Chromosomal microarray (CMA) is a molecular cytogenomic tool for detecting both copy number changes (deletions and duplications) and copy-neutral regions of homozygosity (ROH).
Infinium® CytoSNP-850K BeadChip Array
- 850,000 SNPs with ~15x redundancy of each marker.
- Probes spaced ~1.8 kb and average resolution of ~10 kb.
- Targets microdeletion/microduplication syndrome regions with enriched coverage for more than 3,200 known disease genes.
- Detect regions of homozygosity (ROH) resulted from uniparental disomy (UPD) or identity by descent.
Prenatal CMA testing options:
- Chromosomal microarray and routine chromosome analysis
- Chromosomal microarray and 5-cell chromosome analysis
- Standard chromosome analysis and if results normal, REFLEX to chromosomal microarray
- FISH aneuploidies screen with REFLEX
- IF FISH abnormal, reflex to chromosome analysis
- IF FISH normal, reflex to chromosomal microarray and 5-cell chromosome analysis
Indications for prenatal CMA
- Abnormal ultrasound fidnings
- Confirmation of NIPS results
- Family history of chromosomal abnormality
- Others
Pregnancy loss CMA test options:
- Chromosomal microarray
- Chromosomal microarray and 5-cell chromosome analysis
- Routine chromosome analysis and if results normal, REFLEX to chromosomal microarray
Indications for pregnancy loss CMA
- Spontaneous miscarriages
- Induced termination due to fetal anomalies
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 includes DNA amplification, a labeling process to provide allele and intensity data, followed by hybridization to the BeadChip array. BeadChips are scanned using a two-channel high-resolution laser imager and analyzed using BlueFusionstudio software.
For reporting of copy number variations (CNVs), thresholds are ≥1 Mb for deletions/losses and ≥2 Mb for duplications/gains. Smaller findings in clinically significant regions may also be reported. Common CNVs listed in the Database of Genomic Variants usually are not reported. While NOT diagnostic, SNP data may allow 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 ROHs cover ≥5% of autosomal genome.
For the 5-cell chromosome analysis, a minimum of 5 metaphase cells are analyzed and 3 karyotypes are prepared at ≥400-450 band level.
Regardless of the specific testing option selected, prenatal testing of a CVS specimen includes FISH aneuploidies screen.
Limitations
SNP CMA may reveal whole genome mosaicism suggestive of presence of two different genomes, 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 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 karyotype analysis will not detect subtle chromosomal rearrangements. The 5-cell chromosome analysis will not adequately detect possible mosaicism.
Sample must be accompanied by a completed Test Request Form and Waiver for Microarray testing. Indicate 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 healthcare providers.
Follow-up Testing
Colorado Genetics Laboratory recommends that parental/familial testing be considered when a genomic imbalance is detected by chromosomal microarray. Please see current policy – Familial Follow-up After Abnormal Microarray.
Microarray Billing Policy
References
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.
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.
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.
Wapner RJ, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 367:2175-84, 2012.
Reddy UM, et al., Karyotype versus Microarray Testing for Genetic Abnormalities after Stillbirth. The New England Journal of Medicine 367:23:2185-2193, 2013.
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.
