Cancer Cytogenetics Oncology Microarray - Targeted Gene and Region Panel

Chromosomal microarray (CMA) testing in oncology, including hematologic malignancies in blood and bone marrow and fresh and fixed (FFPE) solid tumors, provides information that can be critical for diagnosis, prognosis and treatment.   CMA detects copy number changes (deletion, duplication and amplification) on a scale from genome-wide to individual genes. In addition to oligonucleotides to detect copy number, the Oncology microarray also contains single-nucleotide polymorphisms (SNPs) to uncover copy-neutral loss of heterozygosity (CN-LOH), associated with gene conversion in cancer.    

The KDL Targeted Gene and Region Panel Oncology Microarray is currently developed and available for targeted testing of the following conditions only (see note*):

1. Glioma
2. Neuroblastoma
3. Wilms Tumors
4. Melanoma
5. Chronic Lymphocytic Leukemia (CLL)

• Generally, the Oncology microarray will detect all copy number changes currently assessed by FISH but will also detect many additional targets and can also detect CN-LOH.The array has been validated for use on FFPE (tumor fraction >40%) and bone marrow/blood (malignant cell fraction >20%).
• Due to limits of detection, the Oncology array is NOT INTENDED FOR FOLLOW-UP STUDIES, eg recurrence, relapse, MRD, etc.
• For CLL, the intended use of the Oncology microarray is for patients at presentation; custom FISH probes may be created for follow-up in specific patients.
• Also, with CLL, a break-apart FISH probe for IGH will be run at no additional cost.
• Reflex testing with additional probes may be performed at a cost, after consultation with referring provider.

Region and gene-level target lists for the individual panels above were created using current guidelines (when applicable), literature (including WHO classification), current laboratory practices and experience and consultation with clinical colleagues. 

Information regarding the specific copy number change and CN-LOH targets for each panel is available by contacting the laboratory. 

*Note: Personalized region and gene targeting may be available – please contact our laboratory. 

FFPE samples receive pathologist review to guide DNA extraction.

DNA is labeled and hybridized to an Oxford Genome Technology CytoSure Consortium Cancer +SNP array; content and build is as recommended by the Cancer Genomics Consortium (CGC).  The array is comprised of a collection of oligonucleotide probes with whole-gene CNV resolution of more than 500 cancer-associated genes, enhanced coverage of 130 cancer-associated genomic regions, in addition to whole-genome coverage for CNV and LOH analysis.  This array contains 180,000 elements in total (oligonucleotides + SNPs).   Data are interpreted and reported according to current guidelines (Mikhail et al. 2019).

FFPE

• A paraffin block or 
• 18 unstained FFPE slides at room temperature. Preferred slice thickness is 5 micrometer on positively charged slides.
• Fresh frozen tumor samples.
• Tumor samples should be selected from viable areas, with as little normal or necrotic material as possible.
• Please avoid needle biopsies when possible, as they generally do not yield sufficient DNA for this test platform.

Blood and/or Bone Marrow
Blood and/or bone marrow may be collected in either EDTA or NaHep vacutainer tubes.
Bone marrow may also be collected using a pre-heparinized plastic syringe (use 0.2 cc sodium heparin,1000 unit/mL) and transferred to a centrifuge tube with transport media.

• Adult: 3-5mL, as noted above
• Child: 1-2mL, as noted above
• Infant:1-2mL, as noted above

Special note for patients who have received blood products:

• For recipients of packed red blood cells or platelets, please wait at least 2 weeks to draw blood for this test.

• For recipients of whole blood products, please wait 4 weeks to draw blood for this test.

After collection:
Keep all samples at room temperature and ship as soon as possible.  Contact Client Services at (855) 535-1522 for shipping kits and instructions.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

Weekly

7-12 days Contact Lab at 855-KDL-1LAB (535-1522)

• Package and ship specimen at room temperature.
• Do not use the cold pack provided in the KDL shipping kit. 
• Ship via overnight express, using the FedEx priority overnight label provided.
• Contact Client Services at (855) 535-1522 for shipping kits and instructions.

Mikhail et al. 2019 Genetics in Medicine 21(9)

Informing all builds:
WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues 2017 Eds. Swerdlow et al. IARC

Glioma:
Louis et al. 2016 Acta Neuropath 131(6)
Cimino et al. 2017 Acta Neuropath Commun 5(1).
Buckner et al. 2017 Nat Rev Neurol 13(6).
Crespo et al. 2011 J Mol Diag 13(6).

Neuroblastoma:
Spitz at al.  2006 Genes Chromosomes Cancer 45(12)
Fischer et al. 2010 Genome Med 2(31)
Colon et al. 2011 Adv Pediatr 58(1)  

CLL:
Chun et al. Cancer Genet. 2018 Dec;228-229:236-250
Fang et al. 2018 American Journal of Hematology 94(3)
Braekeleer et al. 2016 Mol Clin Oncol 4(5)

Wilms tumor:
Gadd et al. 2017 Nat Genet. 9(10)
Gratias et al. 2016 J Clin Oncol.  34(26)
Krepischi et al. 2016 Molecular Cytogenetics 9(20)

Melanoma:
Ardakani et al. 2017 Pathology 49
Chandler et al. 2012 Arch Pathol Lab Med 136