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2p16 deletion

Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Maren Kaufmann, Roderick A F MacLeod, Hans G Drexler
To identify novel cancer-related genes targeted by copy number alterations, we performed genomic profiling of T-cell acute lymphoblastic leukemia (T-ALL) cell lines. In 3/8, we identified a shared deletion at chromosomal position 2p16.3-p21. Within the minimally deleted region, we recognized several candidate tumor suppressor (TS) genes, including FBXO11 and FOXN2. An additional deletion at chromosome 14q23.2-q32.11 included FOXN3, highlighting this class of FOX genes as potential TS. Quantitative expression analyses of FBXO11, FOXN2, and FOXN3 confirmed reduced transcript levels in the identified cell lines...
January 31, 2017: Leukemia & Lymphoma
Aggeliki Dimopoulos, Robert J Sicko, Denise M Kay, Shannon L Rigler, Charlotte M Druschel, Michele Caggana, Marilyn L Browne, Ruzong Fan, Paul A Romitti, Lawrence C Brody, James L Mills
BACKGROUND: Hypoplastic right heart syndrome (HRHS) is a rare congenital defect characterized by underdevelopment of the right heart structures commonly accompanied by an atrial septal defect. Familial HRHS reports suggest genetic factor involvement. We examined the role of copy number variants (CNVs) in HRHS. METHODS: We genotyped 32 HRHS cases identified from all New York State live births (1998-2005) using Illumina HumanOmni2.5 microarrays. CNVs were called with PennCNV and prioritized if they were ≥20 Kb, contained ≥10 SNPs and had minimal overlap with CNVs from in-house controls, the Database of Genomic Variants, HapMap3, and Childrens Hospital of Philadelphia database...
December 23, 2016: Birth Defects Research. Part A, Clinical and Molecular Teratology
Haiping Dai, Stefan Ehrentraut, Stefan Nagel, Sonja Eberth, Claudia Pommerenke, Wilhelm G Dirks, Robert Geffers, Srilaxmi Kalavalapalli, Maren Kaufmann, Corrina Meyer, Silke Faehnrich, Suning Chen, Hans G Drexler, Roderick A F MacLeod
Primary mediastinal B-Cell lymphoma (PMBL) is a recently defined entity comprising ~2-10% non-Hodgkin lymphomas (NHL). Unlike most NHL subtypes, PMBL lacks recurrent gene rearrangements to serve as biomarkers or betray target genes. While druggable, late chemotherapeutic complications warrant the search for new targets and models. Well characterized tumor cell lines provide unlimited material to serve as preclinical resources for verifiable analyses directed at the discovery of new biomarkers and pathological targets using high throughput microarray technologies...
2015: PloS One
Mathew Wallis, Yoshinori Tsurusaki, Trent Burgess, Peter Borzi, Naomichi Matsumoto, Noriko Miyake, Deanna True, Chirag Patel
We describe a male patient with dual genetic diagnoses of atypical hand-foot-genital syndrome (HFGS) and developmental delay. The proband had features of HFGS that included bilateral vesicoureteric junction obstruction with ectopic ureters, brachydactyly of various fingers and toes, hypoplastic thenar eminences, and absent nails on both 4th toes and right 5th toe. The atypical features of HFGS present were bilateral hallux valgus malformations and bilateral preaxial polydactyly of the hands. Chromosomal microarray analysis identified a de novo 0...
March 2016: American Journal of Medical Genetics. Part A
Linh T T Duong, Louise K Hoeffding, Kirsten B Petersen, Charlotte D Knudsen, Johan H Thygesen, Laura L Klitten, Niels Tommerup, Andrés Ingason, Thomas Werge
CNVs spanning the 2p16.3 (NRXN1) and the 15q11.2 gene rich region have been associated with severe neuropsychiatric disorders including schizophrenia. Recently, studies have also revealed that CNVs in non-coding regions play an essential role in genomic variability in addition to disease susceptibility. In this study, we describe a family affected by a wide range of psychiatric disorders including early onset schizophrenia, schizophreniform disorder, and affective disorders. Microarray analysis identified two rare deletions immediately upstream of the NRXN1 gene affecting the non-coding mRNA AK127244 in addition to the pathogenic 15q11...
December 2015: European Journal of Medical Genetics
Tugce B Balci, Sarah L Sawyer, Jorge Davila, Peter Humphreys, David A Dyment
Microdeletions of 2p15-16.1 have been reported in 15 patients with a recognizable syndrome of dysmorphic features, intellectual disability and microcephaly. Facial features include telecanthus, short palpebral fissures, epicanthal folds, a broad nasal root, smooth and long philtrum and large ears. Brain malformations can be observed in this syndrome and include hypoplasia of the corpus callosum and a simplified cortical gyral pattern. Case reports have narrowed the critical region of the neurodevelopmental phenotype to a region that spans the B-cell CLL/lymphoma 11A (BCL11A) gene...
