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https://www.readbyqxmd.com/read/28331547/application-of-high-resolution-genomic-profiling-in-the-differential-diagnosis-of-liposarcoma
#1
Magdalena Koczkowska, Beata Stefania Lipska-Ziętkiewicz, Mariola Iliszko, Janusz Ryś, Markku Miettinen, Jerzy Lasota, Wojciech Biernat, Agnieszka Harazin-Lechowska, Anna Kruczak, Janusz Limon
BACKGROUND: Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28316110/proteasome-ubiquitin-receptor-psmd4-is-an-amplification-target-in-breast-cancer-and-may-predict-sensitivity-to-parpi
#2
Marlena S Fejzo, Lee Anderson, Hsiao-Wang Chen, Enrique Guandique, Ondrej Kalous, Dylan Conklin, Dennis J Slamon
Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme involved in DNA repair under investigation as a chemotherapeutic target. Current randomized phase 3 trials of PARPi in metastatic breast cancer are limited to patients with documented BRCA1/2 mutations and no biomarker of PARPi beyond BRCA status is available. In an effort to identify novel biomarkers for PARP inihibition, we created a cell line (HCC1187/TALRES) resistant to the PARP1 inhibitor talazoparib. Herein we show by array-CGH that HCC1187/TALRES has a selective loss of the proteasome ubiquitin receptor PSMD4 amplicon resulting in significant down-regulation of PSMD4...
March 18, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28314280/embryonal-origin-of-mtscc-of-kidney-may-explain-its-morphological-heterogeneity-diagnostic-impact-of-genetic-analysis
#3
Daniel Banyai, Fanni Vastag, Maria Yusenko, Peter Bugert, Gyula Kovacs
BACKGROUND/AIM: Previous genetic and morphologic characterisation of mucinous tubular and spindle cell carcinoma (MTSCC) have yielded controversial results. The aim of this study was to explain the phenotypic heterogeneity of MTSCC diagnosed by genetic means. MATERIALS AND METHODS: We analyzed 7 MTSCC by array CGH and microsatellite allelotyping and by histology for morphological variation. We worked-up two entire kidneys with MTSCC to find microscopic alterations...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28306341/implantation-potential-of-mosaic-embryos
#4
Belén Lledó, Ruth Morales, Jose Antonio Ortiz, Helena Blanca, Jorge Ten, Joaquín Llácer, Rafael Bernabeu
Chromosomal mosaicism is a relatively common finding in human IVF embryos. However, the association between mosaicism in trophoectoderm and inner mass cells, the mechanisms involved, and its effects on implantation are far from established. We retrospectively reanalyzed array-CGH results from 1,362 trophoectoderm biopsies. We detected chromosomal mosaicism in 183 blastocysts (13.4%). A decrease in the clinical pregnancy rate when we compared the cycles where only mosaic embryos were transferred (26.9%) vs. euploid embryos were transferred (40...
March 17, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28304131/copy-number-variation-in-19-italian-multiplex-families-with-autism-spectrum-disorder-importance-of-synaptic-and-neurite-elongation-genes
#5
Carla Lintas, Chiara Picinelli, Ignazio Stefano Piras, Roberto Sacco, Claudia Brogna, Antonio M Persico
Autism Spectrum Disorder (ASD) is endowed with impressive heritability estimates and high recurrence rates. Its genetic underpinnings are nonetheless very heterogeneous, with common, and rare contributing variants located in hundreds of different loci, each characterized by variable levels of penetrance. Multiplex families from single ethnic groups represent a useful means to reduce heterogeneity and enhance genetic load. We screened 19 Italian ASD multiplex families (3 triplets and 16 duplets, total N = 41 ASD subjects), using array-CGH (Agilent 180 K)...
March 17, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28295210/cnvs-analysis-in-a-cohort-of-isolated-and-syndromic-dd-id-reveals-novel-genomic-disorders-position-effects-and-candidate-disease-genes
#6
Eleonora Di Gregorio, Evelise Riberi, Elga Fabia Belligni, Elisa Biamino, Malte Spielmann, Ugo Ala, Alessandro Calcia, Irene Bagnasco, Diana Carli, Giorgia Gai, Mara Giordano, Andrea Guala, Roberto Keller, Giorgia Mandrile, Carlo Arduino, Antonella Maffè, Valeria Giorgia Naretto, Fabio Sirchia, Lorena Sorasio, Silvana Ungari, Andrea Zonta, Giulia Zacchetti, Flavia Talarico, Patrizia Pappi, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Marta Ferrero, Alessandro Brussino, Elisa Savin, Marina Gandione, Alessandra Pelle, Daniela Francesca Giachino, Mario De Marchi, Gabriella Restagno, Paolo Provero, Margherita Cirillo Silengo, Enrico Grosso, Joseph D Buxbaum, Barbara Pasini, Silvia De Rubeis, Alfredo Brusco, Giovanni Battista Ferrero
Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect Copy Number Variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes...
