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Following State Permit, NY Genome Center's Clinical Lab Prepares to Submit Exome, Genome Tests


NEW YORK (GenomeWeb) — The New York Genome Center's new clinical laboratory has obtained a permit from the New York State Department of Health and is preparing to submit its first clinical sequencing test — an exome test for inherited disorders — to the state this month, Clinical Sequencing News has learned.

By the end of this year, the lab plans to also submit a whole-genome test for inherited, or constitutional, disorders and a whole-genome and transcriptome test for cancer.

In March, the NYGC hired Vaidehi Jobanputra as its director of molecular diagnostics and head of the clinical laboratory. Jobanputra, who is certified in clinical cytogenetics and clinical molecular genetics by the American Board of Medical Genetics, retains an academic appointment in clinical pathology at Columbia University. She also serves as a co-director of Columbia's Laboratory of Personalized Genomic Medicine, which already offers an exome test for constitutional disorders and recently launched a clinical cancer exome and transcriptome test.

NYGC's clinical lab obtained its New York State permit, which serves as the equivalent of CLIA certification, in late May in the categories of molecular genetic testing and oncology testing of molecular and cellular tumor markers. In addition, Jobanputra plans to obtain CAP accreditation for the lab.

To obtain the state permit, which is granted through the department of health's Clinical Laboratory Evaluation Program, CLEP, it submitted a cystic fibrosis test and a KRAS test for colorectal cancer. However, it does not plan to offer either test as a service, as its sole focus will be on exome and genome sequencing tests, which have yet to be approved by the state.

The lab is currently equipped with two Illumina HiSeq 2500 systems and will soon obtain one unit of the genome center's Illumina HiSeq X Ten system for whole-genome sequencing. Several units are already installed in the research production lab.

Right now, the clinical lab has a staff of nine, including six bioinformaticians — four with expertise in cancer, and two to analyze data for constitutional disorders — and will hire additional personnel once its service ramps up. "We're in a really good situation because we have the sequencing capacity and we have the bioinformatics support that we need," Jobanputra said, and can draw on the NYGC's experience with exome and genome sequencing and interpretation for research purposes.

Its first sequencing test, an exome test for inherited disorders, is in late-stage validation and is scheduled to be submitted to New York state this month.

According to Jobanputra, the department of health does not have specific guidelines for the validation of this type of test, but she is using guidelines developed by the Centers for Disease Control for next-generation sequencing-based clinical tests and applying her knowledge from signing out genetic tests at Columbia. Columbia's PGM laboratory has been offering its exome test since last year and has obtained conditional approval for it.

The exome test will have a turnaround time of six to eight weeks, faster than many other laboratories, which often require 12 weeks. Such fast turnaround is possible because many steps in the bioinformatics pipeline have been automated, Jobanputra said, the result of the NYGC already having sequenced many exomes for research purposes. Also in contrast to other clinical laboratories, the lab will use genotyping to ensure that the correct patient was sequenced, she added.

The report will include incidental findings in the 56 genes recommended by the American College of Medical Genetics and Genomics.

While the price of the exome test has not been determined yet, it will be "very competitive," according to Jobanputra. The lab will not bill individual patients or practices, or deal with reimbursement, but will have accounts for institutions who want to send samples.

The reason to start with an exome test is that several of the NYGC's institutional founding members expressed an interest in this test, she said. And while other institutions, including Columbia, offer similar tests, Jobanputra said that the NYGC does not plan to compete with them. "There is a large volume of patients in New York," she said, and several New York hospitals are looking to outsource exome sequencing.

While awaiting conditional approval for the exome test, the lab plans to work on the validation of its next two tests, a whole-genome sequencing test for constitutional disease and a genome and transcriptome test for cancer, which it plans to submit by the end of the year.

The genome test for constitutional disease could eventually replace the exome test, but it will also be geared at patients where the exome came back negative.

The cancer genome test, which will report single nucleotide variants, copy number variants, and gene fusions, will be somewhat unique as most other clinical labs analyze gene panels rather than the whole genome. It will address patients where a more focused approach did not yield any results, as well as patients with cancer that cannot be unambiguously classified, Jobanputra said. Again, demand from member institutions has been driving the development of the test. "There are hospitals that really want us to go very quickly with the cancer whole genomes," she said.

The test will also likely be used as part of a glioblastoma research study that the New York Genome Center is conducting in collaboration with IBM. That study, announced in March, "is going to help us get our hands wet," Jobanputra said.