As next-generation sequencing (NGS) becomes more popular in clinical settings, partnerships are forming to enable the application of this new technology for diagnostic applications. In January, two NGS firms announced partnerships with organizations with backgrounds in molecular diagnostics. Life Technologies announced a partnership with Boston Children’s Hospital (BCH) to establish Claritas Genomics, which will develop NGS diagnostic tests. Illumina announced the expansion of its partnership with Partners HealthCare, a nonprofit comprised of 11 hospitals, originally announced in September 2012, to include pilot sites for the use of Illumina’s sequencing technology with Partners HealthCare’s GeneInsight Suite. Both partnerships will expand to include other partners. The partnerships aim to help the use of NGS grow in the clinical market by addressing some of the bioinformatics issues that currently limit clinical implementation.

Life Technologies is a strategic investor in Claritas Genomics, a spinoff of BCH. The partnership will incorporate BCH’s background in bioinformatics and assay development at its CLIA-certified Genetic Diagnostic Lab to validate clinical tests on the Ion Proton benchtop sequencer. “Through a set of network collaborations and via electronic communications, we plan to provide interpretive services around the world,” said David Margulies, MD, director of the Gene Partnership at BCH. According to Mark Gardner, director of Business Development, Medical Sciences, at Life Technologies, the investment is designed to accelerate the adoption of NGS for clinical usage. “We clearly have a desire for [Claritas Genomics] to do well and to grow and to attract more volume, and that will be good for our Ion [Torrent] business, but frankly, it will also be good for the development of the market because most [highly multiplexed genomic analyses] are not currently deployed wide scale using NGS.” The hospital’s bioinformatics and assays were originally developed for research applications. “The assets at Children’s are derivatives of certain standard bioinformatics tools that were originally created elsewhere,” said Dr. Margulies. “There are some completely innovative pieces of it, the bulk of the tools originated from the Human Genome Project and the Broad [Institute].” The partnership will initially focus on inherited disorders in children. “Most disorders that are genetic in nature can present in childhood in a more severe manner, so the work that we do for inherited disorders of children will also pertain to the inheritable diseases in adults,” said Dr. Margulies.

Illumina and Partners HealthCare’s GeneInsight Network now consists of ARUP Laboratories, Mount Sinai Genetic Testing Laboratory and the New York Genome Center. The Network will utilize Partners HealthCare’s GeneInsight Suite, a platform featuring three components: GeneInsight Lab to manage and interpret genetic testing data; GeneInsight Clinic to deliver test results and updates to physicians; and GeneInsight Network to share genetic data among labs and physicians. The partnership has adapted the GeneInsight software for NGS by making it compatible with Illumina’s BaseSpace cloud computing platform, MyGenome iPad application and LIMS. “Laboratories can integrate their GeneInsight Lab knowledge base with their NGS data analysis pipelines by directly including their clinical variant interpretations and variant frequencies,” said Rich Copp, vice president of Communications at Partners HealthCare. Like Claritas Genomics, the Network aspires to broaden the market for clinical NGS. “This technology aims to help patients and also have an impact on the field nationally.” The partnership will use Illumina’s MiSeq benchtop sequencer.

Usage of NGS in the clinical setting is increasing. One estimate is that 40–50 labs currently use NGS for clinical testing (see IBO 8/31/12). Use is growing for several reasons; one being the decreasing cost of NGS. According to the National Human Genome Research Institute, the current cost of DNA sequencing is $0.07 per megabase. Another reason is the advantages of NGS for clinical diagnosis. Unlike other technologies, NGS can provide information on large regions of the genome, as well as diagnose conditions for which a genetic cause cannot be found through other types of testing. In addition, Illumina’s and Life Technologies’ introduction of smaller, less expensive, easier-to-use and faster sequencers has made the technology more accessible to clinical labs. Both companies are pursuing FDA approval for the systems. On Life Technologies’ 2012 third-quarter conference call, President and COO Mark P. Stevenson disclosed that 20%–30% of Ion Proton customers are in clinical settings. In Illumina’s 2012 first-quarter conference call, President and CEO Jay Flatley announced that the firm had initiated discussions with approximately 100 clients interested in utilizing MiSeq for clinical use.

Several organizations have been working to specifically address NGS processes in the clinical setting. In 2012, the Center for Disease Control and Prevention formed a working group to address quality assurance and control issues specific to clinical NGS. In July 2012, the College of American Pathologists released the first standards in the US for labs that utilize clinical NGS (see IBO 8/31/12). In November 2012, the American Medical Association announced that it would inform and educate physicians on clinical NGS.

