Chromosomal Microarray: CytoScan SNP Array POC

Condition Description

At least 50% of first trimester miscarriages are caused by a chromosomal imbalance. Chromosomal microarray analysis of uncultured products of conception (POC) samples increases the likelihood of detecting clinically significant genetic imbalances as compared to conventional G-banded analysis. Since the Chromosomal Microarray, CytoScan SNP Array POC uses DNA extracted from uncultured cells, rather than cultured cells, tissue culture failure is avoided. Microarray testing detects smaller imbalances than conventional G-banded analysis, especially since POC samples often have poor chromosome morphology. The CytoScan SNP Array POC detects triploidy, trisomy, monosomy, and chromosome deletions and duplications. This test is a cost effective method to detect chromosomal imbalances, which is important to determine the recurrence risk for future pregnancies.

Schaeffer et al. (2004) Am J Hum Genet; 74:1168-1174.

Genes (0)


The CytoScan SNP Array POC is warranted for the evaluation of any spontaneous pregnancy loss and can provide a diagnosis and recurrence risk for future pregnancies.


DNA isolated from the POC 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 POC consists of 2.6 million markers (including 750,000 SNPs) which allows for the detection of both copy number variation (CNV) and large stretches [>10 Megabases (Mb)] of absence of heterozygosity (AOH), which can result from uniparental disomy (UPD) or common parental descent. The design is based on recommendations from the International Standards for Cytogenomic Arrays (ISCA) Consortium (Baldwin et al. (2008) Genet Med; 10(6):415-429).


Deletions and duplications of 400 kilobases (kb) or greater are detected and will be reported. Smaller deletions or duplications in regions of known microdeletion/microduplication syndromes or in clinically relevant genes will also be reported.

This test is designed to detect whole and partial chromosome UPD, long stretches of absence of heterozygosity (AOH) greater than 3 Mb, and AOH in clinically relevant regions.  In addition, this test can also detect triploidy, a common cause of miscarriages. Possible UPD will be reported when a chromosome has at least one homozygous regions >10 Mb. Homozygosity due to apparent common descent will be reported when >5% of the autosomal genome is present in long stretches of AOH. These regions of AOH will be specified to consider recessive risk alleles.

Chromosomal Microarray, CytoScan SNP Array POC will not detect balanced translocations, balanced inversions, imbalances smaller than the resolution of this array, point mutations, or low level mosaicism (usually less than 25%).

Specimen Requirements

Listed below are EGL's preferred sample criteria. For any questions, please call 470.378.2200 and ask to speak with a laboratory genetic counselor (
Submit only 1 of the following specimen types
Whole Blood (Sodium heparin)

Sodium Heparin (Green Top)
Infants and Young Children (<2 years of age): 2-3 ml
Children > 2 years of age to 10 years old: 3-5 ml
Older Children & Adults: 5-10 ml
Autopsy: 2-3 ml unclotted cord or cardiac blood
Collection and Shipping
Ship sample at room temperature for receipt at EGL within 24 hours of collection. Do not refrigerate or freeze. Not accepted on Saturday. (Late Friday colections may be stored at room temperature over the weekend for Monday receipt.)
Products of Conception

Sterile container with EGL transport media|If EGL media is not available, other sterile culture media can be used (RPMI, Hanks Solution)
≥15-30 mg chorionic villi/placental tissue using sterile technique. Place in sterile tube(s) with transport media.
Tissues fixed in formalin cannot be used.
The laboratory cannot legally accept entire fetuses/stillbirths. Must be a part of an individual.
Collection and Shipping
Must be received in securely closed, sterile container with sterile culture media. If fetal demise occurred more than 48-72 hours prior to retrieval of tissue and delivery to the Lab, fetal tissue is unlikely to grow. In this case, placenta is most likely to grow.Refrigerate until time of shipment. Ship sample at room temperature for receipt at EGL within 24 hours of collection.

Special Instructions

Maternal cell contamination studies are warranted to rule out the possibility of maternal cells in female products of conception.  Submit a 5cc maternal whole blood sample in an EDTA tube. Test code: CMCCS. CPT code: 81265 (x1).

Sample Storage and Data Usage:  As a participant in the ISCA (International Standard Cytogenomic Array) Consortium, EGL Genetics retains patient samples indefinitely for validation, educational purposes and/or research. The submitted clinical information and test results are also included in a HIPAA-compliant, de-identified public database as part of the National Institute of Health\'s effort to improve diagnostic testing. For information about the database visit the consortium website at Confidentiality of each sample is maintained.

Patients may request to have their samples discarded upon test completion and to opt-out of participation in the database by:
1) Checking the box provided on the test requisition or consent form
2) Calling the laboratory at 470-378-2200 and asking to speak with a laboratory genetic counselor
  • Maternal cell contamination studies (CMCCS)
  • Targeted testing by FISH is available to family members of an individual with a deletion or duplication detected by microarray.
  • Prenatal Chromosomal Microarray (EmArray Cyto) (CMPRE)
  • EmArray Cyto (VA)
  • EmArray Cyto+SNP (CMSNP)

How to Order