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Cytogenomics

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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
#1
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
#2
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
#3
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
#4
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...
March 18, 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
#5
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
#6
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...
December 30, 2016: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27707671/cytogenetics-in-the-management-of-children-and-adult-acute-lymphoblastic-leukemia-all-an-update-by-the-groupe-francophone-de-cytog%C3%A3-n%C3%A3-tique-h%C3%A3-matologique-gfch
#15
REVIEW
Laurence Baranger, Wendy Cuccuini, Christine Lefebvre, Isabelle Luquet, Christine Perot, Isabelle Radford, Marina Lafage-Pochitaloff
Cytogenetic analyses (karyotype and, if necessary, appropriate complementary FISH analyses) are mandatory at diagnosis in acute lymphoblastic leukemia (ALL) as their results are taken into account in therapeutic protocols due to their diagnostic and prognostic values. In some cases, karyotype can be completed by other techniques (RT-PCR, RQ-PCR, DNA content, SNP-array, MLPA…) that can be equally or more informative than FISH. Here, we have tempted to establish guidelines concerning karyotype and FISH analyses according to the most recent data of the litterature which is reviewed here, completing the 2008 WHO classification with the recent new cytogenomic entities such as Ph-like ALL and indicating possible therapeutic implications...
October 1, 2016: Annales de Biologie Clinique
https://www.readbyqxmd.com/read/27665090/subtelomeric-copy-number-variations-the-importance-of-4p-4q-deletions-in-patients-with-congenital-anomalies-and-developmental-disability
#16
Gil M Novo-Filho, Marília M Montenegro, Évelin A Zanardo, Roberta L Dutra, Alexandre T Dias, Flavia B Piazzon, Taís V M M Costa, Amom M Nascimento, Rachel S Honjo, Chong A Kim, Leslie D Kulikowski
The most prevalent structural variations in the human genome are copy number variations (CNVs), which appear predominantly in the subtelomeric regions. Variable sizes of 4p/4q CNVs have been associated with several different psychiatric findings and developmental disability (DD). We analyzed 105 patients with congenital anomalies (CA) and developmental and/or intellectual disabilities (DD/ID) using MLPA subtelomeric specific kits (P036 /P070) and 4 of them using microarrays. We found abnormal subtelomeric CNVs in 15 patients (14...
2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27639374/comprehensive-genomic-characterization-of-five-canine-lymphoid-tumor-cell-lines
#17
Sarah C Roode, Daniel Rotroff, Kristy L Richards, Peter Moore, Alison Motsinger-Reif, Yasuhiko Okamura, Takuya Mizuno, Hajime Tsujimoto, Steven E Suter, Matthew Breen
BACKGROUND: Leukemia/lymphoma cell lines have been critical in the investigation of the pathogenesis and therapy of hematological malignancies. While human LL cell lines have generally been found to recapitulate the primary tumors from which they were derived, appropriate characterization including cytogenetic and transcriptional assessment is crucial for assessing their clinical predictive value. RESULTS: In the following study, five canine LL cell lines, CLBL-1, Ema, TL-1 (Nody-1), UL-1, and 3132, were characterized using extensive immunophenotyping, karyotypic analysis, oligonucleotide array comparative genomic hybridization (oaCGH), and gene expression profiling...
September 17, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27614666/genomic-copy-number-analysis-of-her2-equivocal-breast-cancers
#18
Katherine B Geiersbach, Carlynn Willmore-Payne, Alexandra V Pasi, Christian N Paxton, Theresa L Werner, Xinjie Xu, Carl T Wittwer, H Evin Gulbahce, Erinn Downs-Kelly
OBJECTIVES: Guidelines for HER2 testing define an equivocal range for HER2 using two approved testing methods, immunohistochemistry (IHC) and in situ hybridization (ISH). We investigated genome-wide copy number alterations in this subgroup. METHODS: Ten breast cancers with equivocal HER2 status by both IHC and ISH were analyzed by single-nucleotide polymorphism cytogenomic microarray (SNP array). DNA ploidy analysis by flow cytometry was performed on nine cases with sufficient material remaining...
October 2016: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/27450648/post-mortem-cytogenomic-investigations-in-patients-with-congenital-malformations
#19
Alexandre Torchio Dias, Évelin Aline Zanardo, Roberta Lelis Dutra, Flavia Balbo Piazzon, Gil Monteiro Novo-Filho, Marilia Moreira Montenegro, Amom Mendes Nascimento, Mariana Rocha, Fabricia Andreia Rosa Madia, Thais Virgínia Moura Machado Costa, Cintia Milani, Regina Schultz, Fernanda Toledo Gonçalves, Cintia Fridman, Guilherme Lopes Yamamoto, Débora Romeo Bertola, Chong Ae Kim, Leslie Domenici Kulikowski
Congenital anomalies are the second highest cause of infant deaths, and, in most cases, diagnosis is a challenge. In this study, we characterize patterns of DNA copy number aberrations in different samples of post-mortem tissues from patients with congenital malformations. Twenty-eight patients undergoing autopsy were cytogenomically evaluated using several methods, specifically, Multiplex Ligation-dependent Probe Amplification (MLPA), microsatellite marker analysis with a MiniFiler kit, FISH, a cytogenomic array technique and bidirectional Sanger sequencing, which were performed on samples of different tissues (brain, heart, liver, skin and diaphragm) preserved in RNAlater, in formaldehyde or by paraffin-embedding...
August 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27385961/cytogenomic-aberrations-in-congenital-cardiovascular-malformations
#20
REVIEW
Mahshid Azamian, Seema R Lalani
Congenital cardiovascular malformations are the most common birth defects, with a complex multifactorial etiology. Genetic factors play an important role, illuminated by numerous cytogenetically visible abnormalities, as well as submicroscopic genomic imbalances affecting critical genomic regions in the affected individuals. Study of rare families with Mendelian forms, as well as emerging next-generation sequencing technologies have uncovered a multitude of genes relevant for human congenital cardiac diseases...
May 2016: Molecular Syndromology
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