Next generation sequencing as a new detection strategy for maternal cell contamination in clinical prenatal samples

Objectives: The maternal cell contamination in chorionic villus or amniotic fluid presents a serious preanalytical risk for prenatal misdiagnosis. The following study presents and validates a novel process for identifying MCC by detecting short tandem repeat markers on Ion Proton system. Initially, MCC testing was performed during the detection of chromosomal abnormalities so as to improve the detection efficiency and accuracy of this method. Material and methods: More than 70 STR loci were selected to establish the detection progress. Capillary electrophoresis was used to compare the next generation sequencing detection results, as well as to identify the optimal STR on Ion Proton system. Evaluation criteria for maternal cell contamination were set, and the automated data analysis was performed. The detection sensitivity was validated via 4 groups with mixed samples and different proportions. Results: Consequently, twenty-three clinical samples were tested to evaluate the detection accuracy. In addition, 14 reli­able STR loci, which were stably detected in more than 25 samples, were found. The detection sensitivity in maternal cell contamination was no less than 20%, while its accuracy reached 100% in clinical samples. Conclusions: Finally, we established and validated a novel detection procedure for maternal cell contamination in clinical prenatal samples using next generation sequencing. This procedure allowed us to simultaneously perform prenatal test­ing and MCC testing. Unlike the traditional capillary electrophoresis, this method is rapid, highly sensitive, and suitable for wide range of clinical applications

Individual-based morphological brain network organization and its association with autistic symptoms in young children with autism spectrum disorder

Individual-based morphological brain networks built from T1-weighted magnetic resonance imaging (MRI) reflect synchronous maturation intensities between anatomical regions at the individual level. Autism spectrum disorder (ASD) is a socio-cognitive and neurodevelopmental disorder with high neuroanatomical heterogeneity, but the specific patterns of morphological networks in ASD remain largely unexplored at the individual level. In this study, individual-based morphological networks were constructed by using high-resolution structural MRI data from 40 young children with ASD (age range: 2-8 years) and 38 age-, gender-, and handedness-matched typically developing children (TDC). Measurements were recorded as threefold. Results showed that compared with TDC, young children with ASD exhibited lower values of small-worldness (i.e., sigma) of individual-level morphological brain networks, increased morphological connectivity in cortico-striatum-thalamic-cortical (CSTC) circuitry, and decreased morphological connectivity in the cortico-cortical network. In addition, morphological connectivity abnormalities can predict the severity of social communication deficits in young children with ASD, thus confirming an associational impact at the behavioral level. These findings suggest that the morphological brain network in the autistic developmental brain is inefficient in segregating and distributing information. The results also highlight the crucial role of abnormal morphological connectivity patterns in the socio-cognitive deficits of ASD and support the possible use of the aberrant developmental patterns of morphological brain networks in revealing new clinically-relevant biomarkers for ASD.China Postdoctoral Science Foundation, Grant/Award Number: 2019M660236; National Natural Science Foundation of China, Grant/Award Numbers: 61901129, 62036003, 81871432, U1808204; The Basque Foundation for Science and from Ministerio de Economia, Industria y Competitividad (Spain) and FEDER, Grant/Award Number: DPI2016-79874-R; the Fundamental Research Funds for the Central Universities, Grant/Award Numbers: 2672018ZYGX2018J079, ZYGX2019Z017; the Sichuan Science and Technology Program, Grant/Award Number: 2019YJ018

Local Stereo Matching Using Adaptive Cross-Region-Based Guided Image Filtering with Orthogonal Weights

Adaptive cross-region-based guided image filtering (ACR-GIF) is a commonly used cost aggregation method. However, the weights of points in the adaptive cross-region (ACR) are generally not considered, which affects the accuracy of disparity results. In this study, we propose an improved cost aggregation method to address this issue. First, the orthogonal weight is proposed according to the structural feature of the ACR, and then the orthogonal weight of each point in the ACR is computed. Second, the matching cost volume is filtered using ACR-GIF with orthogonal weights (ACR-GIF-OW). In order to reduce the computing time of the proposed method, an efficient weighted aggregation computing method based on orthogonal weights is proposed. Additionally, by combining ACR-GIF-OW with our recently proposed matching cost computation method and disparity refinement method, a local stereo matching algorithm is proposed as well. The results of Middlebury evaluation platform show that, compared with ACR-GIF, the proposed cost aggregation method can significantly improve the disparity accuracy with less additional time overhead, and the performance of the proposed stereo matching algorithm outperforms other state-of-the-art local and nonlocal algorithms

