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array comparative hybridization

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https://www.readbyqxmd.com/read/28231327/functionally-focused-algorithmic-analysis-of-high-resolution-microarray-cgh-genomic-landscapes-demonstrates-comparable-genomic-copy-number-aberrations-in-msi-and-mss-sporadic-colorectal-cancer
#1
Hamad Ali, Milad S Bitar, Ashraf Al Madhoun, Makia Marafie, Fahd Al-Mulla
Array-based comparative genomic hybridization (aCGH) emerged as a powerful technology for studying copy number variations at higher resolution in many cancers including colorectal cancer. However, the lack of standardized systematic protocols including bioinformatic algorithms to obtain and analyze genomic data resulted in significant variation in the reported copy number aberration (CNA) data. Here, we present genomic aCGH data obtained using highly stringent and functionally relevant statistical algorithms from 116 well-defined microsatellites instable (MSI) and microsatellite stable (MSS) colorectal cancers...
2017: PloS One
https://www.readbyqxmd.com/read/28231309/improving-molecular-diagnosis-of-aniridia-and-wagr-syndrome-using-customized-targeted-array-based-cgh
#2
Fiona Blanco-Kelly, María Palomares, Elena Vallespín, Cristina Villaverde, Rubén Martín-Arenas, Camilo Vélez-Monsalve, Isabel Lorda-Sánchez, Julián Nevado, María José Trujillo-Tiebas, Pablo Lapunzina, Carmen Ayuso, Marta Corton
Chromosomal deletions at 11p13 are a frequent cause of congenital Aniridia, a rare pan-ocular genetic disease, and of WAGR syndrome, accounting up to 30% of cases. First-tier genetic testing for newborn with aniridia, to detect 11p13 rearrangements, includes Multiplex Ligation-dependent Probe Amplification (MLPA) and karyotyping. However, neither of these approaches allow obtaining a complete picture of the high complexity of chromosomal deletions and breakpoints in aniridia. Here, we report the development and validation of a customized targeted array-based comparative genomic hybridization, so called WAGR-array, for comprehensive high-resolution analysis of CNV in the WAGR locus...
2017: PloS One
https://www.readbyqxmd.com/read/28220983/clinical-and-molecular-cytogenetic-analyses-of-four-families-with-1q21-1-microdeletion-or-microduplication
#3
Hong-Dan Wang, Lin Liu, Dong Wu, Tao Li, Cun-Ying Cui, Lian-Zhong Zhang, Cheng-Zeng Wang
BACKGROUND: Little information is available regarding penetrance of the 1q21.1 copy number variants (CNVs). We explored the clinical significance of 1q21.1 microdeletion or microduplication. METHODS: In four families, chromosome karyotype was analyzed using G-banding karyotype analysis technology, CNVs were detected using array-comparative genomic hybridization (aCGH), and then quantitative polymerase chain reaction (qPCR) was used to validate candidate CNVs. Sequence signature in the breakpoint region was analyzed using UCSC databases...
February 21, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28216909/aneuploidy-screening-by-array-comparative-genomic-hybridization-improves-success-rates-of-in-vitro-fertilization-a-multicenter-indian-study
#4
Aditi Kotdawala, Deven Patel, Javier Herrero, Rajni Khajuria, Nalini Mahajan, Manish Banker
OBJECTIVE: To evaluate the usefulness of preimplantation genetic screening (PGS) using array comparative genomic hybridization (aCGH) in the Indian population. MATERIALS AND METHODS: This is a retrospective, multicenter study including 235 PGS cycles following intracytoplasmic sperm injection performed at six different infertility centers from September 2013 to June 2015. Patients were divided as per maternal age in several groups (<35, 35-36, 37-38, 39-40, and >40 years) and as per indication for undergoing PGS...
October 2016: Journal of Human Reproductive Sciences
https://www.readbyqxmd.com/read/28215484/establishment-and-characterization-of-a-new-human-acinar-cell-carcinoma-cell-line-faraz-icr-from-pancreas
#5
Marzieh Rezaei, Ahmad Hosseini, Saman Nikeghbalian, Abbas Ghaderi
OBJECTIVES: Basic research in the field of acinar cell carcinoma (ACC) as a rare neoplasm of the pancreas is dependent on the availability of pragmatic model such as new pancreatic cancer cell lines. Thus, establishment and characterization of new pancreatic cancer cell lines from ACC origin are deemed important. METHODS: Faraz-ICR cell line was derived from a 58-years old woman with pancreatic acinar cell carcinoma by the collagenase digestion protocol. We characterized the cell line by examining its morphology and cytostructural and functional profile...
