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Colorado Genetics Labs
 

Prenatal SNP Microarray


Test Options that Include Prenatal Microarray:
  • Chromosomal SNP microarray and standard chromosome analysis

  • Chromosomal SNP microarray and 5-cell chromosome analysis

  • Standard chromosome analysis and if results normal, REFLEX to chromosomal SNP microarray on cultured cells

  • ​FISH trisomy screen with REFLEX

    • ​IF FISH abnormal, reflex to standard chromosome analysis

    • IF FISH normal, reflex to chromosomal SNP microarray and 5-cell chromosome analysis

Single nucleotide polymorphism (SNP) based chromosomal microarray (CMA) is a powerful cytogenomic tool for detecting both copy number variation (deletions or duplications) and copy-neutral structural variants such as regions of homozygosity (ROH) and uniparental disomy (UPD).  Detection of submicroscopic abnormalities, including microdeletions and microduplication, may be missed standard chromosome analysis.

For prenatal samples, chromosome analysis is required prior to or along with the microarray testing. The ​chromosome analysis, whether a standard/routine study or an abbreviated 5-cell study, evaluates chromosomes for balanced rearrangements such as inversions and translocations.


Features of the Infinium® CytoSNP-850K BeadChip Array
  • High resolution array containing 850,000 SNPs with ~15x redundancy of each marker

  • Follows the International Collaboration for Clinical Genomics (ICCG) guidelines for chip design

  • Probes spaced ~1.8 kb along genome for a resolution of ~10kb

  • Targets microdeletion/microduplication syndrome regions with enriched coverage for more than 3,200 known disease genes

  • Regions of homozygosity (ROH) evaluated for possible uniparental disomy (UPD) and recent shared ancestry​

  • SNP CMA can detect triploidy and maternal cell contamination (if not at very low levels)


Indications
  • One or more major structural anomalies in the fetus, detected by ultrasound
  • Abnormal prenatal karyotype requiring further characterization
  • Abnormal cell-free fetal DNA screen supporting the presence of a clinically significant microdeletion or microduplication
  • Family history of chromosomal abnormality

If clinically relevant, common aneuploidies, such as Down syndrome or Trisomy 18, should be ruled out by chromosome analysis or fluorescence in situ hybridization (FISH) before CMA testing is pursued.

If cytogenetic evaluation has not been performed previously, standard chromosome analysis or an abbreviated 5-cell chromosome study may provide additional information. In cases of a normal CMA, the cytogenetic analysis will help detect balanced structural rearrangements in the chromosomes, such as translocations and inversions. In cases of imbalances detected by CMA, the cytogenetic analysis may further clarify the abnormal finding(s), such as confirming the presence of a derivative chromosome.

Methodology
Patient DNA is obtained by extraction from direct amniotic fluid, cultured amniocytes, direct chorionic villi sample (CVS) or cultured CVS. The CytoSNP-850K assay utilizes an amplification step for the DNA and hybridizes this to the BeadChip. The assay then uses a labeling process to provide allele and intensity data. BeadChips are scanned using a two-channel high-resolution laser imager and analyzed using Illumina software.

For reporting of copy number variations (CNVs), thresholds are ≥1 Mb for deletions and ≥2 Mb for duplications with reporting of smaller findings in clinically significant regions. Common CNVs listed in the Database of Genomic Variants are not reported. While NOT diagnostic, SNP data allows for detection of regions of homozygosity (ROH) suggestive of UPD (isodisomy) or shared ancestry (consanguinity) with possible implications in the context of recessive disorders. ROH is evaluated at ≥5 Mb with a reporting threshold of ~10 MB. Total percentage of ROH is reported when ≥5%.

For the 5-cell chromosome analysis, a minimum of 5 metaphases are examined and 3 karyotypes are prepared at ≥400-450 band level (standard resolution).

Regardless of the specific testing option selected, prenatal testing of a CVS specimen includes FISH trisomy screen.

Limitations
SNP CMA can detect whole genome mosaicism suggestive of two different genomic cell lines, as in the case of maternal cell contamination.  The presence of maternal cell contamination may limit the interpretation of CMA results.  For products of conception, placenta or chorionic villi sample, when a single female genome is detected, it is assumed to represent the female fetus.  However, the rare possibility that the DNA analyzed is maternal in origin cannot be excluded.

CMA will not detect balanced rearrangements (i.e., inversions, translocations), heterodisomy, or very low level mosaicism.  It will not detect single gene mutations such as single nucleotide mutations/polymorphisms. Abnormalities that are smaller than the resolution of the array may not be detected.

The cytogenetic analysis will not detect very subtle chromosomal rearrangements.  The 5-cell chromosome analysis will not adequately detect possible mosaicism.

Specimen Requirements
If sample volume is insufficient or the direct sample appears compromised (e.g. blood-tinged amniotic fluid), CMA testing will be performed on DNA extracted from cultured cells (thus extending turnaround time).

Amniotic Fluid
  • Submit at least 25-30 ml in sterile, plastic, screw-top tubes at room temperature.
    • IF <25 ml received, CMA will be performed on cultured cells.
  • Label specimen tubes with patient's name and a second identifier.
  • Hold specimen at room temperature and transport to the Colorado Genetics Laboratory as soon as possible.

Chorionic Villi Sample (CVS)

  • Submit at least 20-30 mg in a sterile, plastic, screw-top tubes filled with sterile transport media at room temperature.
    • ​IF <20 mg received, CMA will be performed on cultured cells.
  • Label specimen tubes with patient's name and a second identifier.
  • Hold specimen at room temperature and transport to the Colorado Genetics Laboratory as soon as possible.

Sample must be accompanied by a completed Test Request Form and Waiver for CytoSNP-850K MicroarrayIndicate the specific prenatal chromosomal microarray option.  Include all pertinent medical and family history and/or a completed Prenatal Chromosomal Microarray Clinical Information Form.

​Interpretation Services
Detailed written report provided with genetic counseling phone consultation available to medical providers.

Follow-up Testing
Colorado Genetics Laboratory recommends that parental/familial testing be considered when a genomic imbalance is detected by chromosomal microarray (CMA).  For copy number changes of uncertain clinical significance, testing of parents is especially important to aid in the interpretation of the finding(s). To expedite parental results, the preferred follow-up testing method typically will be targeted CMA on peripheral blood.


Microarray Billing Policy Effective June 1, 2014

When the new molecular CPT codes became effective January 1, 2013, insurance companies subsequently revised their medical policies regarding medical necessity for chromosomal microarray.  Because of the variability among these policies, waivers for microarray testing have been implemented for all insurance carriers, except Colorado Medicaid.   

Please have your patient complete and sign the Waiver for CytoSNP-850K Microarray form below, and submit it with the specimen for microarray testing.  If the patient’s insurance denies the charges, the patient will be billed at a discounted rate.


References
  1. American College of Obstetricians and Gynecologists. Committee Opinion No. 581: The use of chromosomal microarray analysis in prenatal diagnosis. Obstet Gynecol. 122:1374–7, 2013.
  2. Kearney HM, et al. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 13:680-5, 2011.
  3. South ST, et al. ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 15:901-9, 2013.
  4. Wapner RJ, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 367:2175-84, 2012.​