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array comparative hybridization

Brynn Levy, Ronald Wapner
Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae...
February 2018: Fertility and Sterility
Jingjing Yu, Kashif Javaid, Lingyan Liang, Weihua Wu, Yu Liang, Anran Song, Hongliang Zhang, Wen Shi, Ting-Chang Chang, Hongtao Cao
A visible-blind ultraviolet (UV) photodetector was designed based on three-terminal electronic device of thin-film transistor (TFT) coupled with two-terminal p-n junction optoelectronic device, in hope of combining the beauties of the both devices together. Upon the uncovered back channel surface of amorphous indium-gallium-zinc-oxide (IGZO) TFT, we fabricated PEDOT:PSS/SnOx/IGZO heterojunction structure, through which the formation of p-n junction and directional carrier transfer of photo-generated carriers were experimentally validated...
February 14, 2018: ACS Applied Materials & Interfaces
Irene Scharf, Lisa Bierbaumer, Heidemarie Huber, Philipp Wittmann, Christine Haider, Christine Pirker, Walter Berger, Wolfgang Mikulits
Genomic editing using the CRISPR/Cas9 technology allows selective interference with gene expression. With this method, a multitude of haploid and diploid cells from different organisms have been employed to successfully generate knockouts of genes coding for proteins or small RNAs. Yet, cancer cells exhibiting an aberrant ploidy are considered to be less accessible to CRISPR/Cas9-mediated genomic editing, as amplifications of the targeted gene locus could hamper its effectiveness. Here we examined the suitability of CRISPR/Cas9 to knockout the receptor tyrosine kinase Axl in the human hepatoma cell lines HLF and SNU449...
February 2018: Oncology Letters
Daniel Kaser
Recurrent pregnancy loss is often idiopathic, but numerical and structural chromosomal abnormalities constitute an important cause. Numerical chromosomal abnormalities in the conceptus are primarily due to meiotic nondisjunction; the rate and complexity of embryonic aneuploidy are driven by female age. Structural chromosomal abnormalities (balanced translocations or inversions) can lead to unbalanced gametes depending on specific recombination and segregation patterns during meiosis. The attendant reproductive risk depends on the type of rearrangement and its parental origin...
March 2018: Obstetrics and Gynecology Clinics of North America
Sunita Katari, Mahmoud Aarabi, Angela Kintigh, Susan Mann, Svetlana A Yatsenko, Joseph S Sanfilippo, Anthony J Zeleznik, Aleksandar Rajkovic
STUDY QUESTION: What is the prevalence of somatic chromosomal instability among women with idiopathic primary ovarian insufficiency (POI)? SUMMARY ANSWER: A subset of women with idiopathic POI may have functional impairment in DNA repair leading to chromosomal instability in their soma. WHAT IS KNOWN ALREADY: The formation and repair of DNA double-strand breaks during meiotic recombination are fundamental processes of gametogenesis. Oocytes with compromised DNA integrity are susceptible to apoptosis which could trigger premature ovarian aging and accelerated wastage of the human follicle reserve...
February 7, 2018: Human Reproduction
Yuji Yasukochi, Bin Yang, Toshiaki Fujimoto, Ken Sahara, Takashi Matsuo, Yukio Ishikawa
General odorant binding proteins (GOBPs) and pheromone binding proteins (PBPs) form a monophyletic subfamily of insect odorant binding proteins (OBPs) specific for Lepidoptera, butterflies and moths. The GOBP/PBP genes include six subgroups (GOBP1-2, PBP-A-D) previously reported to form a complex arrayed in a conserved order in representative moths (superfamily Bombycoidea) and butterflies (Nymphalidae). Although our knowledge of lepidopteran genomes has increased greatly recently, the structure of the GOBP/PBP complex has been studied only for species that represent limited lineages of the highly diverged Ditrysia...
2018: PloS One
Arie Berkovitz, Yaron Dekel, Revital Goldstein, Shhadeh Bsoul, Yossy Machluf, Dani Bercovich
STUDY QUESTION: Is there an association between spermatozoon genomic stability and vacuolar morphology and location? SUMMARY ANSWER: The genomic stability of spermatozoa is associated with specific characteristics of vacuolar morphology (depth) and location (cellular compartment, i.e. nucleus and equatorial region). WHAT IS KNOWN ALREADY: Genetic anomalies in sperm are correlated with semen abnormalities, yet the advantage of morphologically based selection of spermatozoa for IVF according to current criteria is controversial...
February 6, 2018: Human Reproduction
Xiangcheng Zhou, Cuicui Zhang, Mi Li, Jian Ma, Qiuping Chen, Shanquan Sun, Liang Zhang
OBJECTIVE To develop a new method for detecting 22q11.2 deletion syndrome (22q11.2 DS) in clinical settings. METHODS Specific primers and fluorescence probes were designed to target the TBX1 gene within the 22q11.2 deletion region and a reference gene RPP30. Multiplexed droplet digital PCR (ddPCR) was run to detect the 22q11.2 microdeletion by calculating the ratio of positive droplet number of TBX1/RPP30. RESULTS Three cases of 22q11.2 microdeletion previously confirmed by array comparative genome hybridization were successfully identified...
