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Cytogenomics

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https://www.readbyqxmd.com/read/29153098/high-amplification-levels-of-mdm2-and-cdk4-correlate-with-poor-outcome-in-patients-with-dedifferentiated-liposarcoma-a-cytogenomic-microarray-analysis-of-47-cases
#1
Robert W Ricciotti, Aaron J Baraff, George Jour, McKenna Kyriss, Yu Wu, Yuhua Liu, Shao-Chun Li, Benjamin Hoch, Yajuan J Liu
Dedifferentiated liposarcoma (DDLS) is characterized at the molecular level by amplification of genes within 12q13-15 including MDM2 and CDK4. However, other than FNCLCC grade, prognostic markers are limited. We aim to identify molecular prognostic markers for DDLS to help risk stratify patients. To this end, we studied 49 cases of DDLS in our institutional archives and performed cytogenomic microarray analysis on 47 cases. Gene copy numbers for 12 loci were evaluated and correlated with outcome data retrieved from our institutional electronic medical records...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29140408/philadelphia-chromosome-like-mixed-phenotype-acute-leukemia-demonstrating-p2ry8-crlf2-fusion-and-jak1-mutation
#2
Sarah M Choi, John K Frederiksen, Charles W Ross, Dale L Bixby, Lina Shao
Objectives: Philadelphia chromosome-like (Ph-like) genetic alterations define a subset of B lymphoblastic leukemia/lymphoma (B-ALL), which represents a separate provisional entity in the World Health Organization 2016 updated classification. However, these alterations have not been described outside the context of B-ALL. Methods: Cytogenomic array and molecular analysis identified a Ph-like signature in a mixed-phenotype acute leukemia (MPAL), B/myeloid, confirmed using conventional immunophenotypic and cytochemical analysis...
November 11, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/29075328/comparative-cytogenetics-in-three-sciaenid-species-teleostei-perciformes-evidence-of-interspecific-chromosomal-diversification
#3
Dongdong Xu, Wagner Franco Molina, Cassia Fernanda Yano, Yurong Zhang, Ezequiel Aguiar de Oliveira, Bao Lou, Marcelo de Bello Cioffi
BACKGROUND: Species belonging to the Sciaenidae family present a karyotype composed by 48 acrocentric chromosomes and are thus considered a striking example of chromosomal conservation. In this family, three species are extensively studied including Larimichthys crocea, Larimichthys polyactis and Nibea albiflora due to their importance in fishery and aquaculture in East Asia. Despite abundant data of population genetics available for some of them, cytogenetic information on these species is still scarce and obtained by conventional cytogenetic protocols...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29069255/cytogenomic-assessment-of-the-diagnosis-of-93-patients-with-developmental-delay-and-multiple-congenital-abnormalities-the-brazilian-experience
#4
Évelin Aline Zanardo, Roberta Lelis Dutra, Flavia Balbo Piazzon, Alexandre Torchio Dias, Gil Monteiro Novo-Filho, Amom Mendes Nascimento, Marília Moreira Montenegro, Jullian Gabriel Damasceno, Fabrícia Andreia Rosa Madia, Thaís Virgínia Moura Machado da Costa, Maria Isabel Melaragno, Chong Ae Kim, Leslie Domenici Kulikowski
OBJECTIVE: The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients...
October 2017: Clinics
https://www.readbyqxmd.com/read/29024107/multi-speed-genome-diploidization-and-diversification-after-an-ancient-allopolyploidization
#5
Terezie Mandáková, Milan Pouch, Klára Harmanová, Shing Hei Zhan, Itay Mayrose, Martin A Lysak
Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere...
October 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29023226/contrasting-evolutionary-paths-among-indo-pacific-pomacentrus-species-promoted-by-extensive-pericentric-inversions-and-genome-organization-of-repetitive-sequences
#6
Nuntaporn Getlekha, Marcelo de Bello Cioffi, Nuntiya Maneechot, Luiz Antônio Carlos Bertollo, Weerayuth Supiwong, Alongklod Tanomtong, Wagner Franco Molina
Pomacentrus (damselfishes) is one of the most characteristic groups of fishes in the Indo-Pacific coral reef. Its 77 described species exhibit a complex taxonomy with cryptic lineages across their extensive distribution. Periods of evolutionary divergences between them are very variable, and the cytogenetic events that followed their evolutionary diversification are largely unknown. In this respect, analyses of chromosomal divergence, within a phylogenetic perspective, are particularly informative regarding karyoevolutionary trends...
October 12, 2017: Zebrafish
https://www.readbyqxmd.com/read/28727969/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#7
E Fletcher, M Porteous, K J McKenzie, E J Maher, M J Evans
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome/genome sequencing and the issues these technologies may generate. A systematic review of fetal postmortems at 12-24 weeks gestation between January 2011 and December 2014 was undertaken. Cases where there was no consent for audit, research, or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths, and neonatal deaths...
July 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28613040/chromosomal-microarray-in-clinical-diagnosis-a-study-of-337-patients-with-congenital-anomalies-and-developmental-delays-or-intellectual-disability
#8
Ivona Sansović, Ana-Maria Ivankov, Adriana Bobinec, Mijana Kero, Ingeborg Barišić
AIM: To determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA). METHOD: CMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA...
