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Cytogenomics

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https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#1
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
#2
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
#3
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
#4
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
#5
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...
November 16, 2016: 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
#6
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
#7
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
#8
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...
October 7, 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
#9
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
#10
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...
September 24, 2016: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/27639374/comprehensive-genomic-characterization-of-five-canine-lymphoid-tumor-cell-lines
#11
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...
2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27614666/genomic-copy-number-analysis-of-her2-equivocal-breast-cancers
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27344147/isolation-and-characterization-of-5s-rdna-sequences-in-catfishes-genome-heptapteridae-and-pseudopimelodidae-perspectives-for-rdna-studies-in-fish-by-c0t-method
#15
Juceli Gonzalez Gouveia, Ivan Rodrigo Wolf, Vivian Patrícia Oliveira de Moraes-Manécolo, Vanessa Belline Bardella, Lara Munique Ferracin, Lucia Giuliano-Caetano, Renata da Rosa, Ana Lúcia Dias
Sequences of 5S ribosomal RNA (rRNA) are extensively used in fish cytogenomic studies, once they have a flexible organization at the chromosomal level, showing inter- and intra-specific variation in number and position in karyotypes. Sequences from the genome of Imparfinis schubarti (Heptapteridae) were isolated, aiming to understand the organization of 5S rDNA families in the fish genome. The isolation of 5S rDNA from the genome of I. schubarti was carried out by reassociation kinetics (C0t) and PCR amplification...
December 2016: Cytotechnology
https://www.readbyqxmd.com/read/27313662/familial-chromosomal-translocation-x-22-associated-with-infertility-and-recurrent-x-mosaicism
#16
Juliana Dourado Grzesiuk, Ciro Silveira Pereira, Carlos Henrique Paiva Grangeiro, Clarissa Gondim Picanço-Albuquerque, Flávia Gaona Oliveira-Gennaro, Filipe Brum Machado, Enrique Medina-Acosta, Ester Silveira Ramos, Maisa Yoshimoto, Lucia Martelli
BACKGROUND: Individuals with apparently balanced translocations, often, show no clinical findings. However, in meiosis, translocations tend to cause errors on chromosome disjunction and the ones involving sex chromosomes have particular implications for the phenotype. Male carriers of balanced X-autosome translocations are almost invariably infertile due to interruption of the spermatogenesis, but the mechanism is not fully understood. CASE PRESENTATION: In this case report, we performed a combination of classical cytogenetics (G-banding), molecular cytogenetics (fluorescence in situ hybridization and X-chromosome inactivation study), and cytogenomics (microarray-based comparative genomic hybridization) techniques for characterization of an inherited (X;22) translocation in a family originally referred for infertility investigation...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27176606/implementation-of-non-invasive-prenatal-testing-by-semiconductor-sequencing-in-a-genetic-laboratory
#17
Annelies Dheedene, Tom Sante, Matthias De Smet, Jean-François Vanbellinghen, Bernard Grisart, Sarah Vergult, Sandra Janssens, Björn Menten
OBJECTIVES: To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS: We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow...
August 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27148332/advancing-eucalyptus-genomics-cytogenomics-reveals-conservation-of-eucalyptus-genomes
#18
Teresa Ribeiro, Ricardo M Barrela, Hélène Bergès, Cristina Marques, João Loureiro, Leonor Morais-Cecílio, Jorge A P Paiva
The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27066507/next-generation-sequencing-based-copy-number-analysis-reveals-low-prevalence-of-deletions-and-duplications-in-46-genes-associated-with-genetic-cardiomyopathies
#19
Ozge Ceyhan-Birsoy, Trevor J Pugh, Mark J Bowser, Elizabeth Hynes, Ashley L Frisella, Lisa M Mahanta, Matt S Lebo, Sami S Amr, Birgit H Funke
BACKGROUND: Diagnostic testing for genetic cardiomyopathies has undergone dramatic changes in the last decade with next generation sequencing (NGS) expanding the number of genes that can be interrogated simultaneously. Exon resolution copy number analysis is increasingly incorporated into routine diagnostic testing via cytogenomic arrays and more recently via NGS. While NGS is an attractive option for laboratories that have no access to array platforms, its higher false positive rate requires weighing the added cost incurred by orthogonal confirmation against the magnitude of the increase in diagnostic yield...
March 2016: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/27020032/spectrum-of-cytogenomic-abnormalities-revealed-by-array-comparative-genomic-hybridization-on-products-of-conception-culture-failure-and-normal-karyotype-samples
#20
Qinghua Zhou, Shen-Yin Wu, Katherine Amato, Autumn DiAdamo, Peining Li
Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples...
March 20, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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