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https://www.readbyqxmd.com/read/28728275/-changes-and-differences-of-dna-methylation-in-human-macrophages-infected-with-virulent-and-avirulent-mycobacterium-tuberculosis
#1
L N Lyu, H Y Jia, Z H Li, Z Q Liu, Z D Zhang
Objective: To profile DNA methylation and compare differentially methylated region (DMR) of macrophages infected with virulent and avirulent strains of Mycobacterium tuberculosis (MTB). Methods: PMA(50 ng/ml) treated THP-1 macrophages were left uninfected or infected with the virulent H37Rv(THP-1/Rv) or avirulent H37Ra(THP-1/Ra). The genomic DNA was then extracted and DNA methylation was profiled via Reduced Representation Bisulfite Sequencing (RRBS). The DNA methylation pattern and DMRs between the tested samples were indentified...
July 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#2
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28724436/expanding-the-phenotype-of-reciprocal-1q21-1-deletions-and-duplications-a-case-series
#3
Martina Busè, Helenia C Cuttaia, Daniela Palazzo, Marcella V Mazara, Salvatrice A Lauricella, Michela Malacarne, Mauro Pierluigi, Simona Cavani, Maria Piccione
BACKGROUND: Recurrent reciprocal 1q21.1 deletions and duplications have been associated with variable phenotypes. Phenotypic features described in association with 1q21.1 microdeletions include developmental delay, craniofacial dysmorphism and congenital anomalies. The 1q21.1 reciprocal duplication has been associated with macrocephaly or relative macrocephaly, frontal bossing, hypertelorism, developmental delay, intellectual disability and autism spectrum disorder. METHODS: Our study describes seven patients, who were referred to us for developmental delay/intellectual disability, dysmorphic features and, in some cases, congenital anomalies, in whom we identified 1q21...
July 19, 2017: Italian Journal of Pediatrics
https://www.readbyqxmd.com/read/28717667/haploinsufficiency-of-bcl11a-associated-with-cerebellar-abnormalities-in-2p15p16-1-deletion-syndrome
#4
Hiroko Shimbo, Takayuki Yokoi, Noriko Aida, Seiji Mizuno, Hiroshi Suzumura, Junichi Nagai, Kazumi Ida, Yumi Enomoto, Chihiro Hatano, Kenji Kurosawa
BACKGROUND: Chromosome 2p15p16.1 deletion syndrome is a rare genetic disorder characterized by intellectual disability (ID), neurodevelopmental delay, language delay, growth retardation, microcephaly, structural brain abnormalities, and dysmorphic features. More than 30 patients with 2p15p16.1 microdeletion syndrome have been reported in the literature. METHODS: Molecular analysis was performed using microarray-based comparative genomic hybridization (array CGH)...
July 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28711366/-contribution-of-chromosomal-microarray-analysis-by-a-multidisciplinary-prenatal-diagnosis-center
#5
C Bartholmot, E Mousty, F Grosjean, Y Petrov, P Khau Van Kien, J Chiesa, V Letouzey
OBJECTIVE: Chromosomal analysis by array CGH is a cytogenetic technique that has opened its application to prenatal diagnosis in recent years. The main objective of the study was to analyze the contribution for couples using chromosomal analysis by array CGH in a CPDPN. METHODS: A retrospective cohort study was conducted in 2015 in a CPDPN. All the patients with array CGH analysis were included in the study. The analysis indications were CN≥3.5mm, ultrasound signs, intra-uterine growth retardation and fetal deaths...
July 12, 2017: Gynecologie, Obstetrique, Fertilite & Senologie
https://www.readbyqxmd.com/read/28700181/-hyperuricemia-and-gene-mutations-a-case-report
#6
Fabio Tattoli, Daniela Falconi, Ornella De Prisco, Gherzi Maurizio, Federico Marazzi, Marita Marengo, Ilaria Serra, Michela Tamagnone, Luca Cordero di Montezemolo, Barbara Pasini, Marco Formica
Hyperuricemia is frequently found in nephrology. The case presented may be useful to clarify some pathogenetic aspects. It is a patient of 18 years, hyperuricaemic. Non-consanguineous parents, hyperuricemia in the paternal line, not neuropsychiatric disorders in the family. Delay in neuromotor acquisitions, average intellectual disabilities, anxiety disorder, obsessive-compulsive personality traits. Normal renal function and renal ultrasound. Evidence of hyperuricemia in 2015. Never gouty episodes and / or lithiasis, initiated allopurinol 100 mg on alternate days, with no side effects, urea in the control range, slightly below normal uricuria...
