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Pregnancy Loss Microarray


Chromosomal microarray (CMA) is a powerful cytogenomic tool for detecting subtle gains of DNA as small as 400 kb and losses of DNA as small as 200 kb. CMA can detect abnormalities in known microdeletion and microduplication syndrome regions, as well as submicroscopic abnormalities that may be missed by standard and high resolution​ chromosome analysis.
 

Features of the 180K CMA

    • High resolution array containing 180,000 oligonucleotide features
    • Follows the International Standard Cytogenomic Arrays (ISCA) consortium guidelines for chip design
    • Features are spaced ~16 kb along the backbone of the genome
    • Increased coverage in disease regions
    • Targeted coverage of 500+ OMIM disease genes, microdeletion/microduplication syndrome regions, and subtelomeres
    • Abnormalities detected at a resolution of 100-200 kb
    • Two different software platforms available for analysis to increase overall accuracy and for quality control
    • Confirmation studies performed on abnormal cases
    • Colorado Genetics Laboratory recommends parental testing be considered when a genomic imbalance is detected by chromosomal microarray.  If parental testing will help clarify the clinical significance of the imbalance, it will be offered at no charge.  Otherwise, parental testing is available as a separate test for an additional charge.

Indications

CMA on tissue is performed to evaluate a pregnancy loss for small gains or losses undetectable by chromosome analysis.

Methodology

CMA involves extraction of fetal DNA from a tissue sample (not placenta), labeling of the DNA, and hybridization to the CytoChip oligo microarray. A laser scanner detects the signal from the CMA slide, and interprets gains and losses relative to a normal control DNA using BlueFuse software. The CMA assay performs a comparison between the patient and control to confirm any gains or losses. Finally, fluorescense in situ hybridization analysis is performed, if necessary, to confirm the abnormality detected.
 

Limitations

CMA will not detect balanced rearrangements (i.e., inversions, translocations) or very low level mosaicism. It will also not detect single gene mutations or single nucleotide mutations/polymorphisms. Abnormalities that are smaller than the resolution of the array also may not be detected.
 
If clinically relevant, common aneuploidies, such as Down syndrome or Trisomy 18, should be ruled out by chromosome analysis or fluorescence in situ hybridization before CMA testing is pursued.
 

Specimen Requirements

  • Submit 3-5 mm3 fetal tissue in a sterile, plastic, screw-top tube filled with sterile transport media.  CGL can provide this media.
  • Hold at room temperature; refrigerate if overnight.
  • At this time, we are unable to accept products of conception or placental tissues where there is concern for maternal cell contamination.
  •  
    Samples must be accompanied by a completed Test Request Form.​​ Indicate chromosomal microarray testing.  Include all pertinent medical and family history and/or a completed Pregnancy Loss Chromosomal Microarray Clinical Information Form.

     
    Reddy UM, et al., Karyotype versus Microarray Testing for Genetic Abnormalities after Stillbirth.  The New England Journal of Medicine 367:23:2185-2193, 2012.