Chromosomal Microarray: CytoScan SNP Array Oncology

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Condition Description

Cytogenetic analysis provides clinically relevant diagnostic, prognostic and therapeutic value to the management of hematologic diseases.  Traditional cytogenetic methods, such as karyotyping and FISH analysis, have historically been used to detect clinically relevant abnormalities; however, technical and analytical limitations make these methods costly, laborious and limited in their detection of chromosome aberrations.

Recently, the utilization of chromosomal microarrays in a clinical setting for the detection and management of hematological disease has provided many advantages over these traditional methods. EGL uses the CytoScan HD SNP Array (Affymetrix) to detect clinically-relevant genomic changes in hematological disorders, such as copy number changes and loss of heterozygosity (LOH). This analysis can interrogate the entire genome for recurrent and novel clinically-relevant copy number variation (CNV) at an increased resolution over FISH or karyotype analysis. 

In addition to CNVs, the CytoScan SNP Array Oncology detects copy-neutral LOH due to acquired UPD, which is not detected by karyotype or FISH analysis.  These regions can contain oncogenes or lead to homozygosity of existing pathogenic variants in tumor suppressor genes, which could confer a growth or proliferative advantage to cancer cells. 

The CytoScan SNP Array Oncology detects mosaicism at levels of 15-20% or higher;  therefore, this test is not recommended for detecting minimal residual disease after therapy. FISH analysis is the preferred test for minimal residual disease monitoring, and FISH probes may be specified at the time of array testing for follow-up after treatment.

Microarray analysis cannot detect balanced translocations, inversions and insertions that may be important for cancer diagnosis and prognosis. Therefore, microarray findings should be interpreted together with other concurrent test results, such as flow cytometry, pathology, FISH and chromosome analysis.

References: 
  • Makishima and Maciejewski (2011) Clin Cancer Res 17(12):3913-3923.
  • Simons et al. (2012) Human Mutation 33(6):941-948

Indications

The CytoScan SNP Array Oncology is indicated for individuals with a diagnosis or suspected diagnosis of a hematological disease.

Methodology

DNA isolated from the hematologic sample is hybridized to an array containing oligonucleotide and SNP probes across the genome to detect copy number imbalances and regions of homozygosity.

The CytoScan SNP Array Oncology consists of 2.6 million copy number markers, of which 750,000 are single nucleotide polymorphisms (SNPs) and 1.9 million are non-polymorphic probes.

Detection

Deletions > 200 kb, duplications > 500 kb, and loss of heterozygosity (LOH) > 10 Mb will be reported. For targeted regions, deletions > 25 kb, duplications > 100 kb, or loss of heterozygosity (LOH) > 5 Mb with clinically-relevant genes will also be reported.

CytoScan SNP Array Oncology will not detect balanced translocations, balanced inversions, imbalances smaller than the resolution of this array, point mutations, or low level mosaicism (less than 20%).

Specimen Requirements

Type: Bone Marrow

Specimen Requirements:

3 mL bone marrow collected in a sodium heparin tube. Specimen stability: 2 weeks if refrigerated.

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample overnight at room temperature for receipt at EGL within 24 hours of collection.

Type: Lymphoma Tissue

Specimen Requirements:

Tumor biopsy collected in transport medium

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample overnight at room temperature for receipt at EGL within 24 hours of collection.

Type: Whole Blood

Specimen Requirements:

In EDTA (purple top) or ACD (yellow top) tube:
Infants (<2 years): 2-3 ml
Children (>2 years): 3-5 ml
Older Children & Adults: 5-10 ml Specimen stability: 2 weeks if refrigerated.

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Special Instructions

Microarray findings should be interpreted together with other concurrent test results, such as flow cytometry, pathology, FISH and chromosome analysis.  Please provide these results when submitting the sample or when the results are available. 

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