New York Genome Center Launches First LDT, Whole Exome Sequencing
By Bio-IT World Staff
March 30, 2015 | The New York Genome Center (NYGC) announced today that it has received approval from the New York State Department of Health to offer clinical whole exome sequencing for individuals with constitutional disorders. This is the first laboratory-developed test, or LDT, from the Center to be cleared for clinical diagnostic use.
LDTs have been under careful scrutiny since last year’s FDA guidance on the regulatory oversight of such tests. (See, What You Need to Know About the FDA’s Push to Regulate Laboratory Developed Tests)
Physicians in New York State will be able to order the test on behalf of their patients. Under the plan now approved by the state, the Center will offer trio testing: clinical diagnostic exome sequencing for affected children and their parents. Typically, clinical exome sequencing can take up to 12-14 weeks, but Vaidehi Jobanputra, Ph.D., FACMG, Director of Molecular Diagnostics at the New York Genome Center, who led the work to develop the new test, hopes to return most results within 6-8 weeks. This rapid turnaround time is realistic for the Center because it uses an automated analysis pipeline to ensure that each case is handled not only rapidly but also carefully, precisely and systematically. (See, Toby Bloom on the New York Genome Center’s Crystallizing Clinical Vision)
“Many of the patients we hope to help have been on what the field refers to as a diagnostic odyssey. They have gone from one doctor or hospital to another, trying to figure out what is causing their symptoms,” said Jobanputra.
Analyzing sequencing data in the context of family relationships increases the likelihood of identifying genetic variants that may be contributing to symptoms observed in the child. The laboratory will also accept affected or unaffected relatives to provide additional context and help guide interpretation on a case-by-case basis. The clinical exome test is also available for adult patients.
The test was validated using Agilent exome capture reagents to prepare samples for sequencing on the Illumina HiSeq2500 platform. In addition to variants associated with the reported clinical phenotype, the laboratory will report secondary findings in medically actionable genes as per the American College of Medical Genetics and Genomics (ACMG) guidelines (See, ACMG Changes Recommendations on Incidental Findings and Opting Out).
Patients will have the option to opt out of these findings on the informed consent that must accompany each test request. Patients also will be able to opt in to learning their carrier status for autosomal recessive conditions in genes recommended by the ACMG and the American Congress of Obstetricians and Gynecologists (ACOG) for reproductive carrier screening.
"This allows NYGC to bring state of the art medical care—which today includes genomic sequencing—to patients throughout New York," said Robert Darnell, MD, PhD, President and Scientific Director of NYGC. “Integration of this capability with the research and clinical needs of our partner institutions will enable us, together, to better identify genetic variants and thereby advise doctors how to more specifically treat the root cause of what makes patients sick."
The laboratory is preparing to submit additional LDTs, including a whole exome sequencing test for cancer, a whole genome sequencing test for genetic disorders and a whole genome sequencing test for cancer. Earlier this month, the Center announced that Harold Varmus, director of the National Cancer Institute (NCI) at the National Institutes of Health (NIH) and co-winner of the Nobel Prize, was joining Weill Cornell Medical College’s faculty as the Lewis Thomas University Professor of Medicine, effective April 1. In conjunction with his appointment at Weill Cornell, Dr. Varmus will work with NYGC as a Senior Associate Core Member to promote the use of cancer genomics throughout the New York region.
