Clinical Implementation of Chromosomal Microarray Analysis: Summary of 2513 Postnatal Cases

BACKGROUND: Array Comparative Genomic Hybridization (a-CGH) is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA). METHODS AND FINDINGS: CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5%) of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872) with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524) abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs) of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS: This large set of clinical results demonstrates the significantly improved sensitivity of CMA for the detection of clinically relevant genomic imbalances and highlights the need for comprehensive genetic counseling to facilitate accurate clinical correlation and interpretation

Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

<p>Abstract</p> <p>Background</p> <p>Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL). We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence <it>in situ </it>hybridization (FISH).</p> <p>Results</p> <p>Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23.</p> <p>Conclusions</p> <p>Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future.</p

Coarctation of the aorta and mild to moderate developmental delay in a child with a de novo deletion of chromosome 15(q21.1q22.2)

BACKGROUND: Deletion of 15q21q22 is a rare chromosomal anomaly. To date, there have been nine reports describing ten individuals with different segmental losses involving 15q21 and 15q22. Many of these individuals have common features of growth retardation, hypotonia and moderate to severe mental retardation. Congenital heart disease has been described in three individuals with interstitial deletion involving this region of chromosome 15. CASE PRESENTATION: We report a child with coarctation of the aorta, partial agenesis of corpus callosum and mild to moderate developmental delay, with a de novo deletion of 15q21.1q22.2, detected by the array Comparative Genomic Hybridization (CGH). We utilized chromosome 15-specific microarray-based CGH to define the chromosomal breakpoints in this patient. CONCLUSION: This is the first description of mapping of an interstitial deletion involving the chromosome 15q21q22 segment using the chromosome 15-specific array-CGH. The report also expands the spectrum of clinical phenotype associated with 15q21q22 deletion

Wave-current-surge interaction in a changing climate over a shallow continental shelf region

Wave climate over the North Indian Ocean region experienced a paradigm shift in the recent past, indicating an increase in the extremes. Wind-waves and swell climatology have shown an increasing trend over this region, having direct implications on the coastal zone dynamics surrounding the mainland and island features. The present study aims to investigate the wave-current-surge interaction characteristics over a shallow continental shelf region between India and Sri Lanka using the state-of-art coupled ADCIRC-SWAN model. In particular, a case study performed during tropical cyclone Madi (2013) demonstrates the extreme wave-current-surge interaction mechanism over varying nearshore bathymetric features. Study investigated the wave reflection and transmission characteristics in both the absence and presence of the proposed navigation channel (known as Sethusamudram project) in a coastal vulnerability context. Construction of the channel may result in westward shift of hazardous coastal water zones attributed to storm tides. The navigation channel expects to enhance both extreme waves and storm surge by 1% and 4%, respectively. Synthetic experiments, considering an increase in sea level rise by 0.4 m expected by 2050, indicate that wave activity can increase by 3% with marginal variations in storm tide. Simulations performed with a 7% rise in tropical cyclone intensity reveals a substantial increase in storm surge (10%) and significant wave (20%) heights along the coastal belt. (C) 2021 Elsevier B.V. All rights reserved

Modulation Instability of Hydro-Elastic Waves Blown by a Wind with a Uniform Vertical Profile

An interesting physical phenomenon was recently observed when a fresh-water basin is covered by a thin ice film that has properties similar to the property of a rubber membrane. Surface waves can be generated under the action of wind on the air–water interface that contains an ice film. The modulation property of hydro-elastic waves (HEWs) in deep water covered by thin ice film blown by the wind with a uniform vertical profile is studied here in terms of the airflow velocity versus wavenumber. The modulation instability of HEWs is studied through the analysis of coefficients of the nonlinear Schrödinger (NLS) equation with the help of the Lighthill criterion. The NLS equation is derived using the multiple scale method in the presence of airflow. It is demonstrated that the potentially unstable hydro-elastic waves with negative energy appear for relatively small wind speeds, whereas the Kelvin–Helmholtz instability arises when the wind speed becomes fairly strong. Estimates of parameters of modulated waves for the typical conditions are given