February 8, 2017: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
https://www.readbyqxmd.com/read/28199399/mirna-148a-serves-as-a-prognostic-factor-and-suppresses-migration-and-invasion-through-wnt1-in-non-small-cell-lung-cancer
#6
Yong Chen, Lingfeng Min, Chuanli Ren, Xingxiang Xu, Jianqi Yang, Xinchen Sun, Tao Wang, Fang Wang, Changjiang Sun, Xizhi Zhang
Lung cancer is the leading cause of cancer death in the world, and aberrant expression of miRNA is a common feature during the cancer initiation and development. Our previous study showed that levels of miRNA-148a assessed by quantitative real-time polymerase chain reaction (qRT-PCR) were a good prognosis factor for non-small cell lung cancer (NSCLC) patients. In this study, we used high-throughput formalin-fixed and paraffin-embedded (FFPE) lung cancer tissue arrays and in situ hybridization (ISH) to determine the clinical significances of miRNA-148a and aimed to find novel target of miRNA-148a in lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28196407/comprehensive-genomic-and-phenotypic-characterization-of-germline-fh-deletion-in-hereditary-leiomyomatosis-and-renal-cell-carcinoma-hlrcc
#7
Cathy D Vocke, Christopher J Ricketts, Maria J Merino, Ramaprasad Srinivasan, Adam R Metwalli, Lindsay A Middelton, James Peterson, Youfeng Yang, W Marston Linehan
Hereditary leiomyomatosis and renal cell carcinoma (HLRCC) is a familial cancer syndrome associated with the development of cutaneous and uterine leiomyomas, and an aggressive form of type 2 papillary kidney cancer. HLRCC is characterized by germline mutation of the FH gene. This study evaluated the prevalence and clinical phenotype of FH deletions in HLRCC patients. Patients with phenotypic manifestations consistent with HLRCC who lacked detectable germline FH intragenic mutations were investigated for FH deletion...
February 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28188593/re-analysis-of-aneuploidy-blastocysts-with-an-inner-cell-mass-and-different-regional-trophectoderm-cells
#8
Jin Huang, Liying Yan, Sijia Lu, Nan Zhao, Jie Qiao
PURPOSE: The purpose of this study is to explore which part of the trophectoderm best represents the inner cell mass after aCGH analysis. METHODS: Fifty-one preimplantation genetic diagnosis/preimplantation genetic screening of abnormal blastocysts diagnosed by array comparative genomic hybridization were included in this study. Blastocysts were thawed, incubated for 3 to 4 h, and then biopsied. Four regions were biopsied per blastocyst, including the inner cell mass (ICM), trophectoderm (TE) cells opposite the ICM, TE cells at the upper right of the ICM, and TE cells at the lower right of the ICM...
February 10, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28184250/meiotic-outcome-in-two-carriers-of-y-autosome-reciprocal-translocations-selective-elimination-of-certain-segregants
#9
Harita Ghevaria, Roy Naja, Sioban SenGupta, Paul Serhal, Joy Delhanty
BACKGROUND: Reciprocal Y autosome translocations are rare but frequently associated with male infertility. We report on the meiotic outcome in embryos fathered by two males with the karyotypes 46,X,t(Y;4)(q12;p15.32) and 46,X,t(Y;16)(q12;q13). The two couples underwent preimplantation genetic diagnosis (PGD) enabling determination of the segregation types that were compatible with fertilization and preimplantation embryo development. Both PGD and follow up analysis were carried out via fluorescence in situ hybridization (FISH) or array comparative genomic hybridization (aCGH) allowing the meiotic segregation types to be determined in a total of 27 embryos...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28183588/a-cytocompatible-micro-nano-textured-surface-with-si-doped-titania-mesoporous-arrays-fabricated-by-a-one-step-anodization
#10
Huibing Liu, Xiaobo Huang, Hanwu Yu, Xiaoning Yang, Xiangyu Zhang, Ruiqiang Hang, Bin Tang
To mimic the hierarchical structure of bone tissues, a hybrid micro/nano-textured titanium surface with Si-doped TiO2 mesoporous arrays is fabricated by a one-step high current anodization (HCA). Specifically, the HCA is carried out in a electrolyte containing NO3(-) and SiO3(2-). The NO3(-) in the electrolyte is demonstrated to play a key role in mediating the formation of honeycombed TiO2 mesoporous arrays, which are different than the nanotubes formed by the mediating of F(-) ion in the conventional anodization...
