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array comparative hybridization

Ludmila Volozonoka, Dmitry Perminov, Liene Korņejeva, Baiba Alkšere, Natālija Novikova, Evija Jokste Pīmane, Arita Blumberga, Inga Kempa, Anna Miskova, Linda Gailīte, Violeta Fodina
PURPOSE: To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing. METHODS: Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out...
April 23, 2018: Journal of Assisted Reproduction and Genetics
Yanan Wang, Wei Bao, Yuan Liu, Shiyu Wang, Shengjie Xu, Xi Li, Yanli Li, Sufang Wu
Epithelial ovarian cancer (EOC) is a highly lethal gynecological malignancy, and cisplatin resistance is usually correlated with the poor prognosis of EOC. Increasing evidence indicates that the dysregulation of miRNAs is related to chemotherapy sensitivity. In this study, we revealed that miR-98-5p, a member of the let-7 family, was enriched in cisplatin-resistant EOC cells compared with cisplatin-sensitive cells, and could promote cisplatin resistance in EOC cells. Further studies showed that miR-98-5p could directly target the 3'-UTR of Dicer1 and suppress its expression, causing global miRNA downregulation...
April 18, 2018: Cell Death & Disease
Daniel Y Li, Albert Busch, Hong Jin, Ekaterina Chernogubova, Jaroslav Pelisek, Joakim Karlsson, Bengt Sennblad, Shengliang Liu, Shen Lao, Patrick Hofmann, Alexandra Bäcklund, Suzanne M Eken, Joy Roy, Per Eriksson, Brian Dacken, Deepak Ramanujam, Anne Dueck, Stefan Engelhardt, Reinier A Boon, Hans-Henning Eckstein, Joshua M Spin, Philip S Tsao, Lars Maegdefessel
Background -Long noncoding RNAs (lncRNAs) have emerged as critical molecular regulators in various biological processes and diseases. Here we sought to identify and functionally characterize lncRNAs as potential mediators in abdominal aortic aneurysm (AAA) development. Methods -We profiled RNA transcript expression in two murine AAA models, Angiotensin II (ANGII) infusion in ApoE-/- mice ( n =8) and porcine pancreatic elastase (PPE) instillation in C57BL/6 wildtype mice ( n =12). The lncRNA H19 was identified as one of the most highly up-regulated transcripts in both mouse aneurysm models compared to sham-operated controls...
April 18, 2018: Circulation
Shinya Akatsuka, Guang Hua Li, Shinya Toyokuni
Evolution of the species and carcinogenesis are similar in that genomic alterations are the key events. Oxidative stress derived from various etiologies is one of the major causes of carcinogenesis by inducing mutations in the genome. Persistent oxidative stress in the renal proximal tubules through Fenton reaction catalyzed by ferric nitrilotriacetate (Fe-NTA) generates renal cell carcinoma (RCC) in mice and rats. Here, in order to observe the species difference in oxidative stress-induced carcinogenesis and to obtain an insight regarding the characteristics of each species, we compared the genomic alterations using array-based comparative genome hybridization among RCCs in Mutyh knockout/wild-type mice (C57BL/6 background) induced by Fe-NTA, RCCs in F1 hybrids of Brown-Norway/Fischer-344 wild-type rats and clear cell renal cell carcinoma (CCRCC)/papillary renal cell carcinoma (PRCC) of humans...
April 18, 2018: Free Radical Research
Dong Wu, Tao Li, Qiaofang Hou, Xiaodong Huo, Xin Wang, Tao Wang, Yanli Yang, Hongli Liu, Shixiu Liao
OBJECTIVE: To carry out genetic analysis on a child with developmental delay and multiple malformation. METHODS: The karotypes of the child and her parents were analyzed with routine chromosomal G-banding. Their genomic DNA was analyzed with array comparative genomic hybridization (aCGH). RESULTS: The karyotype of the proband was determined as 46,XX,del(6)(q22),inv(6)(p21.1q21), while no karyotypic abnormality was detected in her parents. aCGH has identified in the child a de novo 800 kb deletion encompassing the RUNX2 gene at 6p21...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Margherita Francescatto, Marco Chierici, Setareh Rezvan Dezfooli, Alessandro Zandonà, Giuseppe Jurman, Cesare Furlanello
BACKGROUND: High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies. RESULTS: In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data...
April 3, 2018: Biology Direct
Eric S Surrey, Mandy Katz-Jaffe, Rebecca L Surrey, Amy Snyder Small, Robert L Gustofson, William B Schoolcraft
OBJECTIVE: To study the impact of the arcuate uterus on euploid blastocyst-stage embryo transfer outcomes after comprehensive chromosomal screening (CCS). DESIGN: Controlled retrospective trial. SETTING: Tertiary care assisted reproduction technology (ART) center. PATIENT(S): Consecutive patients undergoing in vitro fertilization and euploid embryo transfer after CCS during 2014. INTERVENTION(S): Ultrasound examinations and office hysteroscopy; array comparative genomic hybridization to perform CCS after a trophectoderm biopsy...
