The development of a rapid assay for prenatal testing of common aneuploidies and microdeletion syndromes.

OBJECTIVE: To develop a novel, rapid prenatal assay for pregnancies with high likelihood of normal karyotypes, using BACs-on-Beads(™) technology, a suspension array-based multiplex assay that employs Luminex(®) xMAP(®) technology, for the detection of gains and losses in chromosomal DNA. METHODS: Fifteen relatively common microdeletions were selected that are not detectable, or may be missed, by karyotyping and usually do not present with abnormal ultrasound findings. Chromosomes 13, 18, 21, X, and Y were included. We validated the assay with 430 samples. RESULTS: All microdeletions and aneuploidies were correctly identified, except for a 69,XXX incorrectly identified as a normal female and a male with ∼20% maternal cell contamination (MCC) that could not be distinguished from 69,XXY. MCC became apparent at 20 to 30%. Mosaicism was identified at 30 to 35% abnormal cells. CONCLUSION: We have developed an alternative to fluorescence in situ hybridization (FISH) aneuploidy screening and microarray analysis in otherwise normal pregnancies undergoing invasive testing. We demonstrated that the assay will detect all microdeletions and aneuploidies of regions covered on the assay. We developed analytical software that displays results for well-characterized syndromes but not abnormalities of unclear clinical significance. This assay is likely to be preferred by women seeking testing beyond routine karyotyping but who desire more information than provided by aneuploidy FISH.

Somatic/gonadal mosaicism in a syndromic form of ectrodactyly, including eye abnormalities, documented through array-based comparative genomic hybridization.

Split hand/foot malformation (SHFM) is characterized by underdeveloped or absent central digital rays, clefts of hands and feet, and variable syndactyly of the remaining digits. SHFM is a heterogeneous condition caused by abnormalities at one of multiple loci, including SHFM1 (SHFM1 at 7q21-q22), SHFM2 (Xq26), SHFM3 (FBXW4/DACTYLIN at 10q24), SHFM4 (TP63 at 3q27), and SHFM5 (DLX1 and DLX 2 at 2q31). SHFM3 is unique in that it is caused by submicroscopic tandem chromosome duplications of FBXW4/DACTYLIN. In order to show that array-based comparative genomic hybridization should be considered an essential aspect of the genetic analysis of patients with SHFM, we report on a family with two brothers who have ectrodactyly. Interestingly, both also have ocular abnormalities. Their sister and both parents are healthy. DNA of all five family members was analyzed using oligonucleotide-based DNA microarray and quantitative PCR. The two affected brothers were found to have a small duplication of approximately 539 kb at 10q24.32. The patients' sister and father do not have the microduplication, but qPCR showed that mother's DNA carries the duplication in 20% of blood lymphocytes. In this family, two children were affected with ectrodactyly having a duplication over the SHFM3 locus. The mother, who shows no clinical features of ectrodacytyly, is a mosaic for the same duplication. Therefore, we demonstrate that somatic/gonadal mosaicism is a mechanism that gives rise to SHFM. We also suggest that ocular abnormalities may be part of the clinical description of SHFM3.

Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome.

Prader-Willi syndrome (PWS) is a neurobehavioral disorder manifested by infantile hypotonia and feeding difficulties in infancy, followed by morbid obesity secondary to hyperphagia. It is caused by deficiency of paternally expressed transcript(s) within the human chromosome region 15q11.2. PWS patients harboring balanced chromosomal translocations with breakpoints within small nuclear ribonucleoprotein polypeptide N (SNRPN) have provided indirect evidence for a role for the imprinted C/D box containing small nucleolar RNA (snoRNA) genes encoded downstream of SNRPN. In addition, recently published data provide strong evidence in support of a role for the snoRNA SNORD116 cluster (HBII-85) in PWS etiology. In this study, we performed detailed phenotypic, cytogenetic, and molecular analyses including chromosome analysis, array comparative genomic hybridization (array CGH), expression studies, and single-nucleotide polymorphism (SNP) genotyping for parent-of-origin determination of the 15q11.2 microdeletion on an 11-year-old child expressing the major components of the PWS phenotype. This child had an ∼236.29 kb microdeletion at 15q11.2 within the larger Prader-Willi/Angelman syndrome critical region that included the SNORD116 cluster of snoRNAs. Analysis of SNP genotypes in proband and mother provided evidence in support of the deletion being on the paternal chromosome 15. This child also met most of the major PWS diagnostic criteria including infantile hypotonia, early-onset morbid obesity, and hypogonadism. Identification and characterization of this case provide unequivocal evidence for a critical role for the SNORD116 snoRNA molecules in PWS pathogenesis. Array CGH testing for genomic copy-number changes in cases with complex phenotypes is proving to be invaluable in detecting novel alterations and enabling better genotype-phenotype correlations.

