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Qiping Hu, Hongyan Chai, Wei Shu, Peining Li
Background: Constitutional ring chromosomes are rare orphan chromosomal disorders. Ring chromosome syndrome featuring growth retardation and mild to intermediate intellectual disability is likely caused by the dynamic behavior of ring chromosome through cell cycles. Chromosomal and regional specific phenotypes likely result from segmental losses and gains during the ring formation. Although recent applications of genomic copy number and sequencing analyses revealed various ring chromosome structures from an increasing number of case studies, there was no organized effort for compilating and curating cytogenomic and clinical finding for ring chromosomes...
2018: Molecular Cytogenetics
Radka Symonová, W Mike Howell
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species...
February 14, 2018: Genes
Melissa Stosic, Brynn Levy, Ronald Wapner
Chromosomal microarray analysis (CMA) identifies microdeletions and duplications undetected on karyotype analysis. Copy number variants (CNVs) occur in 1% to 1.7% of all pregnancies, with clinical implications. All women undergoing invasive testing for routine indications should be offered microarray. Clinically significant CNVs are seen in approximately 6% of pregnancies with ultrasound anomalies, making CMAs the current standard of cytogenomic analysis. Clinicians should be familiar with different technologies and laboratory reporting practices...
March 2018: Obstetrics and Gynecology Clinics of North America
Gloria T Haskell, Yajuan J Liu, Hui Chen, Beiyun Chen, Reid G Meyer, Jason A Yuhas, Katherine B Geiersbach
Objectives: To develop and test an integrated approach to human epidermal growth factor receptor 2 (HER2) copy number analysis in breast cancer using in situ hybridization (ISH) and cytogenomic microarray (CMA). Methods: CMA was performed on four clinical breast cancer samples with nonclassical patterns of HER2 ISH results. Integrated analysis was performed by correlating the data from pathology review, ISH, and CMA. Results: Integrated analysis provided a more comprehensive view of the genomic copy number landscape that informed HER2 copy number analysis, but ISH provided essential data in all cases...
January 29, 2018: American Journal of Clinical Pathology
Silvia Bragagnolo, Mileny E S Colovati, Malu Z Souza, Anelise G Dantas, Maria F F de Soares, Maria I Melaragno, Ana B Perez
The oculoauriculovertebral spectrum (OAVS) is characterized by anomalies involving the development of the first and second pharyngeal arches during the embryonic period. The phenotype is highly heterogeneous, involving ears, eyes, face, neck, and other systems and organs. There is no agreement in the literature for the minimum phenotypic inclusion criteria, but the primary phenotype involves hemifacial microsomia with facial asymmetry and microtia. Most cases are sporadic and the etiology of this syndrome is not well known...
January 25, 2018: American Journal of Medical Genetics. Part A
Jennifer Reiner, Laura Pisani, Wanqiong Qiao, Ram Singh, Yao Yang, Lisong Shi, Wahab A Khan, Robert Sebra, Ninette Cohen, Arvind Babu, Lisa Edelmann, Ethylin Wang Jabs, Stuart A Scott
Bardet-Biedl syndrome (BBS) is a recessive disorder characterized by heterogeneous clinical manifestations, including truncal obesity, rod-cone dystrophy, renal anomalies, postaxial polydactyly, and variable developmental delays. At least 20 genes have been implicated in BBS, and all are involved in primary cilia function. We report a 1-year-old male child from Guyana with obesity, postaxial polydactyly on his right foot, hypotonia, ophthalmologic abnormalities, and developmental delay, which together indicated a clinical diagnosis of BBS...
2018: NPJ Genomic Medicine
Sarah M Choi, Rajan Dewar, Patrick W Burke, Lina Shao
Partial tandem duplication (PTD) of the KMT2A (MLL) gene is a poor prognostic factor in acute myeloid leukemia, but its significance in the context of myelodysplastic syndrome (MDS) is unknown. Here, we used cytogenomic array to identify MLL-PTD in a group of MDS patients and compared their clinicopathologic characteristics with a cohort of high-risk MDS patients without MLL-PTD. We show that MLL-PTD defines a subset of MDS characterized by high blast count, normal karyotype, and extremely poor prognosis exceeding that of non-MLL-PTD high risk MDS, including those with complex karyotype...
January 19, 2018: Haematologica
Taboada Xoana, Rey Magalí, Bouza Carmen, Viñas Ana
Repetitive DNA plays a fundamental role in the organization, size and evolution of eukaryotic genomes. The sequencing of the turbot revealed a small and compact genome, as in all flatfish studied to date. The assembly of repetitive regions is still incomplete because it is difficult to correctly identify their position, number and array. The combination of classical cytogenetic techniques along with high quality sequencing is essential to increase the knowledge of the structure and composition of these sequences and, thus, of the structure and function of the whole genome...
December 12, 2017: Gene
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
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 20, 2017: American Journal of Clinical Pathology
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
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
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 postpolyploid 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 intertribal hybridization between ancestors of Crucihimalayeae (n = 8; maternal genome) and Smelowskieae (n = 7; paternal genome), both native to the Northern Hemisphere...
November 2017: Molecular Ecology
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
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
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
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
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
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
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
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