Spatiotemporal Matching Cost Function Based on Differential Evolutionary Algorithm for Random Speckle 3D Reconstruction

Random speckle structured light can increase the texture information of the object surface, so it is added in the binocular stereo vision system to solve the matching ambiguity problem caused by the surface with repetitive pattern or no texture. To improve the reconstruction quality, many current researches utilize multiple speckle patterns for projection and use stereo matching methods based on spatiotemporal correlation. This paper presents a novel random speckle 3D reconstruction scheme, in which multiple speckle patterns are used and a weighted-fusion-based spatiotemporal matching cost function (STMCF) is proposed to find the corresponding points in speckle stereo image pairs. Furthermore, a parameter optimization method based on differential evolutionary (DE) algorithm is designed for automatically determining the values of all parameters included in STMCF. In this method, since there is no suitable training data with ground truth, we explore a training strategy where a passive stereo vision dataset with ground truth is used as training data and then apply the learned parameter value to the stereo matching of speckle stereo image pairs. Various experimental results verify that our scheme can realize accurate and high-quality 3D reconstruction efficiently and the proposed STMCF exhibits superior performance in terms of accuracy, computation time and reconstruction quality than the state-of-the-art method based on spatiotemporal correlation

In situ fabrication of high-permeance ZIF-8 tubular membranes in a continuous flow system

A high-permeance ZIF-8 membrane was successfully synthesized on the inner side of a porous hollow fiber ceramic tube in a simple flow system via in situ direct growth method. The continuously pumping fresh nutrients through the inner-surface favor increasing the heterogeneous nucleation of ZIF-8 crystals and the formation of continuous ZIF-8 membrane, thus leading to a high performance ZIF-8 membrane. The achieved ZIF-8 membrane was thin and dense, and has only a thickness of about 2.5 mu m. The membrane demonstrated remarkably high H-2 permeance of 1.9 x 10(-6) mol m(-2) s(-1) and excellent molecular sieving performance with H-2/N-2, and H-2/CH4 ideal selectivities of 12.9 and 15.6, respectively. (C) 2014 Elsevier B.V. All rights reserved

A Novel Graphic-Aided Algorithm (gNIPT) Improves the Accuracy of Noninvasive Prenatal Testing

Noninvasive Prenatal Testing (NIPT) has advanced the detection of fetal chromosomal aneuploidy by analyzing cell-free DNA in peripheral maternal blood. The statistic Z-test that it utilizes, which measures the deviation of each chromosome dosage from its negative control, is now widely accepted in clinical practice. However, when a chromosome has loss and gain regions which offset each other in the z-score calculation, merely using the Z-test for the result tends to be erroneous. To improve the performance of NIPT in this aspect, a novel graphic-aided algorithm (gNIPT) that requires no extra experiment procedures is reported in this study. In addition to the Z-test, this method provides a detailed analysis of each chromosome by dividing each chromosome into multiple 2 Mb size windows, calculating the z-score and copy number variation of each window, and visualizing the z-scores for each chromosome in a line chart. Data from 13537 singleton pregnancy women were analyzed and compared using both the normal NIPT (nNIPT) analysis and the gNIPT method. The gNIPT method had significantly improved the overall positive predictive value (PPV) of nNIPT (88.14% vs. 68.00%, p=0.0041) and the PPV for trisomy 21 (T21) detection (93.02% vs. 71.43%, p=0.0037). There were no significant differences between gNIPT and nNIPT in PPV for trisomy 18 (T18) detection (88.89% vs. 63.64%, p=0.1974) and in PPV for trisomy 13 (T13) detection (57.14% vs. 50.00%, p=0.8004). One false-negative T18 case in nNIPT was detected by gNIPT, which demonstrates the potency of gNIPT in discerning chromosomes that have variation in multiple regions with an offsetting effect in z-score calculation. The gNIPT was also able to detect copy number variation (CNV) in chromosomes, and one case with pathogenic CNV was detected during the study. With no additional test requirement, gNIPT presents a reasonable solution in improving the accuracy of normal NIPT