April 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28181798/shape-morphing-materials-from-stimuli-responsive-hydrogel-hybrids
#11
Seog-Jin Jeon, Adam W Hauser, Ryan C Hayward
The formation of well-defined and functional three-dimensional (3D) structures by buckling of thin sheets subjected to spatially nonuniform stresses is common in biological morphogenesis and has become a subject of great interest in synthetic systems, as such programmable shape-morphing materials hold promise in areas including drug delivery, biomedical devices, soft robotics, and biomimetic systems. Given their ability to undergo large changes in swelling in response to a wide variety of stimuli, hydrogels have naturally emerged as a key type of material in this field...
February 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28168103/in-situ-morphometric-survey-elucidates-the-evolutionary-systematics-of-the-eurasian-himantoglossum-clade-orchidaceae-orchidinae
#12
Richard M Bateman, Attila Molnár V, Gábor Sramkó
BACKGROUND AND AIMS: The charismatic Himantoglossum s.l. clade of Eurasian orchids contains an unusually large proportion of taxa that are of controversial circumscriptions and considerable conservation concern. Whereas our previously published study addressed the molecular phylogenetics and phylogeography of every named taxon within the clade, here we use detailed morphometric data obtained from the same populations to compare genotypes with associated phenotypes, in order to better explore taxonomic circumscription and character evolution within the clade...
2017: PeerJ
https://www.readbyqxmd.com/read/28167835/magnetoresistive-sensors-for-measurements-of-dna-hybridization-kinetics-effect-of-tina-modifications
#13
G Rizzi, M Dufva, M F Hansen
We present the use of magnetoresistive sensors integrated in a microfluidic system for real-time studies of the hybridization kinetics of DNA labeled with magnetic nanoparticles to an array of surface-tethered probes. The nanoparticles were magnetized by the magnetic field from the sensor current. A local negative reference ensured that only the specific binding signal was measured. Analysis of the real-time hybridization using a two-compartment model yielded both the association and dissociation constants kon, and koff...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28159702/a-case-of-feingold-type-2-syndrome-associated-with-keratoconus-refines-keratoconus-type-7-locus-on-chromosome-13q
#14
Fabio Sirchia, Eleonora Di Gregorio, Gabriella Restagno, Enrico Grosso, Patrizia Pappi, Flavia Talarico, Elisa Savin, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Barbara Pasini, Jodhbir S Mehta, Alfredo Brusco
We report on a 58-year old woman with microcephaly, mild dysmorphic features, bilateral keratoconus, digital abnormalities, short stature and mild cognitive delay. Except for keratoconus, the phenotype was suggestive for Feingold syndrome type 2 (FGLDS2, MIM 614326), a rare autosomal dominant disorder described in six patients worldwide, due to the haploinsufficiency of MIR17HG, a micro RNA encoding gene. Karyotype showed a de novo deletion on chromosome 13q, further defined by array-Comparative Genomic Hybridization (a-CGH) to a 17...
January 31, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28155655/between-species-differences-in-gene-copy-number-are-enriched-among-functions-critical-for-adaptive-evolution-in-arabidopsis-halleri
#15
Vasantika Suryawanshi, Ina N Talke, Michael Weber, Roland Eils, Benedikt Brors, Stephan Clemens, Ute Krämer
BACKGROUND: Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively. Arabidopsis halleri is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28145543/synergizing-the-multiple-plasmon-resonance-coupling-and-quantum-effects-to-obtain-enhanced-sers-and-pec-performance-simultaneously-on-a-noble-metal-semiconductor-substrate
#16
Tao Yang, Wenna Liu, Lidong Li, Junhong Chen, Xinmei Hou, Kuo-Chih Chou
Aiming to achieve the synergistic enhancement of the surface-enhanced Raman scattering (SERS) and photoelectrocatalytic (PEC) performance on a noble metal-semiconductor, such as Au nanoparticles (NPs)-TiO2 nanotube arrays (TiO2 NTAs@hybrid Au NPs), theoretical calculation and experiments are performed. Theoretical calculation indicates that both the SERS and PEC performance can be enhanced by coupling different sized Au NPs on TiO2 NTAs based on synergizing the multiple plasmon resonance coupling and quantum effects...
