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Oncology SNP Array Karyotyping, Oncology Molecular Karyotyping

Microarray, SNP, oncology array, genetic, GSNPG

Test Codes

EPIC: LAB6769

Department

Cytogenetics

Instructions

Test Limitations
SNP Array cannot detect:

1. Balanced chromosome rearrangements such as translocations, balanced insertions, or inversions.
2. Low-level mosaicism.
3. An abnormality in a region not represented on the array.

Specimen Collection Criteria

Collect: Peripheral blood OR bone marrow, as described below:

• Bone Marrow: 2-3 mL in a Dark Green-top Sodium Heparin tube. (Minimum: 1.0 mL)
• Peripheral Blood: 5-7 mL in a Dark Green-top Sodium Heparin tube. (Minimum: 3.0 mL)

Gently invert tube to mix specimen.

NOTE: A copy of the completed requisition must accompany the specimen which must include patient name, date of birth, requesting physician, clinical indication, test requested, and specimen source.

Physician Office/Draw Specimen Preparation

Do not freeze specimen. Store bone marrow or peripheral blood at room temperature (20-26°C or 68-78.8°F) prior to courier pickup. For delays in transport (greater than 24 hours from the time of collection), refrigerate (2-8°C or 36-46°F) the specimen.

Preparation for Courier Transport

Transport: 2-3 mL bone marrow (minimum: 1.0 mL) or 5-7 mL peripheral blood (minimum: 3.0 mL), at room temperature (20-26°C or 68-78.8°F).

Rejection Criteria

• Improperly labeled specimens.
• Frozen specimens.
• Cracked or compromised specimen tubes.
• Specimens received greater than 72 hours past the time of collection.

In-Lab Processing

Specimens are processed immediately upon receipt in the Laboratory.

Storage

Specimen Stability for Testing:

Room Temperature (20-26°C or 68-78.8°F): 24 hours 
Refrigerated (2-8°C or 36-46°F): 72 hours
Frozen (-20°C/-4°F or below): Unacceptable

Specimen Storage in Department Prior to Disposal:

Refrigerated (2-8°C or 36-46°F): 7 days. A backup cell pellet is maintained for three weeks past sign-out of the final report. Extracted DNA is maintained for one year.

Laboratory

Royal Oak Cytogenetics Laboratory

Performed

Monday – Friday, 8:00 am – 5:00 pm.
Results are available 10-14 days after the laboratory receives insurance pre-authorization. Additional time may be needed for reflex testing of abnormal results.

Reference Range

Positive or negative for chromosome abnormality. A comprehensive interpretative report will be provided.

Test Methodology

Affymetrix CytoScan™ HD Single Nucleotide Polymorphism (SNP) Array.

Clinical Utility

The importance of identifying chromosome abnormalities in cancer, especially in hematolymphoid disorders, has long been well established as they provide diagnostic, prognostic, and therapeutic information critical to proper patient management. Furthermore, the identification by both conventional karyotyping and FISH of recurrent balanced or unbalanced chromosome changes in specific disorders has permitted the elucidation of the genetic mechanisms that underlie their malignant origins, thus providing the basis for the development of specific treatments. FISH panels are now routinely utilized in evaluation of hematological disorders including myelodysplastic syndrome, acute myeloid leukemia, chronic lymphocytic leukemia, pediatric acute lymphoblastic leukemia, and plasma cell myeloma. Recent advances in chromosome array technology have provided an opportunity to examine the whole genome of cancer cells at a level of resolution far greater than what is achievable by previous methods including FISH. A single nucleotide polymorphism (SNP) DNA array can detect genomic gain or loss at a very high level of resolution and can also provide genotype information which permits detection of copy number neutral loss of heterogeneity (acquired uniparental disomy or aUPD). The Beaumont SNP Oncology array test utilizes the Affymetrix CytoScan™ HD SNP array which provides the broadest coverage and highest performance for detecting both copy number altering and copy number neutral aberrations. In the last several years, a number of different neoplastic conditions have been studied using SNP array analysis. These conditions include chronic lymphocytic leukemia, myelodysplastic syndromes, acute myeloid leukemia (especially with a normal karyotype), plasma cell myeloma, B-cell lymphomas, and solid tumors. These studies have demonstrated a greater sensitivity compared with traditional FISH studies for identifying unbalanced chromosome abnormalities. SNP array can detect complex genomic changes not apparent by either karyotype or FISH, changes which have been correlated with a poorer prognosis in most cases. As a demonstration of the clinical importance of SNP analysis in patients with hematological malignancies, Dougherty et al (2011) performed array analysis on 180 samples from children with a suspected or confirmed hematological malignancy. Of these 180 bone marrow or lymph node biopsies, 130 (72%) revealed aberrations not seen by karyotype. SNP array analysis has also provided valuable, and previously unattainable in a high throughput fashion, information in renal cell carcinoma, neuroblastoma, and glial tumors. At the present time, there is strong supporting data to recommend the use of SNP-array karyotyping in all newly diagnosed cases of CLL, MDS, AML negative for karyotype abnormalities as well as for FLT3 and NPM1 mutations, renal cell carcinomas with equivocal histology, and neuroblastoma.

Reference

1. Song J and Shao H (2016): SNP Array in Hematopoietic Neoplasms: A Review.  Microarrays 5(1).
2. Lacobucci I et al (2013): Use of Single Nucleotide Polymorphism Array Technology to Improve the Identification of Chromosomal Lesions in Leukemia.  Curr Cancer Drug Targets 13(7): 791-810.
3. Simons A et al (2012):  Genome-Wide Arrays in Routine Diagnostics of Hematological Malignancies.  Hum Mut 33(6): 941-948.
4. Yi, JH et al (2011): Adverse Prognostic Impact of Abnormal Lesions Detected by Genome-Wide Single Nucleotide Polymorphism Array-Based Karyotyping Analysis in Acute Myeloid Leukemia with Normal Karyotype. J Clin Oncol 29(35), 4702-4708.
5. Ouillette, P et al (2011): Acquired Genomic Copy Number Aberrations and Survival in Chronic Lymphocytic Leukemia. Blood 118(11):3051-3061.

CPT Codes

81406

NOTE: SNP arrays are generally performed in the outpatient setting.

Contacts

Last Updated

12/30/2022