NeoARRAY™ SNP/Cytogenetic Profile

Enhanced SNP microarray for high-resolution detection of unbalanced chromosome abnormalities and loss of heterozygosity

The NeoARRAY SNP/Cytogenetic Profile is molecular karyotyping that extends the reach of FISH and cytogenetics in hematologic disease and solid tumors. It detects and defines chromosome defects throughout the genome, and enables you to:

  • Scan the entire genome for chromosomal imbalances at resolution ~10-25 times higher than conventional karyotyping
  • Reveal cryptic abnormalities in samples with normal cytogenetic results
  • Obtain detailed description of deletions, duplications, and amplifications (collectively called copy number variants or CNVs)
  • Better define breakpoints in small or complex unbalanced rearrangements in many cases
  • Characterize unknown material in marker chromosomes or complex karyotypes
  • Detect regions of acquired uniparental disomy (UPD, also called copy-neutral loss of heterozygosity or LOH) which are associated with poor prognosis in a growing number of tumors
  • Focus on over 500 cancer genes with enhanced probe density
  • Produce cytogenetic results from samples that fail or do not divide well in culture
  • Determine genotype of a large number of SNPs

 

Test overview

The NeoARRAY analyzes genomic DNA from the patient’s blood, marrow, tumor, or POC sample using the Affymetrix CytoScan HD Array platform, which provides the best coverage of the genome commercially available. The array contains over 2.6 million probes, both SNP and oligo type, for sensitivity and specificity of >99% in detecting abnormalities >400 kb. Clinically significant abnormalities are summarized in text and table format in a comprehensive report that denotes disease association and relevance of the findings to therapy and prognosis.

Contact us for more information about NeoARRAY. 

 

Ordering information

The NeoARRAY is available for fresh hematological and solid tumor specimens.

Specimen requirements:

  • Peripheral blood: 5 mL in EDTA tube.
  • Bone marrow: 2 mL in EDTA tube.
  • Fresh tumor tissue: 0.5 – 1 cm3 in RPMI.

Specimen requirements for NeoARRAY on Products of Conception (without cytogenetics):

  • POC (products of conception): Dissected chorionic villi or known fetal tissue (preferred). Please send at least 50-100 mg villi or 0.5 – 1 cm3 tissue(s) to our Irvine, CA laboratory.
  • Uterine contents or tissue of mixed fetal/maternal origin: Please send at least 50-100 mg villi or 0.5 -1 cm3 tissue(s) to our Nashville, TN laboratory.
  • Place tissue in RPMI: Note type of tissue(s) sent on the test requisition and whether it is fetal in origin or mixed maternal/fetal. Please see our contact page for the shipping addresses.

Specimen requirements for cytogenetics reflex to NeoARRAY on Products of Conception:

  • POC (products of conception): Please send at least 50-100 mg villi or 1 – 1.5 cm3 tissue(s) to our Nashville, TN laboratory.
  • Note: Dissected chorionic villi or known fetal tissue(s) are preferred, but uterine contents or tissue of mixed fetal/maternal origin is acceptable and will be processed. Please include villi if sending tissue from a fetal demise. Tissues placed in formalin are unacceptable.
  • Place tissue in RPMI: Note type(s) of tissue on test requisition, and send to our Nashville, TN facility. Please see our contact page for the shipping address.

Client information for POC cytogenetics with reflex to NeoARRAY:

  • Clients may request POC cytogenetics with reflex to NeoARRAY if the POC culture fails or if cytogenetic results are normal. If there is no cell attachment or growth after 14 days in culture, a cytogenetics failure report will be issued and NeoARRAY will be performed. If there is limited cell attachment after 14 days in culture, NeoGenomics will contact the client for instructions. When array testing is not performed, a fee will be charged for DNA extraction (which is performed upon specimen receipt).

Shipping and transport: Use cold pack for transport, making sure cold pack is not in direct contact with specimen. Ship same day as drawn whenever possible; specimens <48 hours old preferred.

TAT: 14 days

 

Limitations of testing

As with all chromosomal microarray tests, detection limits apply to the NeoARRAY. Abnormalities present at a frequency of <20% may not be reliably detected. Therefore, microarray analysis is not appropriate for minimal residual disease monitoring. This test does not detect balanced translocations and inversions. FISH and/or targeted molecular testing are available for some of these rearrangements. Variants that do not meet NeoGenomics’ thresholds for size or clinical significance will not be reported.

 

Recommended reading

  1. Simons A, et al. Genome-wide arrays in routine diagnostics of hematological malignancies. Hum Mutation. 2012;33(6):941-948.
  2. Maciejewski JP, et al. Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Brit J Haematol. 2009;146:479-488.
  3. Dougherty MJ, et al. Clinical utilization of high-resolution single nucleotide polymorphism based oligonucleotide arrays in diagnostic studies of pediatric patients with solid tumors. Cancer Genet. 2012;205:42-54.
  4. Bullinger L, Frohling S. Array-based cytogenetic approaches in acute myeloid leukemia: clinical impact and biological insights. Seminars Oncol. 2012;39(1):37-46.
  5. O’Malley DP, et al. Comparison of aCGH to FISH and cytogenetics in prognostic evaluation of chronic lymphocytic leukemia. Int J Lab Hematol. 2011;33(3):283-244.

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