Multiplex ligation-dependent probe amplification and array comparative genomic hybridization analyses for prenatal diagnosis of cytogenomic abnormalities

Abstract

BackgroundThe aims of this study were to evaluate the clinical utility of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (aCGH) analyses on prenatal cases and to review prenatal ultrasound findings of cytogenomic syndromes.ResultsOf the 54 prenatal cases analyzed, cytogenomic abnormalities were characterized in 14 cases. In four fetuses with abnormal ultrasound findings, a 40.701 Mb duplication of 8q22.3-q24.3 and a 23.839 Mb deletion of 7q33-q36.3 derived from a paternal balanced translocation, a de novo 13.062 Mb deletion of 11q24.1-q25 for Jacobsen syndrome, a de novo 19.971 Mb deletion of 7q11.23-q21.3 for type 1 split-hand/foot malformation (SHFM1), and a de novo 28.909 Mb duplication of 3q21.1-q25.1 were detected. A 699.8 Kb deletion at 5p15.33 for Cri du Chat syndrome was confirmed in a fetus with abnormal MLPA result. A fetus with abnormal maternal screening was detected with a de novo distal 1.747 Mb duplication at 2q37.1-q37.2 and a 6.664 Mb deletion at 2q37.2-q37.3. Of the eight cases referred by history of spontaneous abortions, derivative chromosomes 11 from paternal carriers of a balanced 8q/11q and a 10q/11q translocation were noted in two cases, simple aneuploids of trisomy 2 and trisomy 21 were seen in three cases, and compound aneuploids of two or three chromosomes were found in three cases. Post-test genetic counseling was performed with detailed genomic information and well characterized postnatal syndromic features.ConclusionsThese results demonstrated that coupling MLPA screening and aCGH analysis are a cost-effective approach to detect cytogenomic abnormalities in a prenatal setting. The aCGH analysis provided not only genomic maps of breakpoints and gene content of imbalanced regions but also better inference of related phenotypes for genetic counseling. Prenatal ultrasound findings reported in the literature for Jacobsen syndrome, SHFM and Cri du Chat syndrome were summarized for use as diagnostic references.

Genomic analysis in the clinic: benefits and challenges for health care professionals and patients in Brazil

“…Apart from WES and WGS, genomic strategies used in the field of molecular cytogenetics (i.e. array comparative genomic hybridization-aCGH) to identify unbalanced chromosomal abnormalities and copy number variants (CNV) are increasingly common in dysmorphology and in prenatal diagnosis; for certain disorders (as intellectual disability, autism and multiple congenital anomalies), aCGH is considered an appropriate first-tier diagnostic test (Xu et al 2014;South et al 2013). Finally, current technical limitations of NGS make it inadequate for disorders caused by expansion of oligonucleotide repeats, CNV and alterations in highly repetitive DNA regions (Bras et al 2012).…”

Copy number changes and methylation patterns in an isodicentric and a ring chromosome of 15q11-q13: report of two cases and review of literature

“…The NDN gene also contains methylation probes while it has a known tendency to over-digest resulted in variable results. The experiment procedures were performed following the manufacturer’s protocol [ 18 , 42 ]. The MS-MLPA data was imported into the software Coffalyser.Net (designed by MRC-Holland) to analyze both the copy number variation and the methylation profile.…”

Prenatal diagnosis: the clinical usefulness of array comparative genomic hybridization

“…1 The possibility of replacing karyotyping by aCGH or by aCGH in addition to multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence-polymerase chain reaction (QF-PCR) has been increasingly discussed among scientific community, namely in fetus with ultrasound abnormalities. 3,5–7…”