Clinical Utility of Chromosomal Microarray Analysis of DNA from Buccal Cells: Detection of Mosaicism in Three Patients

Abstract

Mosaic chromosomal abnormalities are relatively common. However, mosaicism may be missed due to multiple factors including failure to recognize clinical indications and order appropriate testing, technical limitations of diagnostic assays, or sampling tissue (s) in which mosaicism is either not present, or present at very low levels. Blood leukocytes have long been the "gold standard" sample for cytogenetic analysis; however, the culturing process for routine chromosome analysis can complicate detection of mosaicism since the normal cell line may have a growth advantage in culture, or may not be present in the cells that produce metaphases (the lymphocytes). Buccal cells are becoming increasingly utilized for clinical analyses and are proving to have many advantages. Buccal swabs allow for simple and noninvasive DNA collection. When coupled with a chromosomal microarray that contains single nucleotide polymorphic probes, analysis of buccal cells can maximize a clinician's opportunity to detect cytogenetic mosaicism. We present three cases of improved diagnosis of mosaic aberrations using buccal specimens for chromosomal microarray analysis. In each case, the aberration was either undetectable in blood or present at such a low level it likely could have gone undetected. These cases highlight the limitations of certain laboratory methodologies for identifying mosaicism. We also present practice implications for genetic counselors, including clinic workflow changes and counseling approaches based on increasing use of buccal samples.

Chromosomal Microarray Analysis of Consecutive Individuals with Autism Spectrum Disorders Using an Ultra-High Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders

“…CMA yields significant rates of pathogenic or potentially pathogenic (VOUS) results [2,11,12,13,14,15,16,17,18,19,20], which have clinical utility for the case-by-case clinical management of individuals with these individually rare disorders [23,24,25,26,27,28,29,30,31,32,33,34]. …”

“…Collectively this trend has resulted in corresponding increases in the clinical value of CMA testing [11,12,13,14,15,16,17,18,19,20,21,24,25,26,27,28,29,30,31,32,33,34]. In addition to guidelines on the clinical indications for CMA, the American College of Medical Genetics and Genomics (ACMG) has issued guidance on the appropriate content and design of such arrays and specifically opined that, “It is desirable to have enrichment of probes targeting dosage-sensitive genes known to result in phenotypes consistent with common indications for a genomic screen (e.g., intellectual disability, developmental delays, autism, and congenital anomalies)” [22].…”

“…Such critical regions that did not contain >1 probe/1000 bp on the baseline array were supplemented with additional probe content to provide improved detection of smaller deletions and duplications. Additional probe enrichment was of genomic regions identified by our prior studies and elsewhere in the medical literature of published copy number variants and individual genes associated with DD/ID/ASD [23,24,25,26,27,28,29,30,31,32,33,34,35,36]. The increase in analytical sensitivity resulting from this additional 3.3% probe content has been calculated to be 2.6% [21].…”

Clinical Performance of an Ultrahigh Resolution Chromosomal Microarray Optimized for Neurodevelopmental Disorders

“…CMA is the guideline-recognized first-tier test in the evaluation of MCA, DD/ID, and ASD, [2–6] and yields significant rates of abnormal or potentially abnormal (VOUS) results [7–17] with clinical utility for the management of individuals with these disorders [28, 29, 32–39]. Since the introduction of this technology, the total genomic content in terms of probes on CMAs has progressively increased, leading to higher diagnostic yields and resolution of abnormalities [10, 14–17] with corresponding increases in clinical value of these tests [32–40].…”

Confirmation of mosaic trisomy 22 in an infant with failure to thrive

“…When available, comparative genomic hybridization is the preferred method of diagnosis 14 as its positive yield is higher than with conventional karyotyping. In addition, the use of a buccal cells 15 or fibroblasts 16 for testing is more likely to identify the abnormality.…”