A simple and scalable method for preparing low-defect ZIF-8 tubular membranes

Substrate modification by an ultrathin ZnO layer followed by surface activation promotes homogeneous surface nucleation and the growth of a low-defect ZIF-8 tubular membrane that exhibits superb gas permeation and permselectivity

The Comparison of the Performance of Four Whole Genome Amplification Kits on Ion Proton Platform in Copy Number Variation Detection

Abstract With the development and clinical application of genomics, more and more concern is focused on single-cell sequencing. In the process of single-cell sequencing, whole genome amplification is a key step to enrich sample DNA. Previous studies have compared the performance of different WGA strategies on Illumina sequencing platforms, but there is no related research aimed at Ion Proton platform, which is also a popular next-generation sequencing platform. Here by amplifying cells from six cell lines with different karyotypes, we estimated the data features of four common commercial WGA kits (PicoPLEX WGA Kit, GenomePlex Single Cell Whole Genome Amplification Kit, MALBAC Single Cell Whole Genome Amplification Kit, and REPLI-g Single Cell Kit), including median absolute pairwise difference, uniformity, reproducibility, and fidelity, and examined their performance of copy number variation detection. The results showed that both MALBAC and PicoPLEX could yield high-quality data and had high reproducibility and fidelity; and as for uniformity, PicoPLEX was slightly superior to MALBAC

Identification and characteristics of microRNAs from <it>Bombyx mori</it>

Abstract Background MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression by targeting messenger RNAs (mRNAs) and causing mRNA cleavage or translation blockage. Of the 355 Arthropod miRNAs that have been identified, only 21 are B. mori miRNAs that were predicted computationally; of these, only let-7 has been confirmed by Northern blotting. Results Combining a computational method based on sequence homology searches with experimental identification based on microarray assays and Northern blotting, we identified 46 miRNAs, an additional 21 plausible miRNAs, and a novel small RNA in B. mori. The latter, bmo-miR-100-like, was identified using the known miRNA aga-miR-100 as a probe; bmo-miR-100-like was detected by microarray assay and Northern blotting, but its precursor sequences did not fold into a hairpin structure. Among these identified miRNAs, we found 12 pairs of miRNAs and miRNA*s. Northern blotting revealed that some B. mori miRNA genes were expressed only during specific stages, indicating that B. mori miRNA genes (e.g., bmo-miR-277) have developmentally regulated patterns of expression. We identified two miRNA gene clusters in the B. mori genome. bmo-miR-2b, which is found in the gene cluster bmo-miR-2a-1/bmo-miR-2a-1*/bmo-miR-2a-2/bmo-miR-2b/bmo-miR-13a*/bmo-miR-13b, encodes a newly identified member of the mir-2 family. Moreover, we found that methylation can increase the sensitivity of a DNA probe used to detect a miRNA by Northern blotting. Functional analysis revealed that 11 miRNAs may regulate 13 B. mori orthologs of the 25 known Drosophila miRNA-targeted genes according to the functional conservation. We predicted the binding sites on the 1671 3'UTR of B. mori genes; 547 targeted genes, including 986 target sites, were predicted. Of these target sites, 338 had perfect base pairing to the seed region of 43 miRNAs. From the predicted genes, 61 genes, each of them with multiple predicted target sites, should be considered excellent candidates for future functional studies. Biological classification of predicted miRNA targets showed that "binding", "catalytic activity" and "physiological process" were over-represented for the predicted genes. Conclusion Combining computational predictions with microarray assays, we identified 46 B. mori miRNAs, 13 of which were miRNA*s. We identified a novel small RNA and 21 plausible B. mori miRNAs that could not be located in the available B. mori genome, but which could be detected by microarray. Thirteen and 547 target genes were predicted according to the functional conservation and binding sites, respectively. Identification of miRNAs in B. mori, particularly those that are developmentally regulated, provides a foundation for subsequent functional studies.</p