IGM Clinical Laboratory

IGM Clinical Laboratory

The Institute for Genomic Medicine (IGM) Clinical Laboratory at Nationwide Children’s Hospital (NCH) provides a variety of cytogenetic and molecular genetic tests for genetic conditions and cancers.

The laboratory is accredited by the College of American Pathologists (CAP) and certified by the Clinical Laboratory Improvement Amendments (CLIA) and aims to provide the high quality testing. Board-certified laboratory directors, technologists, supervisors, genetic counselors, laboratory scientists and staff are continually improving testing technologies and service to patients and providers. The laboratory integrates clinical practice with research and the IGM Technology Development team to rapidly incorporate innovative methods into diagnostic testing.

Learn about our Guide to Services.

Whole Exome Sequencing

The IGM Clinical Laboratory offers Whole Exome Sequencing (WES) to Nationwide Children’s patients. WES used next-generation sequencing to simultaneously analyze the protein coding regions (exons) of known genes in the human genome. This test is intended for patients who likely have an underlying genetic disorder but without a clear diagnosis. WES can identify changes in a patient’s DNA that may cause or contribute to his or her medical condition or phenotype. The sequencing data are analyzed using a specially developed bioinformatics pipeline and carefully interpreted within the context of the patient’s disease phenotype. Optimal testing includes sequencing of the patient and both parents to compare variants in the patient to those in the parents, which can help identify autosomal recessive conditions and variants that are unique to the patient (de novo). As a result, WES may find genetic changes that are unrelated to the patient’s medical condition or may reveal information about familial relationships. Due to the complex nature of this test, genetic counseling and informed consent are essential parts of the WES testing process.

Learn about our Whole Exome Sequencing FAQs.

Cytogenetics

The laboratory performs cytogenetic chromosome analysis (karyotype) to detect numerical and structural chromosomal abnormalities that may be associated with birth defects, infertility, miscarriages, stillbirths, developmental delays or disabilities, and disorders of sexual differentiation. Our laboratory can perform chromosome analyses on peripheral blood, amniotic fluid, products of conception, skin biopsy, and periumbilical blood (PUBS) samples.

Fluorescence in situ Hybridization (FISH)

FISH testing is used to detect specific  alterations in a patient’s chromosomes. FISH testing involves labeling specific chromosomal regions with a fluorescent probe to determine if  there is a deletion, duplication, amplification, or translocation of  the targeted region.

Our laboratory offers a variety of FISH-based tests:

  • AneuVysion for the detection of common numerical chromosome abnormalities in prenatal and products of conception (POC) samples

  • Locus specific probes for common microdeletion and microduplication syndromes (e.g. Williams syndrome, Smith Magenis syndrome, Prader–Willi Syndrome, etc.)

  • Locus specific probes for familial chromosomal abnormalities

  • Locus specific probes for pediatric cancers (e.g. MYCH, MYC, ALK, FOXO1, etc.)

Chromosomal Microarray Analysis

Chromosomal microarray analysis is a useful technique to identify gains and losses of chromosomal regions across the genome and detect large regions of homozygosity (ROH). The laboratory uses comparative genomic hybridization (CGH) for detection of copy number variants and single nucleotide polymorphism (SNP) analysis for detection of ROH. Presence of ROH is not diagnostic of any disorder, but it can suggest an increased risk for imprinting disorders and recessive genetic disorders.

Microarray analysis is frequently ordered for individuals with multiple congenital anomalies and developmental delays. It can also be performed in the prenatal setting for a fetus with ultrasound abnormalities with unknown cause.

Chromosomal microarray analysis can also be performed on neuroblastoma and Wilms tumor samples to test for segmental aberrations and prognostic indicators.

Molecular Genetic Testing - Inherited Diseases

The IGM clinical laboratory offers numerous different DNA tests that can be used to diagnose genetic disorders and identify disease carriers. We offer a wide array of molecular tests, such as single gene analysis by Sanger sequencing, gene panel tests through next generation sequencing, methylation analyses, uniparental disomy testing, common mutation testing, and bone marrow transplant monitoring.

Molecular Genetic Testing - Cancer

IGM Cancer Genomics Protocol

IGM has partnered with the Hematology/Oncology department at Nationwide Children’s to develop a genomics protocol for comprehensive clinical- and research-based testing for patients with pediatric cancers and/or hematologic disorders. Initially, this translational research and clinical focus will be on patients with relapsed or treatment refractory disease and/or rare tumor types. Research results may be confirmed under CAP/CLIA standards and utilized for patient management, informing diagnosis, evaluating eligibility for targeted therapeutics and clinical trials, and providing information on prognosis. Patient data will also facilitate research studies to further elucidate the biology of pediatric cancers to broaden our understanding of the disease and help future patients.

The IGM Clinical Laboratory also tests cancer specimens for risk assignment and targeted therapy. We serve as a centralized clinical testing laboratory for the Children’s Oncology Group (COG), and offer the same assays for patients not enrolled on COG trials. Samples for COG trials are banked at Nationwide Children’s through the Biopathology Center.

Acute Lymphoblastic Leukemia (ALL)

Pediatric acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, comprising 75% of pediatric leukemia cases. Recent studies involving IGM faculty led to the implementation of diagnostic sequencing and screening technologies for real-time identification of a subset of patients with a Philadelphia chromosome-like expression profile. These patients have drastically poor outcomes. Identification of the kinase alteration may lead to a more targeted, precise treatment for children and adults with this specific form of ALL.

Assays available:

Targeted RNA Sequencing - Archer DX analysis
JAK Sanger sequencing analysis
IL7R Sanger sequencing analysis
MRD analysis by flow (through NCH Clinical Flow Cytometry Laboratory)

Neuroblastoma (NBL)

Testing for neuroblastoma is primarily for risk assignment and includes MYCN amplification, DNA ploidy analysis, and pathology assessment. Recent studies suggest that a subset of patients with whole chromosome gains have a better prognosis than those with segmental abnormalities. Also, patients with ALK somatic changes may benefit from targeted therapy. Testing available for neuroblastoma patients includes:

MYCN FISH to test for amplification (greater than 4x increase over control probe)

ALK FISH to test for amplification
ALK targeted Sanger sequencing
DNA ploidy analysis (through Nationwide Children’s Clinical Flow Cytometry laboratory)
Loss of Heterozygosity (chromosomal regions 1p and 11q)
Copy number/SNP microarray (not available on FFPE tissue)

Medulloblastoma

Identification of medulloblastoma patient with abnormalities of the WNT pathway may lead to decreased therapy for these lower-risk patients. If beta-catenin immunohistochemistry is positive, CTNNB1 sequence analysis is performed to confirm an abnormality. This testing is being performed as part of the NCH Headstart 4 initiative, as well as the recent COG ACNS1422 study.

Beta-catenin immunohistochemistry (through Anatomic Pathology laboratory)
CTNNB1 (gene encoding beta-catenin) Sanger sequencing
MYCN FISH to rule out amplification
MYC FISH to rule our amplification

Wilms tumor

Loss of Heterozygosity (chromosomal regions 1p and 16q)