Chromosomal microarray (CMA) is a molecular cytogenomic test for detecting both copy number changes (deletions and duplications) and copy-neutral absence of heterozygosity (AOH) .  

Indications for CMA

• Spontaneous pregnancy loss
• Pregnancy termination due to anomalies
• Intrauterine Growth Restriction
• Stillbirth/Neonatal death
  

Test Uses

CMA can be used for detection of the following genomic changes:

• Copy Number Variants (CNV) – duplications or deletions of chromosomal material
  • Pathogenic and Likely Pathogenic CNVs are always reported
  • Variants of Uncertain Significance (VUS) are reported if they meet reportable criteria
  • Benign and Likely Benign CNVs are not reported
• Absence of Heterozygosity (AOH) – areas of identical chromosomal material
  • AOH is not diagnostic but may narrow down areas and/or autosomal recessive genes of interest to direct further testing
  • AOH of 5% or more of the autosomal genome will be reported due to the increased likelihood of shared ancestry/identity by descent. Close consanguinity is predicted when 10% or more of the autosomal genome is identical
  • Uniparental Isodisomy is detectable by CMA while heterodisomy is not. Additional testing for imprinted disorders may be recommended
• Mosaicism of a second cell population at greater than ~20%
• CNV classification is determined according to Riggs, et al. (2020). 

Follow-Up Testing

CGL often recommends follow-up studies to further elucidate positive CMA results. Recommendations, if any, appear in the proband’s result report. Follow-up testing may include:

• proband and/or parental karyotype to evaluate for a chromosome rearrangement
• parental and/or family member CMA testing for the CNV detected
  • When a VUS is detected, two close biological family members can be tested by CMA without additional charge if relevant to patient care
• proband molecular, methylation, or biochemical testing of a gene or region of interest at an outside laboratory

Limitations

CMA will NOT detect balanced rearrangements (i.e. inversions, translocations, etc.), heterodisomy, or reliably identify low-level mosaicism (below ~20%). For mosaic conditions, CMA cannot differentiate between specific number of copies present (e.g. trisomy of a whole chromosome arm vs. tetrasomy in 50% of cells tested). It also does not detect deletions and duplications with limited probe coverage, gene expansions, variants within mitochondrial DNA, or single nucleotide variants/polymorphisms. CNVs that are smaller than the resolution of the CMA may not be detected or reported. CNVs determined to be benign or likely benign are not reported. Typically, carrier status is not reported unless possibly relevant to the patient’s reported symptoms to guide further testing. Contact the laboratory if there is a specific region or gene(s) of interest.

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 or placenta, when a single female genome is detected, it is assumed to represent the female fetus. However, the possibility that the specimen analyzed is maternal in origin cannot be excluded; MCC testing (see below) is required to rule out this possibility.

Reporting Thresholds

*Smaller AOH or copy number variants may be reported if likely to have relevant clinical significance.

Methods

Extracted DNA is processed on the Illumina® Infinium Global Diversity bead array. The Infinium Global Diversity bead array targets approximately 4885 genes in accordance with the most recent ICCG recommendations. The Infinium Global Diversity bead array is scanned on Illumina’s iScan Platform. Using single nucleotide polymorphism (SNP) probes, the array can detect genomic copy number losses and gains, known as copy number variants (CNVs), with a resolution of approximately 5 kb across the genome. NxClinical software (Bionano Inc.) is used to analyze and interpret the data. CNVs devoid of relevant gene content or that are common CNVs in the general population (listed in the Database of Genomic Variants) may not be reported. Due to probe placement on the chromosomal microarray (CMA), the smallest size CNV that is detectable is variable by region.

Genomic linear positions are given relative to the Genome Reference Consortium Human Genome build 37 (hg19) released by the National Center for Biotechnology Information (NCBI). CNVs are analyzed using publicly available databases and literature. See the following references regarding CMA analysis, interpretation, and reporting: PMID: 31690835, 34131312, 34906464, 27875474.

Turn Around Time

7-21 days