• Test Code:
    6510
  • Department:
    Constitutional Cytogenetics
  • Test Synonyms:
    Array comparative genomic hybridizationaCGHMicroarrayCompetitive genomic hybridizationChromosome microarrayPrenatal
  • CPT Code(s):
    81229
Background:

Chromosomal microarray (CMA), also known as array comparative genomic hybridization (aCGH), is a molecular technique that relies on a competition between labeled patient and reference DNA for hybridization to an array of immobilized target sequences.  CMA facilitates the simultaneous detection of thousands of target sequence and has become the gold standard for assessment of genomic imbalance, particularly submicroscopic imbalance (<5Mb).  Our SNP array is based on the ISCA 60K oligonucleotide + 120K SNP design and can detect both copy number changes and long contiguous stretches of homozygosity (LCSH) which can reflect uniparental disomy, among others (see ‘Methodology’ below). 

Recently, the American College of Obstetricians and Gynecologists issued a committee opinion statement with the Society for Maternal Fetal Medicine concerning prenatal microarray: “In patients with a fetus with one or more major structural abnormalities identified on ultrasonographic examination and who are undergoing invasive prenatal diagnosis, chromosomal microarray analysis is recommended. This test replaces the need for fetal karyotype.  In patients with a structurally normal fetus undergoing invasive prenatal diagnostic testing, either fetal karyotyping or a chromosomal microarray analysis can be performed.  Most genetic mutations identified by chromosomal microarray analysis are not associated with increasing maternal age; therefore, the use of this test for prenatal diagnosis should not be restricted to women aged 35 years and older.” 

Methodology:

DNA is extracted from uncultured amniocytes or chorionic villi (CVS), fluorescently labeled and hybridized (with labeled reference DNA) to an Oxford Genome Technology-designed ISCA +SNP array, printed by Agilent.  The ISCA+ SNP array is comprised of a collection of specific probes that enable a high resolution analysis for copy number change detections for a variety of genetic disorders in ISCA defined regions.  This array combines long oligonucleotide probes for accurate copy number detections with single nucleotide polymorphism (SNP) probes to detect loss of heterozygosity (LOH) and uniparental disomy (UPD).  Any statistically-significant genetic changes are compared against all known databases and relevant literature.

Abnormal findings are confirmed using an independent Cytogenetics (FISH or chromosome analysis) or Molecular (quantitative PCR) technique.  Reports include comprehensive interpretation and recommendations by ABMG-certified Clinical Cytogeneticists. 

(Note: When parental studies are necessary for interpretation, the parental studies will be performed at no charge.)

Specimen Requirements:

HANDLE ALL SPECIMENS ASEPTICALLY AND TRANSPORT TO OUR LAB IMMEDIATELY.

Maternal blood sample must accompany all samples:
3ml in EDTA. FISH for chromosomes X and Y is performed on all amniotic fluid/CVS submitted for microarray. If those results indicate a female fetus, a maternal cell rule out study will be performed at no additional charge.

Amniotic Fluid:  18-24 mL.

  • Discard or separately collect first one or two mL fluid (can be used for AFP).
  • If fluid is bloody, add 0.5 mL sodium heparin (1000 units/mL) to each 10 mL of fluid and mix well. 

CVS:  Collection of Samples:

  •  Transport medium is available from our laboratory upon request.  [Transport medium: 500 ml Ham F-10 (Gibco), 0.5 ml gentamycin, 5 ml sodium heparin (1,000 USP units/ml).  Aliquot 10 ml of transport medium into sterile, screw-cap plastic test tubes.  The shelf life of the transport media is 3 months at 4°C or 1 year frozen. 

Procedure:

  1. Use approximately half of medium (5ml) in vial for syringe receiving villi.
  2. Pour remaining half of medium from vial into sterile Petri dish.
  3. Villi are transferred from syringe to Petri dish for evaluation.  If sample contains a number of red blood cells, more medium may be added to dilute for better visualization.  It may also be necessary to rinse syringe with fresh medium.
  4. If an adequate sample is obtained (an adequate amount of villi is 20-25 mg), use forceps and sterile technique to transfer villi to one of the vials that still contain medium.  Samples 5-10 mg will be accepted with disclaimer due to small sample size.
  5. Label vial with patient name, date of birth, and gestational age.
  6. Keep at room temperature and transport to laboratory as soon as possible.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information, including reason for referral, ethnicity, clinical history, and family history.

Test Performed (Days):

Mon-Sat

Turn Around Time:

7-10 days - See Additional Information

Shipment Sensitivity Requirements:

  • Keep specimen at room temperature during transit. 
  • Shipping supplies can be provided to you upon request.
  • DO NOT use the cold pack provided in the KDL shipping kit. 
  • Ship the specimen overnight express, using the FedEx priority overnight label provided. 
  • The specimen must arrive at the lab no more than 24 hours after collection.
  • Contact Client Services at (855) 535-1522 for shipping supplies or additional instructions if needed.

References:

  1. Miller et al. 2010 AJHG 86, 749-764
  2. Manning and Hudgins 2010 Professional Practice and Guidelines Committee.  Genet Med. 12, 742-745.
  3. ACOG/SMFM committee opinion on microarray testing.  https://www.acog.org/Resources_And_Publications/Committee_Opinions/Committee_on_Genetics/The_Use_of_Chromosomal_Microarray_Analysis_in_Prenatal_Diagnosis
  4. Rehder et al. American College of Medical Genetics and Genomics: standards and guidelines for documenting suspected consanguinity as an incidental finding of genomic testing. Genet Med 2013 15, 150-152.

Additional Info:

***Turn Around Time: Note direct cases will be reported at the low-end of our turnaround time range; in rare cases, turnaround times may be longer because of confirmation studies or because culturing is necessary to acquire sufficient DNA for testing.  These may be 10-18 days – the referring clinician will be kept abreast of the situation.