February 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Haiyu Li, Yongqin Jia, Junning Cheng, Geli Liu, Fangzhou Song
The purpose of this study was to develop an lncRNA signature to improve the prediction of the prognosis of cervical cancer through integration bioinformatics and analysis of TCGA RNA sequencing data. In this study, we established a set of four lncRNA signatures that was significantly associated with recurrence-free survival using the Cox regression model. Functionally, we screened the CC-associated lncRNA NCK1-AS1 as a new candidate lncRNA and regulator which promotes development and progression in CC. qRT-PCR and RNA in situ hybridization (RISH) results showed that NCK1-AS1 was significantly up-regulated in 77...
February 7, 2018: Cell Death & Disease
Shawn P Grogan, Stuart F Duffy, Chantal Pauli, Martin K Lotz, Darryl D D'Lima
Avascular (Avas) meniscus regeneration remains a challenge, which is partly a consequence of our limited knowledge of the cells that maintain this tissue region. In this study, we utilized microarrays to characterize gene expression profiles of intact human Avas meniscus tissue and of cells following culture expansion. Using these data, we examined various 3D culture conditions to redifferentiate Avas cells toward the tissue phenotype. RNA was isolated from either the tissue directly or following cell isolation and 2 weeks in monolayer culture...
February 7, 2018: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
Haiming Lv, Yi Wang, Lei Pan, Leipeng Zhang, Hangchuan Zhang, Lei Shang, Huiying Qu, Na Li, Jiupeng Zhao, Yao Li
In this article, we report the preparation of a TiO2 nanotube array (TNA) film used as a transparent electrochromic material and a TNA/polyaniline patterned hybrid electrochromic film utilized as an information display material. The TNA film was fabricated by an anodizing process, and a surface patterned TNA with extreme wettability contrast (hydrophilic/hydrophobic) on a TNA surface through self-assembly (SAM) and photocatalytic lithography is fabricated. Then the TNA/polyaniline hybrid film was prepared by electrodeposition of aniline in an aqueous solution...
February 7, 2018: Physical Chemistry Chemical Physics: PCCP
Roberto R Capela de Matos, Moneeb A K Othman, Gerson M Ferreira, Elaine S Costa, Joana B Melo, Isabel M Carreira, Mariana T de Souza, Bruno A Lopes, Mariana Emerenciano, Marcelo G P Land, Thomas Liehr, Raul C Ribeiro, Maria Luiza M Silva
Myeloid neoplasms are a heterogeneous group of hematologic disorders with divergent patterns of cell differentiation and proliferation, as well as divergent clinical courses. Rare recurrent genetic abnormalities related to this group of cancers are associated with poor outcomes. One such abnormality is the MECOM gene rearrangement that typically occurs in cases with chromosome 7 abnormalities. MECOM encodes a transcription factor that plays an essential role in cell proliferation and maintenance and also in epigenetic regulation...
February 2018: Cancer Genetics
Aritrick Chatterjee, Roger M Bourne, Shiyang Wang, Ajit Devaraj, Alexander J Gallan, Tatjana Antic, Gregory S Karczmar, Aytekin Oto
Purpose To evaluate whether compartmental analysis by using hybrid multidimensional magnetic resonance (MR) imaging can be used to diagnose prostate cancer and determine its aggressiveness. Materials and Methods Twenty-two patients with prostate cancer underwent preoperative 3.0-T MR imaging. Axial images were obtained with hybrid multidimensional MR imaging by using all combinations of echo times (47, 75, 100 msec) and b values of 0, 750, 1500 sec/mm2, resulting in a 3 × 3 array of data associated with each voxel...
February 2, 2018: Radiology
Guangming Liu, Zhongmei Wen, Xianglan Lu, Young Mi Kim, Xianfu Wang, Rebecca M Crew, Mohamad A Cherry, Shibo Li, Yuanyuan Liu
RATIONALE: With combination of multiple techniques, we have successfully characterized unique, complex chromosomal changes in a patient with chronic lymphocytic leukemia (CLL), a lymphoproliferative disorder. DIAGNOSES: The diagnosis was based on white blood cell, flow cytometry, and immunophenotypes and confirmed by karyotype, fluorescence in situ hybridization, and array comparative genomic hybridization from the patient's blood culture. INTERVENTIONS: The patient was given fludarabine, cyclophosphamide and rituximab (FCR) for 6 cycles...
