Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies

Abstract

Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.

Figure 1

Examples of Genomic Imbalances Detected by a CMA but Not by G-Banded Karyotyping (A) A 10.9 Mb deletion, including more than 60 genes. The deletion includes the Williams-Beuren syndrome region at chromosome region 7q11 but extends beyond the typical breakpoints for this syndrome. The arrow is pointing to the deleted chromosome that was observed by retrospective analysis of G-banded slides. (B) A 7.2 Mb duplication on the long arm of chromosome 11. Again, the arrow is pointing to the chromosome that has the duplication shown by the darker G-positive band.

Figure 2

Evolution of a Constitutional CMA Design (A) Early versions of array-based Comparative Genomic Hybridization (aCGH) platforms used for constitutional cytogenetic testing targeted the subtelomeric and pericentromeric regions and defined microdeletion and microduplication syndromes.^61,62 (B) Later, more extensive coverage was added at the subtelomeric and pericentromeric regions and included additional probes outside the targeted regions; this is so-called “backbone” coverage. (C) Higher-density backbone coverage or high-density genome-wide arrays provide essentially whole-genome coverage, yielding even higher detection rates.

Figure 3

Algorithm for CMA Testing in Patients with Unexplained DD, MR, MCA, and ASD This algorithm assumes that the patient does not present with features of a recognizable syndrome or metabolic disorder or that tests have been negative for a suspected disorder. The first-tier test is a chromosomal copy-number array or CMA. If no copy-number changes are identified, or if only known CNVs that are known to be benign are identified, this testing is considered “normal” (left side of figure), and further clinical evaluation is warranted to determine whether other testing should be pursued on the basis of the clinical presentation. If a CNV is detected within a known, clinically relevant region or gene, or if the CNV is in the genomic backbone and meets recommended size and gene content guidelines, then the result is considered a pathogenic CNV and “abnormal” (right side of figure). For these cases, follow-up analyses include confirmation studies and determination of the mechanism of imbalance in the proband and parental analysis to determine recurrence risk. All other results are considered VOUS until parental analysis is performed to aid in the final clinical interpretation. After the parental analyses of “abnormal” and “VOUS” results, final results may be classified into three major categories: familial variant, abnormal with a low recurrence risk (RR), or abnormal with an increased RR. In addition, the final interpretation may remain VOUS in some instances, even after parental testing.