Cytogenetic microarrays in Manitoba patients with developmental delay

To the Editor: Cytogenetic microarrays have revolutionized conventional cytogenetics by increasing the resolution of the standard karyotype from 5–10 to ,1 Mb using microarray comparative genomic hybridization (aCGH) (1). Targeted microarrays, which cover specific areas of the genome with known clinical significance, and whole genome arrays, which span the entire genome but detect copy number polymorphisms/variants/changes (CNVs) of unknown clinical significance, allow for the comprehensive analysis of hundreds or thousands of distinct genomic loci for DNA copy number losses or gains. Conventional cytogenetics identifies 5–10% abnormalities depending on ascertainment criteria, and microarrays can identify an additional 10–15% of previously undetected abnormalities. The purpose of our study was to determine how many Manitoba patients had unrecognized chromosome imbalances detectable by microarray. Inclusion criteria were unexplained developmental delay (DD) or mental retardation (MR), a normal 550 G-band karyotype, fragile X (FMR1) negative, and at least one of the following additional criteria: multiple congenital anomalies; prenatal growth retardation; postnatal growth abnormalities including microcephaly, short or tall stature, or macrocephaly; facial or non-facial dysmorphisms; or a family history of any of the above clinical criteria in a child with unexplained DD or MR. Exclusion criteria included an identified genetic or environmental diagnosis. A total of 74 children were selected for targeted bacterial artificial chromosome (BAC) microarray analysis using TOP (technical only program) at Combimatrix Molecular Diagnostics (Irvine, CA). The microarray platform used at this time was the CA 1500, which is a targeted array of 1500 BAC clones representing greater than 125 constitutional disorders. All patient microarray abnormalities were confirmed by fluorescent in situ hybridization (FISH); microarray, FISH and karyotype analysis were performed on parents of patients with microarray abnormalities. A total of 7 of 74 (10%) of patients had clinically significant microarray abnormalities, with phenotypes compatible with the specific genomic imbalance observed. The observed frequency is consistent with previous reports (2, 3). These abnormalities are summarized in Table 1. Two of 74 (3%) had unbalanced 1p36 deletions (one interstitial, patient 1; one terminal, patient 2), 2 (3%) (patients 3 and 4) had other subtelomere rearrangements, and the remaining 3 (4%) (patients 5, 6, and 7) had various interstitial deletions. Thus, approximately 5% had subtelomere rearrangements, in agreement with previous estimates (1, 2). Parental microarray studies did not detect any unbalanced cases. However, FISH analyses of the parents of patient 4 (Table 1) showed the presence of a paternal subtelomere translocation: t(12;18)(qter2,pter1;pter2,qter1). In addition, karyotyping the parents of patient 3 (Table 1) fortuitously revealed the presence of a paternal t(1;3)(p36.3;p13), which would not have been otherwise detected as both parents had normal confirmatory subtelomere FISH and microarray results. We recommend confirmatory FISH in all parents of a child with an abnormal microarray result. Parental aCGH may not always be necessary but may be required to provide supportive evidence for the association between a CNV and the clinical presentation. Karyotyping of parents is still recommended for balanced rearrangements. Our targeted microarray study detected 23 the frequency of unbalanced abnormalities as found by conventional karyotyping in our Cytogenetics Laboratory ( 5.4%) (unpublished data) and 103 the full FMR1 mutation in our Molecular Diagnostic Laboratory ( 1%) (unpublished data). Our findings suggest that screening for microarray