NYGC Diagnostic Tests
NYGC’s clinical sequencing laboratory offers tests that are intended to further the mission of NYGC – translating genomic research into clinical solutions for serious disease. The laboratory received New York State Clinical Laboratory Evaluation Program (CLEP) certification from the NY State (NYS) Department of Health (DOH) in May 2014. Its first two genomics laboratory developed tests (LDT), a constitutional whole-exome sequencing (WES) test for undiagnosed disease and a targeted variant test (Sanger-sequencing based assay to confirm the mutations identified by research NGS for constitutional diseases), received CLEP approval from the NYS DOH in March 2015. The clinical lab participates in the College of American Pathologists (CAP) proficiency testing for our CLEP approved clinical tests.
In addition to its own approved tests, NYGC’s clinical laboratory can generate sequencing data for institutions that would like to offer next-generation sequencing laboratory-developed tests but do not have the infrastructure to generate the data. It can also be used to support research efforts that require CLIA-standard grade sequencing data.
Director, Molecular Diagnostics
Yumi Kasai, PhD, DABMG
Associate Director, Clinical Laboratory
For inquiries, please contact us at
CONSTITUTIONAL WHOLE EXOME SEQUENCING TEST FOR UNDIAGNOSED DISEASE
Clinical constitutional whole exome sequencing (WES) is intended for children or adult patients with an undiagnosed condition that suggests an underlying genetic cause. This test involves targeted sequencing of the exome, the subset of genomic DNA that encodes proteins (known as exons), using high throughput DNA sequencing technology. Knowledge of clinically or likely relevant disease causing mutations in exons is changing at a rapid pace, and clinicians may be unable to stay fully aware of these updates. WES enables simultaneous sequencing of a large number of genes that may contain these mutations in a single test, and may also identify entirely new private mutations in genes previously not linked to a disease. Because WES interrogates all protein coding regions, it replaces the potential need for multiple costly single-gene tests, avoids clinician guesswork or bias in gene testing decisions, improves the odds of identifying a high-risk variant and thereby improves diagnostic success rate and the guidance of appropriate clinical management.
NYGC’s clinical constitutional whole exome sequencing test is offered as a trio-test in which the affected child and parents are sequenced together. Sequencing data is analyzed in the context of family relationships to increase the likelihood of identifying genetic variants that may be contributing to the symptoms observed in the child. The clinical lab will also accept samples from just the affected child or individual as well as from other affected or unaffected relatives to provide additional context and help guide interpretation on a case-by-case basis.
NYGC’s clinical laboratory is able to return results within 6-8 weeks, approximately half the time typically required for this type of testing. Because of the complexity of genetic testing and the important implications of the test results, results are sent to the physician and/or genetic counselor, who will then discuss the results with the patient. The results of this test can become part of the patient’s medical record.
A report will be provided indicating the variants that could explain the clinical phenotype. In addition, the clinical lab will report secondary findings in medically actionable genes as per the American College of Medical Genetics and Genomics (ACMG) guidelines. Patients will also be able to opt in to learning their carrier status for autosomal recessive genes recommended by the ACMG and the American Congress of Obstetricians and Gynecologists (ACOG) for reproductive screening.
A physician must order the test using NYGC’s test requisition form and obtain informed consent from each family member (in pediatric cases, the child’s parents) being tested. This test requires 5ml of blood drawn in an EDTA tube or saliva specimen collected in OragenDx collection kit from each family member being tested (all tubes submitted together whenever possible) or DNA extracted in a CLIA-certified laboratory from each family member being tested (all samples submitted together whenever possible). Samples should be shipped to NYGC overnight via FedEx. A courier service may also be feasible.
TARGETED VARIANT TESTING
Our clinical laboratory can use Sanger sequencing to independently confirm findings from exome and/or genome sequencing that was done on a research basis.
Turn around time is within 2-3 weeks. A report will be provided indicating if the test detects the specified variant(s).
A physician must order the test using NYGC’s test requisition form and obtain informed consent from the patient (in pediatric cases, the child’s parents) being tested. This test requires 5ml of blood drawn in an EDTA tube or saliva specimen collected in OragenDx collection kit or DNA extracted in a CLIA-certified laboratory. Samples should be shipped to NYGC overnight via FedEx. A courier service may also be feasible.