December 2017: Medicine (Baltimore)
Mei-Juan Xie, Zhi-Kun Liang, Dan He, Wei-Wen Xu, Ying-Song Wu, Xue-Xi Yang, Ming Li
Rare autosomal aneuploidies (RAAs) can cause miscarriage or other pregnancy complications and lead to inconsistent results of noninvasive prenatal testing (NIPT), but many NIPT providers have not yet started to provide related services. Our aim was to develop a semiconductor sequencing platform (SSP)-based method for detecting RAAs when pregnant women performed NIPT. Fifty-three aneuploidy samples with verified karyotyping or array comparative genomic hybridization (aCGH) results were collected and subjected to RAAs detection using an SSP to develop a method by genomic sequencing...
January 30, 2018: DNA and Cell Biology
Nehir Kurtas, Filippo Arrigoni, Edoardo Errichiello, Claudio Zucca, Cristina Maghini, Maria Grazia D'Angelo, Silvana Beri, Roberto Giorda, Sara Bertuzzo, Massimo Delledonne, Luciano Xumerle, Marzia Rossato, Orsetta Zuffardi, Maria Clara Bonaglia
INTRODUCTION: Phelan-McDermid syndrome (PMS) is caused by SHANK3 haploinsufficiency. Its wide phenotypic variation is attributed partly to the type and size of 22q13 genomic lesion (deletion, unbalanced translocation, ring chromosome), partly to additional undefined factors. We investigated a child with severe global neurodevelopmental delay (NDD) compatible with her distal 22q13 deletion, complicated by bilateral perisylvian polymicrogyria (BPP) and urticarial rashes, unreported in PMS...
January 29, 2018: Journal of Medical Genetics
Ruidie Tang, Sancan Han, Feng Teng, Kai Hu, Zhiming Zhang, Mingxiang Hu, Xiaosheng Fang
Graphene nanodots (GNDs) are one of the most attractive graphene nanostructures due to their tunable optoelectronic properties. Fabricated by polystyrene-nanosphere lithography, uniformly sized graphene nanodots array (GNDA) is constructed as an ultraviolet photodetector (PD) with ZnO nanofilm spin coated on it. The size of GNDA can be well controlled from 45 to 20 nm varying the etching time. It is revealed in the study that the photoelectric properties of ZnO/GNDA PD are highly GNDA size-dependent. The highest responsivity (R) and external quantum efficiency of ZnO/GNDA (20 nm) PD are 22...
January 2018: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
China Nagano, Kandai Nozu, Naoya Morisada, Masahiko Yazawa, Daisuke Ichikawa, Keita Numasawa, Hiroyo Kourakata, Chieko Matsumura, Satoshi Tazoe, Ryojiro Tanaka, Tomohiko Yamamura, Shogo Minamikawa, Tomoko Horinouchi, Keita Nakanishi, Junya Fujimura, Nana Sakakibara, Yoshimi Nozu, Ming Juan Ye, Hiroshi Kaito, Kazumoto Iijima
BACKGROUND: Comprehensive genetic approaches for diagnosing inherited kidney diseases using next-generation sequencing (NGS) have recently been established. However, even with these approaches, we are still failing to detect gene defects in some patients who appear to suffer from genetic diseases. One of the reasons for this is the difficulty of detecting copy number variations (CNVs) using our current approaches. For such cases, we can apply methods of array-based comparative genomic hybridization (aCGH) or multiplex ligation and probe amplification (MLPA); however, these are expensive and laborious and also often fail to identify CNVs...
January 25, 2018: Clinical and Experimental Nephrology
Marieke Hylebos, Guy Van Camp, Geert Vandeweyer, Erik Fransen, Matthias Beyens, Robin Cornelissen, Arvid Suls, Patrick Pauwels, Jan P van Meerbeeck, Ken Op de Beeck
Malignant pleural mesothelioma (MPM) is an aggressive tumor that is often causally associated with asbestos exposure. Comparative genomic hybridization techniques and arrays demonstrated a complex set of copy number variations (CNVs) in the MPM-genome. These techniques however have a limited resolution, throughput and flexibility compared to next-generation sequencing platforms. In this study, the presence of CNVs in the MPM-genome was investigated using an MPM-cohort (N = 85) for which genomic microarray data are available through 'The Cancer Genome Atlas' (TCGA)...
December 26, 2017: Oncotarget
Boris Zagradišnik, Danijela Krgović, Špela Stangler Herodež, Andreja Zagorac, Bogdan Ćižmarević, Nadja Kokalj Vokač
Background: Copy number variations (CNSs) of large genomic regions are an important mechanism implicated in the development of head and neck cancer, however, for most changes their exact role is not well understood. The aim of this study was to find possible associations between gains/losses of genomic regions and clinically distinct subgroups of head and neck cancer patients. Results: Array comparative genomic hybridization (aCGH) analysis was performed on DNA samples in 64 patients with cancer in oral cavity, oropharynx or hypopharynx...
2018: Molecular Cytogenetics
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