March 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28286255/a-further-case-of-brain-lung-thyroid-syndrome-with-deletion-proximal-to-nkx2-1
#7
Mira Kharbanda, Pia Hermanns, Jeremy Jones, Joachim Pohlenz, Iain Horrocks, Malcolm Donaldson
Brain-lung-thyroid syndrome (OMIM #610978) is associated with mutations in the NK2 homeobox 1 (NKX2-1) gene, a transcription factor important in development. 50% of patients are affected by the full triad, comprising congenital hypothyroidism, benign hereditary chorea and infant respiratory distress syndrome. Four cases have previously been reported where a patient has features consistent with brain-lung-thyroid syndrome and a chromosome 14q13 deletion adjacent to, but not disrupting, NKX2-1. We present a patient who has a phenotype consistent with brain-lung-thyroid syndrome, featuring congenital hypothyroidism and choreoathetoid movements with gross motor delay...
March 7, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28285730/new-in-vivo-model-to-analyse-the-expression-of-angiogenic-genes-in-the-borders-of-a-cleft-lip
#8
C François, M L Poli-Merol, C Tournois, P Cornillet-Lefebvre, T Guillard, Z Djerada, M Doco Fenzy, P Nguyen
Defects in the fusion of facial buds can result from an anomaly in tissue development or apoptosis, or both. Our working hypothesis was that anomalies in the development of tissues could be caused by a genetic angiogenic defect. Our main objective was to design a reproducible experimental model to study the expression of angiogenic genes in the borders of cleft lips with or without cleft palate. We therefore prospectively studied seven non-syndromic patients, three with a cleft lip (2 right, 1 left), and four with a cleft lip and palate (1 bilateral, 2 right, 1 left), with no CGH (comparative genomic hybridisation) array, who had primary operations to repair their clefts...
March 9, 2017: British Journal of Oral & Maxillofacial Surgery
https://www.readbyqxmd.com/read/28284561/novel-mutation-in-two-brothers-with-hermansky-pudlak-syndrome-type-3
#9
Kirstin Sandrock-Lang, Ingrid Bartsch, Nina Buechele, Udo Koehler, Carl Philipp Simon-Gabriel, Matthias Eckenweiler, Barbara Zieger
Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder causing oculocutaneous albinism, bleeding disorder and ceroid lipofuscinosis. Platelets from HPS patients are characterized by impaired secretion of dense (δ)-bodies (CD63). Meanwhile, there are ten known human HPS genes, each leading to a particular clinical HPS subtype (HPS1-HPS10). We report on two Turkish brothers showing typical HPS phenotype comprising oculocutaneous albinism and bleeding symptoms. Pathological bleeding time as well as platelet aggregometry analyses revealed impaired platelet function...
March 6, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/28274670/detection-of-copy-number-variations-in-melanocytic-lesions-utilising-array-based-comparative-genomic-hybridisation
#10
Nima Mesbah Ardakani, Carla Thomas, Cleo Robinson, Kym Mina, Nathan Tobias Harvey, Benhur Amanuel, Benjamin Andrew Wood
Distinction between melanocytic naevi and melanoma occasionally poses a diagnostic challenge in ambiguous cases showing overlapping histological features. Melanomas are characterised by the presence of multiple genomic copy number variants (CNVs), while this is not a feature of naevi. We assessed the feasibility and utility of array-based comparative genomic hybridisation (aCGH) to assess CNVs in melanocytic lesions. DNA was extracted from formalin fixed, paraffin embedded (FFPE) sections of unambiguous naevi (n=19) and melanomas (n=19)...
March 5, 2017: Pathology
https://www.readbyqxmd.com/read/28266316/genomic-copy-number-variation-associated-with-clinical-outcome-in-canine-cutaneous-mast-cell-tumors
#11
Paulo C Jark, Deborah B P Mundin, Marcio de Carvalho, Raquel B Ferioli, Letícia A Anai, Fabio A Marchi, Silvia R Rogatto, Renee Laufer-Amorim, Mirela Tinucci-Costa
Mast cell tumors are the most common malignant cutaneous tumors in dogs. Although there are several prognostic factors involved, the clinical and biological behavior of this type of tumor varies greatly, making the best choice of treatment challenging. Molecular techniques can be used to evaluate a large number of genes involved in the neoplastic process and aid in the selection of candidate genes related to prognostic and predicting factors. Identification of the genes associated with tumor development and progression can be performed through the analysis of numerical and structural changes in DNA isolated from tumor cells by array comparative genomic hybridization (aCGH)...
