Illumina's GenoLogics Clarity LIMS but has added customized modules. The lab also streams all operational data into a central database, which can be accessed by all lab employees, allowing them to suggest improvements and spot problems as early as possible.

The lab uses Amazon Web Services for its data analytics and storage, although it has a small data center of its own. In order to keep turnaround times short and to prevent any disruptions, the company uses two independent internet service providers and two high-speed (10 gigabits per second) data lines to transfer sequencing data to the cloud.

Customer samples arriving at the lab are unpacked and prepared for DNA extraction. During the visit, two piles of 240 yellow boxes each containing customers' saliva samples were sitting on a bench to be processed. After the boxes are opened and visually inspected for quality, the saliva tubes are scanned in with their barcodes and go into the DNA extraction lab in batches of 96.

About half of each sample is used to extract DNA, while the other half goes into storage as a backup. Much of the DNA purification process is automated, utilizing Hamilton liquid handling robots to load the samples into 96-well plates and perform other steps of the magnetic bead-based extraction. The lab is set up with three identical robotic stations, which each perform thousands of extractions per day, Becker said, and additional robots could easily be added if needed.

Next stop for the samples is the pre-amplification lab, where the DNA is enzymatically fragmented and adapters are ligated as part of the library preparation process. Again, these steps are performed by identical Hamilton liquid handling stations, and the company's automation team always translates updates to all systems, Becker noted.

To avoid contamination, samples are then transferred to the PCR lab through a transparent pass-through box that can only be opened on one side at a time. This is where the target enrichment for the Exome+ assay takes place, followed by clustering and sequencing on the Illumina machines.

Data from the sequencers first streams onto local hard drives, which can serve as a buffer in the unlikely event that both internet providers are down, before it is uploaded to the Amazon cloud. To prevent any losses from potential power failures, the lab also maintains a backup generator.

Members of the Helix lab review the sequencing and other data, making sure that samples, controls, and runs meet all quality metrics, and issue a technical report. After that, the data goes to Helix's informatics team in San Francisco, which is in charge of the data analysis. The third-party test provider then issues a report containing an interpretation of the results to the consumer.

The scale of the Helix lab operations, and the lab's ability to increase production quickly if needed, are among the main advantages for developers launching their tests in the Helix store, Becker said, even those that operate their own laboratories. "It's a way for them to reach a 'mass market' of individuals," he said.