New York State approves NYGC's Whole Genome and Transcriptome Sequencing for oncology

Reviewed by James Ives, M.Psych. (Editor)Nov 29 2018

The New York Genome Center (NYGC) has received approval from the New York State Department of Health to offer whole genome and RNA transcriptome sequencing in its Clinical Laboratory Evaluation Program (CLEP)-certified laboratory. This is the first approval by New York State for a whole genome sequencing test for oncology, and currently NYGC's Clinical Lab is the only one to offer it.

Whole Genome and Transcriptome Sequencing (WGTS) for oncology is a complex genetic test developed by NYGC scientists that involves sequencing the genome of the tumor, the matched normal (unaffected) specimen, and the transcriptome of the tumor specimen. Unlike gene panels or whole exome sequencing, this new test includes sequencing the coding and non-coding regions of the genome. WGTS doesn't rely on enriching the protein-coding part of the genome or make any assumptions about the most relevant genes. It probes the transcriptome of the tumor, revealing an unbiased and more complete depiction of the patient's cancer from a genomic and molecular perspective. The ultimate advantage of WGTS is that it can lead to more comprehensive disease diagnosis and personalized treatment decisions than tests that sequence only the coding region.

NYGC's WGTS is a test for all types of cancer that aims to examine the similarities and differences among the genomic and cellular alterations found across diverse tumor types. As such, it is indicated for both solid tumors and hematological malignancies where a mutational profile with multiple types of mutations would assist clinicians in determining disease stratification, prognosis, or treatment options, including targeted therapies and eligibility for clinical trials. The test has been validated for fresh, frozen and FFPE (formalin fixed paraffin embedded) specimens. Significant driver and therapeutic-associated mutations are included as part of the NYGC's WGTS clinical report. The laboratory also reports secondary findings from the whole genome sequencing of the germline specimen for variants contributing to cancer predisposition and the ACMG-59 gene list when consented. These germline findings could have a significant impact in the clinical management of patients and their families.

Tom Maniatis, PhD, NYGC's Scientific Director and Chief Executive Officer, noted, "Developing novel approaches to cancer genomics such as WGTS is part of the NYGC's scientific focus, combining state-of-the-art genomic tools and analysis with whole genome sequencing to help identify more effective cancer treatments and therapies based on the tumor's genetic profile."

"Under Governor Cuomo, the biotech sector in New York State has made significant strides, advancing scientific discovery and creating jobs," said Dr. Jill Taylor, Director of the Wadsworth Center, New York State Department of Health. "NYGC's work with this next-generation sequencing test could lead to more comprehensive disease diagnosis and personalized treatment decisions, benefiting clinicians and patients in New York and all across the country."

A recent paper about the WGTS assay developed at the NYGC was published in the Journal of Molecular Diagnostics with Vaidehi Jobanputra, PhD, NYGC's Director of Molecular Diagnostics and Head of the Clinical Lab, as senior author and Kazimierz Wrzeszczynski, PhD, NYGC's Assistant Director of Clinical Oncology Informatics, as first author. They and their clinical team describe the unique WGTS assay they developed and validated, and which New York State approved. This test provides more comprehensive genomic profiles of a patient's tumor than current routine tests. The validation study involved 125 patient-derived tumors (including FFPE specimens) and matched normal specimens for the purpose of interrogating somatic alteration in the patient's tumor. High confidence variant identification standards were determined and validated for whole genome sequencing detection of single nucleotide variants, insertions and deletions, copy number aberrations, structural variants, and RNA sequencing identified fusions. The study demonstrated that the WGTS assay can provide a variant discovery approach suitable for directed oncologic therapeutic applications.

"Whole genome sequencing provides an unbiased representation of a patient's somatic tumor profile," explained Dr. Jobanputra. "When combined with RNA transcriptome sequencing, this comprehensive diagnostic approach can be used to significantly improve diagnosis and potential targeted therapy selection for cancer patients."

The NYGC's Clinical Lab also offers a separate clinical whole genome sequencing test for undiagnosed disease and predisposition testing in ostensibly healthy individuals.