Brian Bunke

BACKGROUND: Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. METHODS: Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. RESULTS: We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down's syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. CONCLUSIONS: In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.).

Array-based molecular cytogenetic techniques have improved the detection of small genomic deletions and duplications not seen on karyotyping. These copy-number variants can be benign or pathogenic, depending on their location and genetic content. Whether microarray analysis reliably detects all chromosome abnormalities diagnosed on standard karyotyping and how often abnormal microarray results are not detected on karyotyping are unknown. This large, prospective study was performed at 29 prenatal centers to assess the capability of microarray analysis to diagnose common chromosome abnormalities and to determine the amount of additional data possible using microarray compared with standard karyotyping. Women presenting with a singleton fetus for chorionic villus sampling or amniocentesis for indications including advanced maternal age, a positive aneuploidy screening result, and ultrasound-detected anomalies were eligible. Each sample was split into 2 portions, one for karyotyping and the other for microarray analysis. Each microarray result was considered as true positive, true negative, false positive, or false negative relative to the karyotype findings. Karyotyping was considered the standard against which the chromosomal microarray was judged for identifying common autosomal and sex-chromosome aneuploidies. Karyotyping and microarray assays were performed according to standard protocols. Variants determined not to be of clinical importance were classified as “likely benign” and were not reported to the participant. The rest were determined to be of potential clinical significance and were reported to the participant. Adequate samples were obtained from 4406 of 6537 women screened. Samples for microarray were available from 4391 women (99.7%), and analysis was successful in 4340 cases (98.8%). The primary analysis included 4282 samples, in which 317 (7.4%) common autosomal and 57 (1.3%) sex-chromosome aneuploidies were identified by standard karyotyping. Microarray analysis identified all of these aneuploidies. All 22 unbalanced rearrangements also were identified by microarray. None of the apparently balanced rearrangements identified on karyotyping were identified by microarray analysis, suggesting that these rearrangements were truly balanced. Seventeen triploid samples (0.4%) were present, none of which were identified on microarray. On microarray, 1399 samples had copy-number variants, of which 1234 (88.2%) were classified as common benign. Thirty-five copy-number variants (0.9%) among the 3822 fetuses were on a predetermined list of pathogenic copy-number variants. Of 130 samples, 36 (27.7%) were likely benign, and 94 were considered of uncertain significance. Sixty-one (64.9%) of these 94 had sufficient clinical relevance to be reported to the participant. Overall, 96 (2.5%) of the 3822 fetal samples with normal karyotypes had a microdeletion or duplication of clinical significance. From fetuses with suspected growth or structural anomalies, 45 (6.0%) of the 755 samples had clinically relevant findings on microarray that were not found on karyotyping. Thirty-four (1.7%) of 1966 women without ultrasound-identified anomalies tested because of older age had a normal karyotype and a clinically relevant finding on microarray as did 12 (1.6%) of 729 women who tested positive on Down syndrome screening. Microarray analysis is equivalent to standard karyotype analysis for prenatal diagnosis of common aneuploidies and can be beneficial for prenatal testing. Patients should be aware of the risks of invasive testing, the frequency and severity of clinically relevant microarray findings, and the more limited identification of common aneuploidies obtainable by noninvasive screening. Still under study are how much incremental information should be sought by prenatal testing and how that information should be introduced into care.

Copy number studies have led to an explosion in the discovery of new segmental duplication-mediated deletions and duplications. We have analyzed copy number changes in 2419 patients referred for clinical array comparative genomic hybridization studies. Twenty-three percent of the abnormal copy number changes we found are immediately flanked by segmental duplications > or =10 kb in size and > or =95% identical in direct orientation, consistent with deletions and duplications generated by non-allelic homologous recombination. Here, we describe copy number changes in five previously unreported loci with genomic organization characteristic of NAHR-mediated gains and losses; namely, 2q11.2, 7q36.1, 17q23, 2q13 and 7q11.21. Deletions and duplications of 2q11.2, deletions of 7q36.1 and deletions of 17q23 are interpreted as pathogenic based on their genomic size, gene content, de novo inheritance and absence from control populations. The clinical significance of 2q13 deletions and duplications is still emerging, as these imbalances are also found in phenotypically normal family members and control individuals. Deletion of 7q11.21 is a benign copy number change well represented in control populations and copy number variation databases. Here, we discuss the genetic factors that can modify the phenotypic expression of such gains and losses, which likely play a role in these and other recurrent genomic disorders.