Although microarray analysis is proficient in characterizing chromosomal imbalances (which ultimately improves patient care),29
clinicians ordering the test need to be aware of the different clinical platforms (e.g., BAC versus oligo, targeted versus whole genome, and SNP), the variation in resolution among arrays and the information each provides. For example, many clinicians are unaware that a whole genome oligoarray can detect clinically significant copy number changes missed on a targeted BAC array30
or that a SNP array can detect long contiguous stretches of homozygosity that can be associated with uniparental disomy or consanguinity, both of which increase the risk for autosomal recessive conditions.
Array resolution is dependent on the number and types of probes used and how they are distributed across the genome.31
BAC probes are larger than oligonucleotide probes used for oligo and SNP arrays (BACs are ~75,000 to 150,000 base pairs in length, whereas oligos are usually ~50 to 60 base pairs long). This translates into reduced breakpoint specificity of copy number abnormalities for the BAC arrays. Higher probe density on oligo arrays allows for copy number evaluation to be based on multiple adjacent probes, enhancing the accuracy of the interpretation. Oligonucleotide array construction tends to have better reproducibility and less batch-to-batch variation than does BAC construction.31
SNP microarrays are applications of microarray technology that also provide genome-wide copy number analysis. In addition to copy number changes, SNP arrays are able to detect so-called “copy number neutral” abnormalities such as segmental uniparental disomy and areas of long contiguous stretches of homozygosity that can give rise to disease, congenital anomalies, or cognitive impairment.32,33
SNP arrays are increasingly being used in the assessment of cognitive impairment or DD, with or without associated anomalies and are likely to be used in the diagnosis of these conditions.9,11
When ordering a CMA, the clinician should be aware of the various platforms currently in use and their limitations. Questioning the laboratory performing the test about coverage of the array in specific regions of interest (e.g., telomeres, X chromosome, and common microdeletions) is justified. The clinician also should understand what type of follow-up tests will be performed, and on whom, in the event of abnormal results. Further, for deletions and duplications, parental studies (by fluorescence in situ hybridization [FISH] or metaphase preparations, if possible) should be conducted to rule out the presence of a chromosomal rearrangement such as an insertion or inherited duplication. Although rare, for a family in which such a rearrangement is found, recurrence risk can be as high as 50%. With increased utilization of a diagnostic test comes a better appreciation of the range of possible and sometimes unexpected results. This is certainly the case with array CGH and identification of what we now understand to be benign CNVs. An international consortium of more than 75 laboratories has been formed to address questions surrounding array-based testing. The International Standard Cytogenomic Array consortium (https://isca.genetics.emory.edu/iscaBrowser/
) is investigating the feasibility of establishing a standardized, universal system of reporting and cataloging CGH results, both pathologic and benign, to provide the clinician with the most accurate and up-to-date information.14
Databases currently available for referencing gene location and function, CNV listings, and up-to-date clinical information for specific abnormalities include the UC Santa Cruz Database (http://www.genome.uscs.edu
), the Toronto Database of Genomic Variants (http://projects/tcag.ca/variation/
), DECIPHER (http://www.sanger.ac.uk/PostGenomics/decip
), and ECARUCA.34
Even though CMA technology has greatly improved since it was initially developed,4
clinicians ordering these tests must be aware of the limitations that remain. Array CGH cannot identify balanced chromosomal rearrangements, such as translocations or inversions, or differentiate free trisomies from unbalanced Robertsonian translocations.13,35,36
Some aneuploidies can be missed, such as XYY if the wrong gender control is used.31
Marker chromosomes may also be missed, depending on the size, marker composition, and array coverage of the specific chromosomal region present on the marker.35
Detection of mosaicism has been reported, but the accuracy of detecting low levels described by some groups37
has been questioned by others.35,36
Recently, Scott et al.38
suggested that mosaicism for an extra chromosome could be detected at the 10% level, whereas mosaicism for deletion or duplication of part of a chromosome could be detectable at the 20–30% level. These findings remain to be replicated by others. Interpretation of the significance of a rare copy number change can be incomplete if parental samples are unavailable for comparison and published data on the CNV are lacking. Finally, triploidy will not be detected by some forms of microarray.
A microarray should not be ordered when a rapid turnaround time is needed (e.g., a STAT newborn analysis), especially if a chromosomal trisomy is suspected. Currently, a STAT G-banded chromosome analysis can be performed within 48 hours. With some array CGH platforms, hybridization alone can take 48 hours. Although technically some arrays may be run in 3–5 days in some laboratories, analysis and confirmation of results with FISH (development of a unique probe can take weeks) and analysis of parental samples and interpretation may take much longer.
Although microarray is a powerful diagnostic tool for the evaluation of chromosomal copy number changes, its use as a first-tier test may not always be appropriate. For example, conventional karyotyping may be more appropriate when a common aneuploidy (e.g., trisomy 21, trisomy 18, or a sex chromosome aneuploidy) is suspected. FISH with a single probe to confirm a suspected diagnosis of a well-described syndrome, such as Williams syndrome, would be a more cost-effective testing methodology. CMA also should not be used in cases of family history of chromosome rearrangement in a phenotypically normal individual or in cases of multiple miscarriages.14
Finally, CMA cannot detect low-level mosaicism or, in some arrays, polyploidy.
- CMA testing for CNV is recommended as a first-line test in the initial postnatal evaluation of individuals with the following:
- Multiple anomalies not specific to a well-delineated genetic syndrome.
- Apparently nonsyndromic DD/ID.
- Autism spectrum disorders.
- Further determination of the use of CMA testing for the evaluation of the child with growth retardation, speech delay, and other less well-studied indications is recommended, particularly by prospective studies and after-market analysis.
- Appropriate follow-up is recommended in cases of chromosome imbalance identified by CMA, to include cytogenetic/FISH studies of the patient, parental evaluation, and clinical genetic evaluation and counseling.