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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
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
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
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
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
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
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
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...
June 25, 2016: Cytotechnology
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
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
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
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
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
Fabíola Araújo Dos Santos, Diego Ferreira Marques, Maria Leandra Terencio, Eliana Feldberg, Luís Reginaldo R Rodrigues
Hoplias malabaricus is a common fish species occurring in white, black and clear water rivers of the Amazon basin. Its large distribution across distinct aquatic environments can pose stressful conditions for dispersal and creates possibilities for the emergence of local adaptive profiles. We investigated the chromosomal localization of repetitive DNA markers (constitutive heterochromatin, rDNA and the transposable element REX-3) in populations from the Amazonas river (white water), the Negro river (black water) and the Tapajós river (clear water), in order to address the variation/association of cytogenomic features and environmental conditions...
March 2016: Genetics and Molecular Biology
Milena Simioni, Isabella Lopes Monlleó, Camila M Costa de Queiroz, Ilanna Fragoso Peixoto Gazzaneo, Diogo L Lima do Nascimento, Reinaldo Luna de Omena Filho, Cristiane Santos da Cruz Piveta, Maricilda Palandi de Mello, Vera L Gil-da-Silva-Lopes
This is the first molecular characterization of a female XY patient with an Xp duplication due to an X;22 translocation. Array CGH detected a copy number gain of ∼36 Mb in the Xp22.33p21.1 region involving 150 genes. Clinical and molecular studies described in the literature have suggested DAX1 duplication as the major cause responsible for a sex reversal phenotype. Additionally, the interaction between genes and their possible role in clinical features are presented to support the discussion on genotype-phenotype correlation in cases of syndromic XY gonadal dysgenesis...
2016: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
Anelisa Gollo Dantas, Adriana Bortolai, Mariana Moysés-Oliveira, Sylvia Takeno Herrero, Adriana Azoubel Antunes, Beatriz Tavares Costa-Carvalho, Vera Ayres Meloni, Maria Isabel Melaragno
We report on a patient conceived via in vitro fertilization (IVF) with a 22q11.2 deletion due to an unusual unbalanced translocation involving chromosomes 6 and 22 in a karyotype with 45 chromosomes. Cytogenomic studies showed that the patient has a 3.3-Mb deletion of chromosome 22q and a 0.4-Mb deletion of chromosome 6p, which resulted in haploinsufficiency of the genes responsible for the 22q11.2 deletion syndrome and also of the IRF4 gene, a member of the interferon regulatory factor family of transcription factors, which is expressed in the immune system cells...
February 2016: Molecular Syndromology
Krzysztof Szczałuba, Anna Jakubiuk-Tomaszuk, Marta Kędzior, Joanna Bernaciak, Jolanta Zdrodowska, Wiesław Kurzątkowski, Marek Radkowski, Urszula Demkow
Identification of submicroscopic chromosomal aberrations, as a cause of structural malformations, is currently performed by MLPA (multiplex ligation-dependent probe amplification) or array CGH (array comparative genomic hybridization) techniques. The aim of this study was the evaluation of diagnostic usefulness of MLPA and array CGH in patients with congenital malformations or abnormalities (at least one major or minor birth defect, including dysmorphism) with or without intellectual disability or developmental delay and the optimization of genetic counseling in the context of the results obtained...
2016: Advances in Experimental Medicine and Biology
Marilyn M Li, Federico A Monzon, Jaclyn A Biegel, Vaidehi Jobanputra, Jennifer J Laffin, Brynn Levy, Annette Leon, Patricia Miron, Michael R Rossi, Gokce Toruner, Karla Alvarez, Gregory Doho, Margaret J Dougherty, Xiaofeng Hu, Shera Kash, Deanna Streck, Iya Znoyko, Jill M Hagenkord, Daynna J Wolff
Cytogenomic microarray analysis (CMA) offers high resolution, genome-wide copy number information and is widely used in clinical laboratories for diagnosis of constitutional abnormalities. The Cancer Genomics Consortium (CGC) conducted a multiplatform, multicenter clinical validation project to compare the reliability and inter- and intralaboratory reproducibility of this technology for clinical oncology applications. Four specimen types were processed on three different microarray platforms-from Affymetrix, Agilent, and Illumina...
November 2015: Cancer Genetics
Roberto Ferreira Artoni, Jonathan Pena Castro, Uedson Pereira Jacobina, Paulo Augusto Lima-Filho, Gideão Wagner Werneck Félix da Costa, Wagner Franco Molina
Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes...
2015: TheScientificWorldJournal
Yingying Qin, Xue Jiao, Joe Leigh Simpson, Zi-Jiang Chen
BACKGROUND: Primary ovarian insufficiency (POI) is characterized by marked heterogeneity, but with a significant genetic contribution. Identifying exact causative genes has been challenging, with many discoveries not replicated. It is timely to take stock of the field, outlining the progress made, framing the controversies and anticipating future directions in elucidating the genetics of POI. METHODS: A search for original articles published up to May 2015 was performed using PubMed and Google Scholar, identifying studies on the genetic etiology of POI...
November 2015: Human Reproduction Update
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