November 17, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/28253504/genomic-characterization-of-a-metastatic-alveolar-rhabdomyosarcoma-case-using-fish-studies-and-cgh-snp-microarray-revealing-foxo1-pax7-rearrangement-with-mycn-and-mdm2-amplification-and-rb1-region-loss
#12
Arivarasan Karunamurthy, Lori Hoffner, Jie Hu, Peter Shaw, Sarangarajan Ranganathan, Svetlana A Yatsenko, Urvashi Surti
Rhabdomyosarcomas (RMS) are rare, heterogeneous, soft tissue sarcomas and a common type of childhood malignancy with a distinct histomorphology. At the molecular level, alveolar rhabdomyosarcoma (ARMS), a subtype of RMS, harbors a signature genetic makeup characterized by specific translocations. The type of translocation and associated genetic aberrations correlate with disease progression, hence we used multiple molecular modalities including high-resolution array comparative genomic hybridization to explore the oncogenic gene fusion and associated copy number variations in a case of metastatic ARMS...
March 3, 2017: Cytogenetic and Genome Research
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
#13
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
#14
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/28215484/establishment-and-characterization-of-a-new-human-acinar-cell-carcinoma-cell-line-faraz-icr-from-pancreas
#15
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/28196407/comprehensive-genomic-and-phenotypic-characterization-of-germline-fh-deletion-in-hereditary-leiomyomatosis-and-renal-cell-carcinoma-hlrcc
#16
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/28176767/intragenic-fmr1-disease-causing-variants-a-significant-mutational-mechanism-leading-to-fragile-x-syndrome
#17
Angélique Quartier, Hélène Poquet, Brigitte Gilbert-Dussardier, Massimiliano Rossi, Anne-Sophie Casteleyn, Vincent des Portes, Claire Feger, Elsa Nourisson, Paul Kuentz, Claire Redin, Julien Thevenon, Anne-Laure Mosca-Boidron, Patrick Callier, Jean Muller, Gaetan Lesca, Frédéric Huet, Véronique Geoffroy, Salima El Chehadeh, Matthieu Jung, Benoit Trojak, Stéphanie Le Gras, Daphné Lehalle, Bernard Jost, Stéphanie Maury, Alice Masurel, Patrick Edery, Christel Thauvin-Robinet, Bénédicte Gérard, Jean-Louis Mandel, Laurence Faivre, Amélie Piton
Fragile-X syndrome (FXS) is a frequent genetic form of intellectual disability (ID). The main recurrent mutagenic mechanism causing FXS is the expansion of a CGG repeat sequence in the 5'-UTR of the FMR1 gene, therefore, routinely tested in ID patients. We report here three FMR1 intragenic pathogenic variants not affecting this sequence, identified using high-throughput sequencing (HTS): a previously reported hemizygous deletion encompassing the last exon of FMR1, too small to be detected by array-CGH and inducing decreased expression of a truncated form of FMRP protein, in three brothers with ID (family 1) and two splice variants in boys with sporadic ID: a de novo variant c...
February 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28165654/identification-of-proteasomal-catalytic-subunit-psma6-as-a-therapeutic-target-for-lung-cancer
#18
Tomohiko Kakumu, Mitsuo Sato, Daiki Goto, Toshio Kato, Naoyuki Yogo, Tetsunari Hase, Masahiro Morise, Takayuki Fukui, Kohei Yokoi, Yoshitaka Sekido, Luc Girard, John D Minna, Lauren A Byers, John V Heymach, Kevin R Coombes, Masashi Kondo, Yoshinori Hasegawa
To identify potential therapeutic targets for lung cancer, we performed semi-genome-wide shRNA screening combined with the utilisation of genome-wide expression and copy number data. shRNA screening targeting 5,043 genes in NCI-H460 identified 51 genes as candidates. Pathway analysis revealed that the 51 genes were enriched for the five pathways, including ribosome, proteasome, RNA polymerase, pyrimidine metabolism and spliceosome pathways. We focused on the proteasome pathway that involved six candidate genes because its activation has been demonstrated in diverse human malignancies, including lung cancer...
February 6, 2017: Cancer Science
https://www.readbyqxmd.com/read/28161066/genomic-profile-in-gestational-and-non-gestational-choriocarcinomas
#19
Julia Bette Homem de Mello, Priscila Daniele Ramos Cirilo, Odair Carlito Michelin, Maria Aparecida Custódio Domingues, Marilza Vieira Cunha Rudge, Silvia Regina Rogatto, Izildinha Maestá
INTRODUCTION: Gestational (GC) (derived from the placenta) and non-gestational (NGC) choriocarcinomas are trophoblastic diseases originated from abnormal proliferation of trophoblastic cells. These rare tumors share similar morphology and pathological features and differ on chemotherapy response, genetic origin and prognosis. In this study, the genomic profile of choriocarcinomas was performed according to their origin (GC or NGC) aiming to better understand these poorly characterized diseases...
February 2017: Placenta
https://www.readbyqxmd.com/read/28159702/a-case-of-feingold-type-2-syndrome-associated-with-keratoconus-refines-keratoconus-type-7-locus-on-chromosome-13q
#20
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...
April 2017: European Journal of Medical Genetics
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