February 1, 2017: Nanoscale
https://www.readbyqxmd.com/read/28133835/the-cut-off-value-for-normal-nuchal-translucency-evaluated-by-chromosomal-microarray-analysis
#17
Idit Maya, Shiri Yacobson, Sarit Kahana, Josepha Yeshaya, Tamar Tenne, Ifaat Agmon-Fishman, Lital Cohen-Vig, Mordechai Shohat, Lina Basel-Vanagaite, Reuven Sharony
OBJECTIVES: An association between isolated, increased nuchal translucency thickness and pathogenic chromosomal microarray analysis (CMA) has been reported. A recent meta-analysis reported that most studies used a 3.5 mm cut-off value. Considering nuchal translucency distribution and the commonly accepted 5% false positive rate in maternal serum screening, nuchal translucency cut-off levels should be reconsidered. This study evaluated the unique contribution of CMA to the investigation of foetuses with mildly increased nuchal translucency (NT) thickness of 3...
January 30, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28133555/familial-case-of-pelizaeus-merzbacher-disorder-detected-by-oligoarray-comparative-genomic-hybridization-genotype-to-phenotype-diagnosis
#18
Kimia Najafi, Roxana Kariminejad, Kaveh Hosseini, Azadeh Moshtagh, Gole Maryam Abbassi, Neda Sadatian, Masood Bazrgar, Ariana Kariminejad, Mohamad Hassan Kariminejad
Introduction. Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive hypomyelinating leukodystrophy characterized by nystagmus, spastic quadriplegia, ataxia, and developmental delay. It is caused by mutation in the PLP1 gene. Case Description. We report a 9-year-old boy referred for oligoarray comparative genomic hybridization (OA-CGH) because of intellectual delay, seizures, microcephaly, nystagmus, and spastic paraplegia. Similar clinical findings were reported in his older brother and maternal uncle...
2017: Case Reports in Genetics
https://www.readbyqxmd.com/read/28120895/genomic-structural-variations-for-cardiovascular-and-metabolic-comorbidity
#19
Maria S Nazarenko, Aleksei A Sleptcov, Igor N Lebedev, Nikolay A Skryabin, Anton V Markov, Maria V Golubenko, Iuliia A Koroleva, Anton N Kazancev, Olga L Barbarash, Valery P Puzyrev
The objective of this study was to identify genes targeted by both copy number and copy-neutral changes in the right coronary arteries in the area of advanced atherosclerotic plaques and intact internal mammary arteries derived from the same individuals with comorbid coronary artery disease and metabolic syndrome. The artery samples from 10 patients were screened for genomic imbalances using array comparative genomic hybridization. Ninety high-confidence, identical copy number variations (CNVs) were detected...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28118382/integrative-variation-analysis-reveals-that-a-complex-genotype-may-specify-phenotype-in-siblings-with-syndromic-autism-spectrum-disorder
#20
Viviane Neri de Souza Reis, João Paulo Kitajima, Ana Carolina Tahira, Ana Cecília Feio-Dos-Santos, Rodrigo Ambrósio Fock, Bianca Cristina Garcia Lisboa, Sérgio Nery Simões, Ana C V Krepischi, Carla Rosenberg, Naila Cristina Lourenço, Maria Rita Passos-Bueno, Helena Brentani
It has been proposed that copy number variations (CNVs) are associated with increased risk of autism spectrum disorder (ASD) and, in conjunction with other genetic changes, contribute to the heterogeneity of ASD phenotypes. Array comparative genomic hybridization (aCGH) and exome sequencing, together with systems genetics and network analyses, are being used as tools for the study of complex disorders of unknown etiology, especially those characterized by significant genetic and phenotypic heterogeneity. Therefore, to characterize the complex genotype-phenotype relationship, we performed aCGH and sequenced the exomes of two affected siblings with ASD symptoms, dysmorphic features, and intellectual disability, searching for de novo CNVs, as well as for de novo and rare inherited point variations-single nucleotide variants (SNVs) or small insertions and deletions (indels)-with probable functional impacts...
2017: PloS One
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