June 14, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/28324502/telomeres-and-nextgen-co-fish-directional-genomic-hybridization-telo-dgh%C3%A2
#9
Miles J McKenna, Erin Robinson, Edwin H Goodwin, Michael N Cornforth, Susan M Bailey
The cytogenomics-based methodology of Directional Genomic Hybridization (dGH™) emerged from the concept of strand-specific hybridization, first made possible by Chromosome Orientation FISH (CO-FISH), the utility of which was demonstrated in a variety of early applications, often involving telomeres. Similar to standard whole chromosome painting (FISH), dGH™ is capable of identifying inter-chromosomal rearrangements (translocations between chromosomes), but its distinctive strength stems from its ability to detect intra-chromosomal rearrangements (inversions within chromosomes), and to do so at higher resolution than previously possible...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315998/chordoid-glioma-of-the-third-ventricle-report-of-a-rapidly-progressive-case
#10
Amalie A Erwood, Jose E Velazquez-Vega, Stewart Neill, David A Solomon, Nicholas Butowski, Adam Nowlan, Erin Dunbar, Daniel J Brat
Chordoid gliomas are slowly growing third ventricular tumors that can be challenging to manage clinically. Rapid progression causing death has not been previously reported for this tumor type. We present and discuss a case of chordoid glioma that arose in a 46-year-old female who presented with progressive fatigue, headache, and altered mental status, attributable to severe hydrocephalus caused by a third ventricular mass. She underwent urgent subtotal resection and ventriculo-peritoneal shunt placements. Post-operative MRI noted residual tumor in the anterior resection cavity...
May 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28274670/detection-of-copy-number-variations-in-melanocytic-lesions-utilising-array-based-comparative-genomic-hybridisation
#11
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)...
April 2017: Pathology
https://www.readbyqxmd.com/read/28035749/genome-compositional-organization-in-gars-shows-more-similarities-to-mammals-than-to-other-ray-finned-fish
#12
Radka Symonová, Zuzana Majtánová, Lenin Arias-Rodriguez, Libor Mořkovský, Tereza Kořínková, Lionel Cavin, Martina Johnson Pokorná, Marie Doležálková, Martin Flajšhans, Eric Normandeau, Petr Ráb, Axel Meyer, Louis Bernatchez
Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period...
November 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#13
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910032/cytogenetic-nomenclature-and-reporting
#14
Marian Stevens-Kroef, Annet Simons, Katrina Rack, Rosalind J Hastings
A standardized nomenclature is critical for the accurate and consistent description of genomic changes as identified by karyotyping, fluorescence in situ hybridization and microarray. The International System for Human Cytogenomic Nomenclature (ISCN) is the central reference for the description of karyotyping, FISH, and microarray results, and provides rules for describing cytogenetic and molecular cytogenetic findings in laboratory reports. These laboratory reports are documents to the referring clinician, and should be clear, accurate and contain all information relevant for good interpretation of the cytogenetic findings...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910022/high-resolution-fiber-fluorescence-in-situ-hybridization
#15
Christine J Ye, Henry H Heng
High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#16
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27853865/adequately-defining-tumor-cell-proportion-in-tissue-samples-for-molecular-testing-improves-interobserver-reproducibility-of-its-assessment
#17
Benoît Lhermitte, Caroline Egele, Noëlle Weingertner, Damien Ambrosetti, Bérengère Dadone, Valérie Kubiniek, Fanny Burel-Vandenbos, John Coyne, Jean-François Michiels, Marie-Pierre Chenard, Etienne Rouleau, Jean-Christophe Sabourin, Jean-Pierre Bellocq
Gene mutation status assessment of tumors has become standard practice in diagnostic pathology. This is done using samples comprising tumor cells but also non-tumor cells, which may dramatically dilute the proportion of tumor DNA and induce false negative results. Increasing sensitivity of molecular tests presently allows detection of a targeted mutation in a sample with a small percentage of tumor cells, but assessment of tumor cellularity remains essential to adequately interpret the results of molecular tests...
January 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27788041/fetal-dysmorphology-still-an-essential-art-analysis-of-the-limitations-of-microarray-in-a-fetal-population-and-a-look-toward-the-genome-sequencing-era
#18
Elaine Fletcher, Mary Porteous, Eddy Maher, Kathryn J McKenzie, Margaret J Evans
Cytogenomic microarray allows assessment of the genome at higher resolutions than traditional karyotyping. The objective of this study is to evaluate the utility of microarray in a routine fetal autopsy setting before the advent of routine fetal exome / genome sequencing and the issues these technologies may generate. A systematic review of fetal post mortems performed between Jan 2011 - Dec 2014 was undertaken. Cases where there was no consent for audit, research or genetic testing were excluded as were cases referred to the Procurator Fiscal, stillbirths and neonatal deaths...
October 27, 2016: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/27766957/copy-number-variations-in-saudi-family-with-intellectual-disability-and-epilepsy
#19
Muhammad I Naseer, Adeel G Chaudhary, Mahmood Rasool, Gauthaman Kalamegam, Fai T Ashgan, Mourad Assidi, Farid Ahmed, Shakeel A Ansari, Syed Kashif Zaidi, Mohammed M Jan, Mohammad H Al-Qahtani
BACKGROUND: Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging. RESULTS: In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID), and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis...
October 17, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27710958/karyotype-and-mapping-of-repetitive-dnas-in-the-african-butterfly-fish-pantodon-buchholzi-the-sole-species-of-the-family-pantodontidae
#20
Petr Ráb, Cassia F Yano, Sébastien Lavoué, Oladele I Jegede, Luiz A C Bertollo, Tariq Ezaz, Zuzana Majtánová, Ezequiel A de Oliveira, Marcelo B Cioffi
The monophyletic order Osteoglossiformes represents one of the most ancestral groups of teleosts and has at least 1 representative in all continents of the southern hemisphere, with the exception of Antarctica. However, despite its phylogenetic and biogeographical importance, cytogenetic data in Osteoglossiformes are scarce. Here, karyotype and chromosomal characteristics of the lower Niger River population of the African butterfly fish Pantodon buchholzi, the sole species of the family Pantodontidae (Osteoglossiformes), were examined using conventional and molecular cytogenetic approaches...
2016: Cytogenetic and Genome Research
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