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Mar 1, 2014 (Vol. 34, No. 5)

NGS Systems Secure Place in Clinic

  • Prenatal Testing

    Click Image To Enlarge +
    Sequenom Laboratories’ MaterniT21 PLUS test is performed at one of the company’s U.S.-based facilities—a lab in San Diego, CA or a lab in Morrisville, NC (near Raleigh). The turnaround for results is about seven days from receipt of the sample in the lab.

    Dirk van den Boom, Ph.D., evp of R&D and CSO, describes Sequenom Laboratories’ MaterniT21™ PLUS noninvasive diagnostic test for fetal chromosomal abnormalities as “the first real example of applying next-generation sequencing in a clinical setting in a high-throughput fashion.” More than 148,000 tests were performed in high-risk pregnant women in 2013, avoiding the risks associated with amniocentesis or chorionic villus sampling to access fetal DNA. The test sequences cell-free DNA in a sample of maternal blood—which includes fragments of fetal DNA—matches the fragments to the chromosome from which they derived, and essentially determines if a chromosome is present in greater than the normal diploid amount.

    “NGS is a good tool for this because of the number of data points you can generate,” says Dr. van den Boom. Sequenom Laboratories implemented the test on Illumina’s HiSeq platform and initially reported on chromosome 21.

    Prenatal testing is a big market, with an estimated 750,000 high-risk pregnancies each year in the U.S. alone. “We started with trisomy 21, but we chose a whole-genome approach so we could add content as we have the clinical data and see the medical need, “ he adds.

    Sequenom next added the capability to detect trisomy 18 and 13 and sex chromosome aneuploidies, and toward the end of last year introduced the Enhanced Sequencing Series as an additional feature to the MaterniT21 PLUS test, which added trisomy 16 and 22 as well as larger clinically relevant chromosomal microdeletions such as those associated with DiGeorge syndrome, Cri-du-chat syndrome, and Prader-Willi/Angelman syndrome.

    The ability to generate a full fetal karyotype by using NGS to analyze a maternal blood sample “is fundamentally in reach within the next couple of years,” predicts Dr. van den Boom. As the company continues to expand its prenatal testing portfolio, it has also begun to explore the power of applying NGS to DNA fragments in the bloodstream to the detection of cancer.

  • Oncology Testing

    According to Andy Felton, director of Life Technologies’ genetic systems division, “oncology testing will be a huge potential market” for NGS. Unlike PCR and Sanger sequencing, it gives you the ability to look at many mutations in parallel—single nucleotide changes, copy number variations, and gene fusions, for example.

    Life Technologies’ Ion PGM System is currently a research use only instrument; the PGM DX platform in development will target the clinical setting and is in the process of completing testing for future registration and listing with the FDA. The company continues to streamline and enhance the automation and ease of use of its research platform, advances it intends to apply to a future clinical testing system.

    Citing the speed of its NGS technology—with a turnaround time of a few hours—and the scalable output as key advantages of the Ion Proton System, Dr. Felton also highlights the ability of the platform’s AmpliSeq technology to accommodate samples as small as 10 ng, as may be common in future clinical testing of FFPE tissue samples.

  • Click Image To Enlarge +
    Genomic Expression asserts that its bait-free RNA sequencing process—which encompasses sample preparation, sequencing, and analysis—can produce results in less than a week while generating a data file of just 30 MB that can be attached to an electronic medical record.

    From a research perspective, the goal of NGS is to obtain as much sequence data as possible—to find that SNP, translocation, or other variant that correlates with disease, but “we ask the opposite question as the researcher,” says Gitte Pedersen, CEO of Genomic Expression. To use RNA-seq in the clinical setting, for example, we want to know “what is the minimum amount of information you need to extract from your sample in order to identify and quantify all of the RNAs.” RNA-seq by itself is not a clinical application, because depending on how the test is analyzed, and who analyzes it, the results can be different, asserts Pedersen.

    To reduce the time, cost, data burden, and complexity of RNA-seq applications to make them faster, easier, and more amenable for use in the development of a companion diagnostic for instance, Genomic Expression produced kits and accompanying software for performing automated RNA-seq that are platform-agnostic and work on existing and emerging NGS instruments. Based on a bait-free target filtering sample preparation method, the process from sample prep to results takes less than a week and generates a data file of 30 MB that can be attached to an electronic medical record.

    Pedersen describes how pharma companies can use RNA-seq to develop companion diagnostics for stratifying patient populations for clinical testing of oncology drugs, for example. As data is collected it can be used to perfect the evolving algorithms and “optimize the definition of the target population based on data points.”

    This exercise to link a companion diagnostic to a cancer therapeutic may have required an array of different markers and multiple testing platforms, but RNA-seq can turn that complexity “into a math exercise with a very high probability of success on one platform with one assay,” Pedersen adds.

    “With the approval of the Illumina MiSeq for clinical applications, we are 90% there, the platforms are there; the last 10% is to develop the algorithms. Our business model is to partner around the last 10%—the content, leveraging our access to fully annotated clinical samples.”

    Pedersen emphasizes the scalability of the Genomic Expression technology, and its broad range of potential applications. How sample- or disease-specific it will be remains to be seen. “We know it works in breast cancer,” she says, and have demonstrated that it could also work in a number of other cancers. Other promising application areas are organ transplantation rejection, cardiovascular and central nervous system disorders, and autoimmune diseases.

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