BackgroundArray comparative genomic hybridization (CGH) is currently the most powerful method for detecting chromosomal alterations in pre and postnatal clinical cases. In this study, we developed a BAC based array CGH analysis platform for detecting whole genome DNA copy number changes including specific micro deletion and duplication chromosomal disorders. Additionally, we report our experience with the clinical implementation of our array CGH analysis platform. Array CGH was performed on 5080 pre and postnatal clinical samples from patients referred with a variety of clinical phenotypes.ResultsA total of 4073 prenatal cases (4033 amniotic fluid and 40 chorionic villi specimens) and 1007 postnatal cases (407 peripheral blood and 600 cord blood) were studied with complete concordance between array CGH, karyotype and fluorescence in situ hybridization results. Among 75 positive prenatal cases with DNA copy number variations, 60 had an aneuploidy, seven had a deletion, and eight had a duplication. Among 39 positive postnatal cases samples, five had an aneuploidy, 23 had a deletion, and 11 had a duplication.ConclusionsThis study demonstrates the utility of using our newly developed whole-genome array CGH as first-tier test in 5080 pre and postnatal cases. Array CGH has increased the ability to detect segmental deletion and duplication in patients with variable clinical features and is becoming a more powerful tool in pre and postnatal diagnostics.

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The Fourier finite-element method (FFEM) on the sphere, which performs with an operation count of O(N 2 log 2 N) for 2N 3 N grids in spherical coordinates, was developed using linear basis functions. Dependent field variables are expanded with the Fourier series in the longitude, and the Fourier coefficients are represented with a series of first-order finite elements. Different types of pole conditions were incorporated into the Fourier coefficients of the scalar and vector variables in order to avoid discontinuity at the poles. For the Laplacian operator, the linear element was defined as a function of the sine of latitude instead of the latitude. The FFEM was applied to the derivatives of the first-and second-order elliptic equations and the transport equations. The scale-selective high-order Laplacian-type filter was implemented as a hyperviscosity. For the first-order derivative the fourth-order convergence rate of the accuracy, as is expected from the theoretical analysis, was achieved. Elliptic equations were found to be solved accurately without pole discontinuity, and the convergence rate turned out to be second order. The cosine bell advection, time-differenced with a thirdorder Runge-Kutta method, showed that the squared-norm error convergence rate was slightly above second order. Both the Gaussian bell advection and the deformational flow produced the theoretical convergence rate of fourth order. The high-order filter was found to be effective in maintaining a quasi-uniform resolution over the sphere, and thus allowed a large time step size. Sensitivity experiments of cosine bell advection over the poles revealed that the CFL number, as defined with the maximum grid size on the global domain, can be taken to be as large as unity.