June 2017: Giornale Italiano di Nefrologia: Organo Ufficiale Della Società Italiana di Nefrologia
https://www.readbyqxmd.com/read/28696559/genetic-testing-for-hereditary-nonpolyposis-colorectal-cancer-hnpcc
#7
Babi Ramesh Reddy Nallamilli, Madhuri Hegde
Hereditary nonpolyposis colorectal cancer (HNPCC), also called Lynch syndrome, is an autosomal dominant cancer syndrome that confers an elevated risk of early-onset colorectal cancer (CRC) and increased lifetime risk for other cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary. Lynch syndrome accounts for up to 3% of all CRC, making it the most common hereditary colorectal cancer syndrome. Germline mutations in methyl-directed mismatch repair (MMR) genes give rise to microsatellite instability (MSI) in tumor DNA...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28695677/combined-genetic-analyses-can-achieve-efficient-diagnostic-yields-for-subjects-with-alagille-syndrome-and-incomplete-alagille-syndrome
#8
Kei Ohashi, Takao Togawa, Tokio Sugiura, Koichi Ito, Takeshi Endo, Kohei Aoyama, Yutaka Negishi, Toyoichiro Kudo, Reiko Ito, Shinji Saitoh
AIM: We evaluated combined genetic analyses with targeted next-generation sequencing (NGS), multiplex ligation probe amplification (MLPA) of Jagged1 (JAG1) genes and microarray comparative genomic hybridisation (CGH) in subjects with Alagille syndrome, incomplete clinical features of Alagille syndrome and biliary atresia. METHODS: Subjects recruited from April 2013 to December 2015 underwent a targeted NGS analysis, including JAG1 and Notch homolog 2 (NOTCH2). If no mutations were detected in JAG1 or NOTCH2, or if copy number variations were suggested by the NGS analysis, we performed an MLPA analysis of JAG1...
July 11, 2017: Acta Paediatrica
https://www.readbyqxmd.com/read/28694329/feminization-of-male-mouse-liver-by-persistent-growth-hormone-stimulation-activation-of-sex-biased-transcriptional-networks-and-dynamic-changes-in-chromatin-states
#9
Dana Lau-Corona, Alexander Suvorov, David J Waxman
Sex-dependent pituitary GH secretory profiles--pulsatile in males and persistent in females--regulate sex-biased, STAT5-dependent expression of hundreds of genes in mouse liver, imparting sex differences in hepatic drug/lipid metabolism and disease risk. Here we examine transcriptional and epigenetic changes induced by continuous-GH infusion (cGH) in male mice, which rapidly feminizes the temporal profile of liver STAT5 activity. cGH repressed 86% of male-biased genes and induced 68% of female-biased genes within 4-days; however, several highly female-specific genes showed weak or no feminization, even after 14-days cGH...
July 10, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28693295/germline-dna-copy-number-variations-as-potential-prognostic-markers-for-non-muscle-invasive-bladder-cancer-progression
#10
Yoshiaki Yamamoto, Yutaka Suehiro, Atomu Suzuki, Ryosuke Nawata, Yoshihisa Kawai, Ryo Inoue, Hiroshi Hirata, Hiroaki Matsumoto, Takahiro Yamasaki, Kohsuke Sasaki, Hideyasu Matsuyama
Accumulating evidence has suggested that germline DNA copy number variations (CNVs) affect various disorders, including human malignancies. However, the significance of CNVs in non-muscle invasive bladder cancer (NMIBC) remains unclear. The purpose of the present study was to identify the role of CNVs in NMIBC. Array comparative genomic hybridization (CGH) analysis was performed to search for candidate CNVs associated with NMIBC susceptibility. Quantitative polymerase chain reaction was carried out to evaluate CNVs associated with patient outcome in 189 NMIBC cases...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28692986/heavy-tailed-noise-suppression-and-derivative-wavelet-scalogram-for-detecting-dna-copy-number-aberrations
#11
Nha Nguyen, An Vo, Haibin Sun, Heng Huang
Most existing array comparative genomic hybridization (array CGH) data processing methods and evaluation models assumed that the probability density function of noise in array CGH is a Gaussian distribution. However, in practice such noise distribution is peaky and heavy-tailed. A more accurate and sufficient model of noise in array CGH data is necessary and beneficial to the detection of DNA copy number variations. We analyze the real array CGH data from different platforms and show that the distribution of noise in array CGH data is fitted very well by generalized Gaussian distribution (GGD)...
July 6, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28691344/combined-tumor-genomic-profiling-and-exome-sequencing-in-a-breast-cancer-family-implicates-atm-in-tumorigenesis-a-proof-of-principle-study
#12
Virginie Bubien, Françoise Bonnet, Jennifer Dupiot-Chiron, Emmanuelle Barouk-Simonet, Natalie Jones, Aurélien de Reynies, Gaëtan MacGrogan, Nicolas Sevenet, Eric Letouzé, Michel Longy
Familial breast cancers (BCs) account for 10-20% of all diagnosed BCs, yet only 20% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes non BRCA1 and non BRCA2 (or BRCAx) families makes grouped studies impossible to perform. Next generation sequencing techniques, however, allow individual families to be studied in order to identify rare and or private mutations but the high number of genetic variants identified need to be sorted using pathogenicity or recurrence criteria...
July 10, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28690986/next-generation-sequencing-and-array-based-comparative-genomic-hybridization-for-molecular-diagnosis-of-pediatric-endocrine-disorders
#13
REVIEW
Maki Fukami, Mami Miyado
Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders...