A tale of two deletions: a report of two novel 20p13 --> pter deletions.

We report on two patients with 1.7 and 1.2 Mb terminal 20p deletions, which have apparently not been reported previously. Both individuals exhibit certain similar features including large fontanelles, ear abnormalities, and seizures. However, even though the deletions are of similar size, there were many disparate features between the two. The deletions in each patient encompass at least 28 genes that may provide useful candidates for ear development and cranial ossification.

Whole-genome microarray analysis in prenatal specimens identifies clinically significant chromosome alterations without increase in results of unclear significance compared to targeted microarray.

OBJECTIVE: To determine the detection rates of whole-genome microarray technology compared to targeted microarray analysis for chromosome abnormalities in prenatal samples submitted for diagnostic testing. METHODS: Microarray analysis using either whole-genome bacterial artificial chromosome (BAC)-based and oligonucleotide (oligo)-based microarrays or targeted BAC microarrays was performed on 182 and 62 prenatal cases, respectively, from North American healthcare providers without previously known chromosome abnormalities or family history of a parent with a known chromosome rearrangement. RESULTS: Microarray analysis identified clinically significant chromosome alterations in 7 out of 182 (3.8%) prenatal specimens, two of which each had two unrelated abnormalities. After excluding two of the cases in which the abnormality would have been identified by routine karyotyping, the diagnostic yield of clinically significant findings was 5 out of 182 (2.7%). One case had a finding of unclear significance (0.5%) and 16 cases had benign copy number variants (CNVs) (8.8%). Targeted microarray analysis combined with previously published data demonstrated detection rates of 0.9% for clinically significant results, 0.5% for results of unclear significance, and 8.0% for benign CNVs. CONCLUSIONS: Whole-genome prenatal aCGH detected clinically significant submicroscopic chromosome abnormalities in addition to chromosome abnormalities that could be identified by concurrent karyotyping without an increase in unclear results or benign CNVs compared to targeted aCGH.

A comparative analysis of ethical and professional challenges experienced by Australian and U.S. genetic counselors.

Ethical issues are an inevitable part of genetic counseling practice. Prior research identified 16 domains of ethical and professional challenges encountered by practitioners in the United States. In order to further validate these domains, the present study surveyed Australian genetic counselors. Sixty-three respondents rated the frequency with which they encountered each domain, and 39 individuals also provided personal anecdotes detailing their most challenging ethical and professional dilemmas. Every domain reportedly was experienced by the Australian sample. However, there were some differences between Australian respondents and U.S. genetic counselors in frequencies of domain occurrence, and in strategies recommended for resolving them. Several anecdotes illustrate challenging situations due to Australia's geography, universal healthcare system, and the genetic counseling profession's evolution in that country. The results generally validate domains identified for U.S. genetic counselors. They further suggest that certain ethical issues may manifest in ways unique to a given country, and therefore they must be addressed in a culturally-appropriate manner.

Comparison of microarray-based detection rates for cytogenetic abnormalities in prenatal and neonatal specimens.

OBJECTIVE: To compare the detection rate by microarray analysis for chromosome abnormalities in a prenatal population to that of a neonatal population referred for diagnostic testing. METHODS: Array comparative genomic hybridization (aCGH) analysis was performed for 151 prenatal cases and compared with the results from 1375 postnatal cases less than 3 months of age. RESULTS: Two of 151 prenatal cases (1.3%) showed a clinically significant cytogenetic abnormality. In contrast, of the 1375 postnatal cases studied, 11.4% showed a cytogenetic abnormality by aCGH. Many of these (40%) were referred for aCGH because of dysmorphic features, a clinical indication unlikely to be identified in the prenatal population. CONCLUSIONS: The chance of detecting a chromosome abnormality in a prenatal population that has already been screened by routine cytogenetics is approximately 1.3%. However, given that many of the abnormal array results in the neonatal population were among those with dysmorphic features as the primary indication for testing, which are not easily identifiable by ultrasound, offering prenatal testing by aCGH to a wider population would likely result in a higher detection rate.