Clinical NGS primarily consists of three types of sequencing: targeted sequencing, exome sequencing and whole genome sequencing (WGS). Targeted sequencing examines rare and common variants in a specific set of genes. Exome sequencing analyzes the approximately 1% of the genome that chiefly encodes protein. WGS analyzes and interprets genetic variations across a patient’s entire genome. Exome sequencing and WGS detect causal variants in genes not previously linked with a disease. Because it costs less to sequence an exome, the partnerships will initially focus on exome sequencing.

NGS is useful for cancer diagnosis because its high levels of coverage can detect low-frequency somatic mutations as well as single nucleotide changes, structural chromosomal changes and copy number variations that have been linked to cancer. It can also filter variants for causative genes to identify Mendelian disorders, such as cystic fibrosis, sickle cell anemia, Tay-Sachs disease and hemophilia. NGS is also used to diagnose heart disease, for which hundreds of loci linked with cardiovascular pathologies have been found.

There are several challenges to implementing NGS in a clinical setting. Challenges for sharing data include access to tertiary data and forming consensus on causal variants. Different labs have their own databases of curated variants. “The GeneInsight software supports connectivity between labs and can be used to facilitate the establishment of networks of laboratories that all agree to share variant-level data,” explained Mr. Copp. “Labs can maintain and track their own curated variants and have autonomy over what they choose to say about them, yet benefit from access to the work others have done as a starting point for any variant.” The more samples that are sequenced, the more information can be obtained regarding characteristics of variant calls, such as strand bias, coverage and mapping quality. “The goal of the GeneInsight Network infrastructure is to enable connectivity between laboratories interested in crowdsourcing the clinical assessment of specific genetic variants. As a workflow tool, the network will serve as an additional reference source for laboratories to visit during the variant interpretation process,” said Mr. Copp. Claritas Genomics also emphasizes sharing for reference and validation. “We’re strong believers that certain anonymized data, such as the prevalence of variation, needs to be shared widely in order to have the safest and most effective possible interpretations,” said Dr. Margulies.

Challenges for data interpretation include the volume of variant data and the laborious procedures to assess the clinical relevance of the data. Each patient has hundreds of rare DNA variants, which can complicate the understanding of a variant’s phenotypic implications. In addition, much of the information about genome variation is poorly understood or unknown, including variant significance. Filtering the relevant information produced by NGS will be a focus of the partnerships. “[BCH is] primarily going to be starting with specific panels and probably exomes,” explained Mr. Gardner. “As one moves to whole genome sequencing, which is their intent, the amount of data goes up quite significantly yet again.” In addition to interpreting the amount of variant data produced, clinical relevance must be established. “Genetic testing labs must track and annotate the variants that they uncover during testing and curate this knowledge as it changes over time,” explained Mr. Copp. “The process of curating variant knowledge involves performing internal assessments to determine if certain variants are segregating with a disease in a lab’s patient population, combing the scientific literature for relevant papers, and leveraging a number of public and private databases and commercial tools to help a lab to assess the clinical significance of a specific genetic variant.”

Another challenge is physician utilization, which involves a physician’s ability to adequately access and interpret a patient’s genetic information. Specific issues are physician education and access to up-to-date variant data. “Reports sent into GeneInsight Clinic include a number of structured data elements that remain linked back to the original testing laboratory. This enables clinicians to get updates and alerts on their patient’s reports as variant-level information evolves in the laboratory’s knowledge base,” said Mr. Copp. “As these changes take place in the lab, alerts are sent out via GeneInsight Clinic to notify clinicians that they have a patient in which there is a new or updated variant knowledge.”

Claritas Genomics will educate physicians through the use of guidelines and access to appropriate information. “At the time of initial ordering, it’s very important to us that we provide guidelines to clinicians indicating the appropriate tests to be ordered in particular clinical settings,” said Dr. Margulies. “We want doctors to order the right tests, and then when we find variation in genes, which might be related to the ordering indication, we want to be sure that we’re providing them with useful interpretations. These interpretations will change over time as new knowledge accrues.” Physician involvement is integral to the partnership. “What makes Claritas unique is that they have a well-developed clinical reference network,” said Mr. Gardner. “They have the full support of the hospital and the right culture to enable themselves to be a hub.”