Funded by both for-profit and not-for-profit organizations, this new gene sequencing center is preparing to offer its first genetic tests for use in patient care

Next-generation gene sequencing for clinical diagnostic applications is moving forward at the New York Genome Center (NYGC). Located in New York City, the center is designed to be a genetic medicine technology incubator and has funding from a number of for-profit and not-for-profit sources.

For pathologists and medical laboratory administrators, this creation and operation of this independent sequencing center is a notable development. It shows the willingness of different organizations to come together and fund a collaborative venture to advance exome sequencing and whole-genome sequencing for clinical purposes.

NYGC’s new clinical laboratory obtained a permit from the New York State Department of Health. It also is preparing to submit its first clinical sequencing test—an exome test for inherited disorders—to the state in August, according to a story published in Clinical Sequencing News and posted on GenomeWeb.

A story published by Clinical Sequencing News noted that, by year-end, NYGC plans to submit a whole-genome test for inherited, or constitutional, disorders and a whole-genome and transcriptome test for cancer. These assays will be submitted to New York State Department of Health’s Clinical Laboratory Evaluation Program (CLEP).

Permit, Equipment in Hand at NYGC

Last May the organization’s clinical laboratory obtained a New York State permit (equal to Clinical Laboratory Improvement Amendment [CLIA]-certification) in categories of molecular genetic testing and oncology testing of molecular and cellular tumors.

Another point of interest for pathologists is that NYGC has purchased the Illumina HiSeq X Ten system for whole-genome sequencing, according to a blog post on AllSeq. NYGC’s clinical lab is also outfitted with two Illumina HiSeq 2500 systems, NYGC’s Web site said.

“We’re in a really good situation, because we have the sequencing capacity and the bioinformatics support that we need,” stated Vaidehi Jobanputra, Ph.D., FACMG, M.S., in the Clinical Sequencing News report. She is NYGC’s Director of Molecular Diagnostics and head of the clinical laboratory, as well as an Assistant Professor of Clinical Pathology at Columbia University. “And we can draw on NYGC’s experience with exome and genome sequencing and interpretation for research purposes,” she added.

Pictured above is Vaidehi Jobanputra, who was named Director of Molecular Diagnostics and head of the clinical laboratory at New York Genome Center in March. She also retains an academic appointment in clinical pathology at Columbia University. (Photo copyright Columbia University.)

Pictured above is Vaidehi Jobanputra, who was named Director of Molecular Diagnostics and head of the clinical laboratory at New York Genome Center in March. She also retains an academic appointment in clinical pathology at Columbia University. (Photo copyright Columbia University.)

NYGC Plans to Offer Quick Turnaround Time, Competitive Prices

Prices for NYGC’s exome test will be “very competitive” with turnaround time of six to eight weeks as compared to 12 weeks required by other labs, Jobanputra told Clinical Sequencing News.

She acknowledged that Columbia University offers similar exome sequencing tests. But she envisions a large volume of patients in New York, as well as state hospitals interested in exome sequencing outsourcing.

In fact, Columbia physicians sequenced the exomes of 150 patients to diagnose unknown disorders over the past year, Dark Daily reported in May.

Other tests reportedly being planned by NYGC are a whole-genome sequencing test for constitutional disease and a genome and transcriptome test for cancer. The genome test for constitutional disease may replace the exome test and be geared at patients where the exome came back negative, Clinical Sequencing News reported.

Meanwhile, the cancer genome test, analyzing whole genomes, will be unique as compared to clinical labs that analyze gene panels, Jobanputra said.

NYGC Collaboration with IBM Helps Center ‘Get Hands Wet’

The cancer genome test relates to a glioblastoma research study NYGC is conducting with IBM. In March, the organizations issued a press release announcing an initiative to accelerate genomic medicine with use of IBM’s Watson cognitive system. A Watson prototype designed specifically for genomic research is being tested.

A story in ZDNet shared that NYGC and IBM plan to:

  1. conduct a joint research study to develop care for glioblastoma, an aggressive brain cancer;
  2. examine DNA-based treatment options by using Watson to correlate data from genome sequencing to journals, studies and records;
  3. identify patterns in genome sequencing and medical data; and,
  4. refine Watson’s algorithms based on the NYGC’s data.

These first exome and whole-genome sequencing assays will “help us get our hands wet,” Jobanputra told Clinical Sequencing News.

Once it obtains regulatory approval for these medical laboratory tests, the NYGC will enter the clinical laboratory market for gene sequencing services. It will be one more competitor in this fast-growing field of laboratory medicine. The interesting question that most pathologists would want answered, however, is whether health insurers will reimburse the NYGC for these advanced genetic tests when physicians order them for clinical purposes?

—Donna Marie Pocius

Related Information:

Following State Permit, New York Genome Center’s Clinical Lab Prepares to Submit Exome, Genome Tests

The $1,000 Genome is One Step Closer to Reality

Researchers at Columbia University Report How Exome Sequencing Helped Diagnose Patients With Unknown Disorders

The New York Genome Center & IBM Watson Group Announce Collaboration to Advance Genomic Medicine

IBM, New York Genome Center Prep Watson Prototype