March 30, 2018: Fertility and Sterility
D Dell'Edera, C Dilucca, A Allegretti, F Simone, M G Lupo, C Liccese, R Davanzo
BACKGROUND: The recurrent ∼ 600 kb 16p11.2 microdeletion is among the most commonly known genetic etiologies of autism spectrum disorder, overweightness, and related neurodevelopmental disorders. CASE PRESENTATION: Our patient is a 2-year-old white girl from the first pregnancy of a non-consanguineous healthy young white couple (father 33-years old and mother 29-years old). Our patient and her parents' DNA were analyzed by comparative genomic hybridization-array platform...
April 3, 2018: Journal of Medical Case Reports
Jenna Friedenthal, Susan M Maxwell, Santiago Munné, Yael Kramer, David H McCulloh, Caroline McCaffrey, James A Grifo
OBJECTIVE: To evaluate whether the use of next generation sequencing (NGS) for preimplantation genetic screening (PGS) in single thawed euploid embryo transfer (STEET) cycles improves pregnancy outcomes compared with array comparative genomic hybridization (aCGH). DESIGN: Retrospective cohort study. SETTING: Single university-based fertility center. PATIENT(S): A total of 916 STEET cycles from January 2014 to December 2016 were identified...
March 28, 2018: Fertility and Sterility
Andrey S Alenin, Israel J Vaughn, J Scott Tyo
In this paper, we present the first in-depth analysis of the bandwidth tradeoffs, error performance, and noise resiliency of full-Stokes micropolarizer array (MPA) designs. By applying our Fourier domain tools that provide a systematic way for arranging information carriers and allocating bandwidth, we develop a number of new full-Stokes MPA layouts and compare them to the existing full-Stokes MPAs in the literature, all of which use 2×2 pixel unit cells to build the MPA. We compare the reconstruction accuracy afforded by these traditional designs with the generalized 2×L family of MPAs, a 3×3 tiling, as well as a 2×2×3 layout that uses multiple snapshots and trades off temporal resolution for spatial resolution...
March 20, 2018: Applied Optics
Jongmin Sim, Do-Hyun Nam, Yuil Kim, In-Hee Lee, Jung Won Choi, Jason K Sa, Yeon-Lim Suh
According to the 2016 World Health Organization classification of tumors of the central nervous system, detecting 1p/19q co-deletion became essential in clinical neuropathology for gliomas with oligodendroglioma-like morphology. Here, we assessed genomic profiles of glioblastoma in 80 cases including 1p/19q status using fluorescent in situ hybridization (FISH), array-comparative genomic hybridization (aCGH), and/or whole exome sequencing (WES). Paraffin-embedded tumor tissues were subjected to FISH analysis, and the corresponding frozen tissues from the same tumors were evaluated for aCGH and/or WES for 1p/19q co-deletion and other genetic parameters, which included IDH1-R132H, ATRX, TP53, CIC, and NOTCH1 mutations and MGMT methylation status...
March 29, 2018: Medical Oncology
Beth Frazer, Hugh Kearney, Jane Cryan, Alan Beausang, Francesca Brett, Michael A Farrell, Patrick G Buckley
The presence of oligodendroglioma-like areas in pilocytic astrocytoma may give rise to pathologic diagnostic uncertainty. This study aims to determine if the oligodendroglioma-like areas present in some pilocytic astrocytomas (PA) possess the signature 1p/19q codeletion that is characteristic of classical oligodendroglioma. Array comparative genomic hybridization was carried out on 12 PA samples, from which oligodendroglioma-like areas were microdissected and used as the template DNA source. 1p/19q codeletions were not found in any of the oligodendroglioma areas in PAs...
March 29, 2018: Clinical Neuropathology
Tanya M Bardakjian, Ingo Helbig, Colin Quinn, Lauren B Elman, Leo F McCluskey, Steven S Scherer, Pedro Gonzalez-Alegre
To determine the diagnostic yield of different genetic test modalities in adult patients with neurological disorders, we evaluated all adult patients seen for genetic diagnostic evaluation in the outpatient neurology practice at the University of Pennsylvania between January 2016 and April 2017 as part of the newly created Penn Neurogenetics Program. Subjects were identified through our electronic medical system as those evaluated by the Program's single clinical genetic counselor in that period. A total of 377 patients were evaluated by the Penn Neurogenetics Program in different settings and genetic testing recommended...
March 28, 2018: Neurogenetics
Clara Franco-Jarava, Hongying Wang, Andrea Martin-Nalda, de la Sierra Daniel Alvarez, Marina García-Prat, Domingo Bodet, Vicenç García-Patos, Alberto Plaja, Francesc Rudilla, Victor Rodriguez-Sureda, Laura García-Latorre, Ivona Aksentijevich, Roger Colobran, Pere Soler-Palacín
There is scarce literature about autoinflammation in syndromic patients. We describe a patient who, in addition to psychomotor and growth delay, presented with fevers, neutrophilic dermatosis, and recurrent orogenital ulcers. Comparative Genomic Hybridization (CGH) array permitted to identify a 13.13Mb deletion on chromosome 6, encompassing 53 genes, and including TNFAIP3 gene (A20). A20 is a potent inhibitor of the NF-kB signalling pathway and restricts inflammation via its deubiquitinase activity. Western blotting and immunoprecipitation assays showed decreased A20 expression and increased phosphorylation of p65 and IkBa...
