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MOgene Launches Clinical Subsidiary to Focus on Testing for Infectious Diseases, Immune Disorders

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NEW YORK (GenomeWeb) – MOgene, a genomics services provider, launched a new subsidiary this week called MOgene Clinical Diagnostics (MOgeneDx) to provide next-generation sequencing-based testing for infectious diseases and immune disorders.

The newly minted subsidiary is preparing to launch its first NGS-based test for the diagnostics market slated for release early next year. The test, dubbed ResistDx, focuses on HIV and, specifically, helps clinicians identify the most appropriate treatment cocktail for HIV-positive patients based on mutations in the viral strains found in the patients' plasma samples.

MOgeneDx will perform the ResistDx test at the company's CLIA-certified laboratory at the Bio-Research & Development Growth Park which is located on the Danforth Plant Science Center's campus in St. Louis, Mo. It will be indicated for recently infected patients, positive patients who've never been treated, patients whose viral load rises while on treatment, people on treatment whose viral load is not dropping, and HIV-infected pregnant women.

Clinicians seeking treatment guidance will send plasma samples to the facility, where MOgene researchers will isolate the viral RNA, amplify it, and then sequence it using an Illumina MiSeq instrument. The raw files then move through a bespoke analysis and interpretation pipeline that identifies variants in the data and compares them to Stanford University's public database of information on HIV and associated treatments, Dun Liang, director of MOgeneDx, told GenomeWeb.

According to the company's website, the test covers the important polymerase gene with genotypic resistance information for three classes of HIV ART drugs including protease and reverse transcriptase inhibitors with integrase inhibitors to be added. The final report, which physicians will receive four to seven days after this process starts, will suggest treatments that the virus is likely to be susceptible to based on the mutations identified as well as supporting information from published literature. Reimbursement for the test uses the existing CPT codes that cover infectious disease genotype analysis.

MOgeneDx's informatics pipeline uses Illumina's BaseSpace to store data but the actual analysis of the information is performed on the company's servers using internally written scripts that are run in an unnamed commercial platform designed to handle things like quality assurance, software version and parameter control, and tracking and auditing. These scripts use mostly open-source solutions that handle data quality control, reference selection, alignment, variant calling, and consensus building. The company also has a script for querying, extracting, and formatting information from the Stanford database.

Rather than choose existing software for its analysis needs, MOgeneDx chose to develop its own solution to ensure the quality of the sequence data analysis procedure and to comply with current and future regulatory requirements, Liang said. The company considered using applications in Illumina's BaseSpace for the analysis but ultimately decided against that, Liang said, because it would require paying a cost per sample, lacked some of the needed tracking and auditing capabilities, and is intended primarily for research use. Also, "we don't have control on it if we want to customize or add more analysis for our future tests," he said. Running the analysis locally also ensures a seamless and automatic flow of information from the sequencing through interpretation and reporting.

Furthermore, since the test is NGS-based, it provides a more comprehensive profile of the viral population and is more sensitive to low level viral mutations than existing genotyping methods, which only provide average information on the viruses in the sample, Liang said. That’s important, Shaukat Rangwala, senior vice president, operations for parent company MOgene, noted, because clinicians would be able to spot viruses with low level mutations at an earlier stage of development — before they become dominant under drug selection pressure — and start preemptive treatments to nip them in the bud.

MOgeneDx is still validating its test internally, which is why it won't be released until next year. As a result, the company is not discussing its validation results in detail at this time, however, Liang said that the test's sensitivity is above 99 percent compared to roughly 75 percent sensitivity achieved by traditional methods. The company also plans to contribute new information from collaborative studies it has going on with physicians to the HIV drug resistance database, Rangwala added.

MOgene, the parent of MOgeneDx, has been incubating the clinical diagnostic concept for several months. The company decided to launch MOgeneDx as a separate subsidiary to differentiate its standard genomics services from its diagnostic offering, Rangwala explained.

The company has been providing services since 2004. The now 16-person firm began its days as an Agilent-certified microarray service provider, but it has since branched out by adding other technologies and services to its portfolio including NGS. In February this year, the company announced that it had completed Illumina CSPro certification for sequencing on HiSeq and MiSeq instruments. In 2012, the company signed an agreement with Lawrence Livermore National Laboratory to provide microbial analysis services using the Lawrence Livermore Microbial Detection Array; and it tapped Fluidigm's Access Array sample preparation platform to provide high-throughput targeted enrichment for its targeted resequencing customers.

In launching its diagnostics business, MOgene opted to stay away from the more expensive and more saturated oncology arena, choosing to focus its available resources instead on infectious diseases, where the genomes are smaller, and immunology, which uses mostly targeted sequencing and requires fewer resources for validation than whole-genome and whole-exome-based tests, Liang told GenomeWeb.

The company has plans to launch another test focused on the hepatitis C virus, which is often a co-infection in HIV cases, and later on to launch a test for detecting viral pathogens in metagenomic samples, and T-cell receptor profiling assay for immunology, Liang said.




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