June 2017: Annals of Pediatric Endocrinology & Metabolism
https://www.readbyqxmd.com/read/28684328/genetics-of-gynaecological-disorders
#14
REVIEW
Dragana J Josifova
From genomic imbalances associated with developmental abnormalities of the female genital tract to the molecular mechanisms underpinning endometriosis and uterine leiomyomatosis, new technologies have allowed the exploration of the genetic contribution and mapping the molecular pathways underpinning common and rare gynaecological conditions. While some of these conditions have historically been considered sporadic, recent research has demonstrated their potentially heritable nature linked to single genes or copy number variants...
July 2017: Best Practice & Research. Clinical Obstetrics & Gynaecology
https://www.readbyqxmd.com/read/28683077/dna-isolation-protocol-effects-on-nuclear-dna-analysis-by-microarrays-droplet-digital-pcr-and-whole-genome-sequencing-and-on-mitochondrial-dna-copy-number-estimation
#15
Elizabeth Nacheva, Katya Mokretar, Aynur Soenmez, Alan M Pittman, Colin Grace, Roberto Valli, Ayesha Ejaz, Selina Vattathil, Emanuela Maserati, Henry Houlden, Jan-Willem Taanman, Anthony H Schapira, Christos Proukakis
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol...
2017: PloS One
https://www.readbyqxmd.com/read/28680000/genetic-heterogeneity-of-dlbcl-not-otherwise-specified
#16
Kennosuke Karube
Diffuse large B-cell lymphoma (DLBCL), not otherwise specified, is the most common malignant lymphoma in the world. The recent progress of molecular techniques has proved its heterogeneity. Gene expression profiling for DLBCL, recently achieved using formalin-fixed paraffin-embedded samples, has identified two molecular subtypes, according to their cell of origin correlated with prognosis. Genomic abnormalities are roughly divided into translocations, amplifications/deletions, and mutations. Translocations involving MYC and BCL2 frequently co-occur in 5%-10% of DLBCL and are associated with aggressive clinical behavior with poor outcomes...
2017: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
https://www.readbyqxmd.com/read/28676910/morphokinetic-parameters-from-a-time-lapse-monitoring-system-cannot-accurately-predict-the-ploidy-of-embryos
#17
Jingye Zhang, Wenrong Tao, Hui Liu, Guanling Yu, Mei Li, Shuiying Ma, Keliang Wu
PURPOSE: This study aimed to test whether there is an association between embryo morphokinetic parameters and ploidy status. METHODS: Patients with high risk of aneuploidy were analyzed by time-lapse microscopy combined with preimplantation genetic screening (PGS). Accordingly, 256 blastocysts from 75 patients were subjected to trophectoderm biopsy and microarray comparative genomic hybridization (array-CGH). Blastocyst development process was analyzed using time-lapse images...
July 4, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28673748/late-solitary-extraocular-recurrence-from-previously-resected-iris-melanoma
#18
Ido Didi Fabian, Caroline Thaung, Lamis AlHarby, Karen Sisley, Hardeep S Mudhar, Rachel E Doherty, Andrew W Stacey, Amit K Arora, Victoria M L Cohen, Mandeep S Sagoo
PURPOSE: To report on cases of late extraocular relapse of previously resected iris melanoma, without concurrent intraocular recurrence. DESIGN: Retrospective case series. METHODS: A retrospective chart review of 4 patients diagnosed with late subconjunctival relapse of previously resected iris melanoma. RESULTS: Three females and one male underwent iris tumour resection and presented to our service with suspicious conjunctival lesions at a median of 22 years later (mean: 21)...
June 30, 2017: American Journal of Ophthalmology
https://www.readbyqxmd.com/read/28659124/cataract-and-optic-disk-drusen-in-a-patient-with-glycogenosis-and-di-george-syndrome-clinical-and-molecular-report
#19
D Allegrini, S Penco, A Pece, A Autelitano, G Montesano, S Paci, C Montanari, A Maver, B Peterlin, G Damante, L Rossetti
BACKGROUND: We report the ophthalmic findings of a patient with type Ia glycogen storage disease (GSD Ia), DiGeorge syndrome (DGS), cataract and optic nerve head drusen (ONHD). CASE PRESENTATION: A 26-year-old white woman, born at term by natural delivery presented with a post-natal diagnosis of GSD Ia. Genetic testing by array-comparative genomic hybridization (CGH) for DGS was required because of her low levels of serum calcium. The patient has been followed from birth, attending the day-hospital every six months at the San Paolo Hospital, Milan, outpatient clinic for metabolic diseases and previously at another eye center...
June 28, 2017: BMC Ophthalmology
https://www.readbyqxmd.com/read/28647497/prediction-of-metastasis-in-advanced-colorectal-carcinomas-using-cgh-data
#20
Ehsan Saghapour, Mohammadreza Sehhati
Logistic Regression Model (LRM) and artificial neural networks (ANNs) as two nonlinear models have been used to establish a novel two-stage hybrid modeling procedure for prediction of metastasis in advanced colorectal carcinomas. Two different datasets were used in training and testing procedures. For the first stage of hybrid modeling procedure, LRM was used to evaluate the contribution of DNA sequence copy number aberrations detected by Comparative Genomic Hybridization in advanced colorectal carcinoma and its metastasis...
September 21, 2017: Journal of Theoretical Biology
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