March 20, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
Maria Stella Vari, Monica Traverso, Tommaso Bellini, Francesca Madia, Francesca Pinto, Pasquale Striano, Carlo Minetti, Federico Zara
We report a de novo 12q22-q23.3 duplication detected by whole-genome array comparative genomic hybridization (array-CGH) in a 5-year-old girl with temporal lobe epilepsy and intellectual disability. The 12Mb duplication encompasses 67 genes, many of which have an established function in brain development and functioning. In particular, it includes DEPDC4, a gene belonging to the IML1 family of proteins involved in G-protein signaling pathways, regulating cells growth and development which also include DEPDC5, which is mutated in autosomal dominant focal epilepsy with variable foci and in few families with familial TLE...
March 2, 2018: Seizure: the Journal of the British Epilepsy Association
Kosuke Ichida, Koichi Suzuki, Taro Fukui, Yuji Takayama, Nao Kakizawa, Fumiaki Watanabe, Hideki Ishikawa, Yuta Muto, Takaharu Kato, Masaaki Saito, Kazushige Futsuhara, Yasuyuki Miyakura, Hiroshi Noda, Tsukasa Ohmori, Fumio Konishi, Toshiki Rikiyama
The impairment of the stability of the chromosomal structure facilitates the abnormal segregation of chromosomes, thus increasing the risk of carcinogenesis. Chromosomal stability during segregation is managed by appropriate methylation at the centromere of chromosomes. Insufficient methylation, or hypomethylation, results in chromosomal instability. The centromere consists of satellite alpha repetitive sequences, which are ideal targets for DNA hypomethylation, resulting in the overexpression of satellite alpha transcript (SAT)...
March 16, 2018: International Journal of Oncology
M T Ibrahim, T Alarcon-Martinez, I Lopez, N Fajardo, J Chiang, R K Koenekoop
CRX is a transcription factor required for activating the expression of many photoreceptor-neuron genes. CRX may be mutated in three forms of human blindness; Leber congenital amaurosis (LCA), cone-rod degeneration (CRD) and retinitis pigmentosa (RP). The pathogenic mechanism in most cases is likely dominant negative, with gain of function. We report a novel, complete homozygous CRX deletion in LCA. We identified a Lebanese family with 3 affected LCA cases. The proband was sequenced by NGS. Quantitative PCR, array comparative genomic hybridization, and long range PCR were performed...
March 22, 2018: Scientific Reports
Ahmed Alfares, Taghrid Aloraini, Lamia Al Subaie, Abdulelah Alissa, Ahmed Al Qudsi, Ahmed Alahmad, Fuad Al Mutairi, Abdulrahman Alswaid, Ali Alothaim, Wafaa Eyaid, Mohammed Albalwi, Saeed Alturki, Majid Alfadhel
PurposeWhole-exome sequencing (WES) and whole-genome sequencing (WGS) are used to diagnose genetic and inherited disorders. However, few studies comparing the detection rates of WES and WGS in clinical settings have been performed.MethodsVariant call format files were generated and raw data analysis was performed in cases in which the final molecular results showed discrepancies. We classified the possible explanations for the discrepancies into three categories: the time interval between the two tests, the technical limitations of WES, and the impact of the sequencing system type...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Bo Geum Choi, Su Kyung Hwang, Jung Eun Kwon, Yeo Hyang Kim
BACKGROUND AND OBJECTIVES: The purpose of the present study was to investigate the advantages and disadvantages of verifying genetic abnormalities using array comparative genomic hybridization (a-CGH) immediately after diagnosis of congenital heart disease (CHD). METHODS: Among neonates under the age of 28 days who underwent echocardiography from January 1, 2014 to April 30, 2016, neonates whose chromosomal and genomic abnormalities were tested using a-CGH in cases of an abnormal finding on echocardiography were enrolled...
March 2018: Korean Circulation Journal
V Pillonel, D Juskevicius, C K Y Ng, A Bodmer, A Zettl, D Jucker, S Dirnhofer, A Tzankov
Nodal marginal zone lymphoma (NMZL) is a rare small B-cell lymphoma lacking disease-defining phenotype and precise diagnostic markers. To better understand the mutational landscape of NMZL, particularly in comparison to other nodal small B-cell lymphomas, we performed whole-exome sequencing, targeted high-throughput sequencing, and array-comparative genomic hybridization on a retrospective series. Our study identified for the first time recurrent, diagnostically useful, and potentially therapeutically relevant BRAF mutations in NMZL...
February 28, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
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