June 2015: European Journal of Medical Genetics
Anne-Claude Tabet, Alain Verloes, Marion Pilorge, Elsa Delaby, Richard Delorme, Gudrun Nygren, Françoise Devillard, Marion Gérard, Sandrine Passemard, Delphine Héron, Jean-Pierre Siffroi, Aurelia Jacquette, Andrée Delahaye, Laurence Perrin, Céline Dupont, Azzedine Aboura, Pierre Bitoun, Mary Coleman, Marion Leboyer, Christopher Gillberg, Brigitte Benzacken, Catalina Betancur
BACKGROUND: Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment...
2015: Molecular Autism
Marina Viñas-Jornet, Susanna Esteba-Castillo, Elisabeth Gabau, Núria Ribas-Vidal, Neus Baena, Joan San, Anna Ruiz, Maria Dolors Coll, Ramon Novell, Miriam Guitart
Deletions in the 2p16.3 region that includes the neurexin (NRXN1) gene are associated with intellectual disability and various psychiatric disorders, in particular, autism and schizophrenia. We present three unrelated patients, two adults and one child, in whom we identified an intragenic 2p16.3 deletion within the NRXN1 gene using an oligonucleotide comparative genomic hybridization array. The three patients presented dual diagnosis that consisted of mild intellectual disability and autism and bipolar disorder...
November 2014: Molecular Genetics & Genomic Medicine
Frederic Esclassan, Jennifer Francois, Keith G Phillips, Sally Loomis, Gary Gilmour
Neurexins are neuronal presynaptic proteins that play a key role in mediation of synapse formation. Heterozygous partial deletions in the neurexin-1 gene (NRXN1, 2p16.3) have been observed in autism spectrum disorder (ASD) patients. NRXN1-α knockout (KO) mice present behavioral impairments that resemble some of the core ASD symptoms of social impairment and inflexibility/stereotypy. At present, a thorough assessment of cognitive function has yet to be completed. Rats, containing a biallelic deletion of the NRNX1-α gene on a Sprague Dawley background were compared to littermate wild types across a range of tasks designed to test functional domains disrupted in ASD and other neurodevelopmental disorders, including sensory perception (prepulse inhibition), attention (latent inhibition), associative learning (instrumental and Pavlovian conditioning), and memory (rewarded alternation T maze and spatial discrimination)...
February 2015: Behavioral Neuroscience
Jaime Imitola, Diana Walleigh, Carol E Anderson, Reena Jethva, Karen S Carvalho, Agustin Legido, Divya S Khurana
A 7-year-old child presented with atypical absence epilepsy. He also had autism and severe cognitive deficit. As part of his diagnostic workup, a chromosomal microarray analysis was performed, which showed novel biallelic deletions in the neurexin 1 gene (NRXN1). His fraternal twin sister, who also had autism and cognitive impairment, was subsequently found to have the same biallelic deletions. Deletions included a 272-282kb loss at band 2p16.3 in one allele and a smaller 135-174-kb loss on the second allele...
June 2014: Seminars in Pediatric Neurology
Milena Crippa, Ilaria Bestetti, Mario Perotti, Chiara Castronovo, Silvia Tabano, Chiara Picinelli, Guido Grassi, Lidia Larizza, Angela Ida Pincelli, Palma Finelli
BACKGROUND: Trichorhinophalangeal syndrome (TRPS) is a rare autosomal dominant genetic disorder characterised by distinctive craniofacial and skeletal abnormalities. TRPS is generally associated with mutations in the TRPS1 gene at 8q23.3 or microdeletions of the 8q23.3-q24.11 region. However, three deletions affecting the same chromosome region and a familial translocation t(8;13) co-segregating with TRPS, which do not encompass or disrupt the TRPS1 gene, have been reported. A deregulated expression of TRPS1 has been hypothesised as cause of the TRPS phenotype of these patients...
May 2, 2014: BMC Medical Genetics
Bérengère Dadone, Damien Ambrosetti, Xavier Carpentier, Valérie Duranton-Tanneur, Fanny Burel-Vandenbos, Jean Amiel, Florence Pedeutour
Metanephric adenomas (MAs) are rare benign tumors that may be difficult to recognize. Specific genetic anomalies might aid in diagnosis, but genomic data are limited and conflicting. Consistent mutations of the BRAF gene have been recently reported in MAs and could become useful as a discriminative marker among renal tumors. We report here a case of MA, showing both a BRAF V600E mutation and a segmental loss within bands 2p16 and 2p24 as the sole quantitative genomic anomaly. We compared the borders and size of the deleted region in our case to those of five cases of MAs previously reported...
September 2013: Cancer Genetics
M Palacín, C Mora, J Chillarón, M J Calonge, R Estévez, D Torrents, X Testar, A Zorzano, V Nunes, J Purroy, X Estivill, P Gasparini, L Bisceglia, L Zelante
The cDNAs of mammalian amino acid transporters already identified could be grouped into four families. One of these protein families is composed of the protein rBAT and the heavy chain of the cell surface antigen 4F2 (4F2hc). The cRNAs of rBAT and 4F2hc induce amino acid transport activity via systems b(0,+) -like and y(+)L -like inXenopus oocytes respectively. Surprisingly, neither rBAT nor 4F2hc is very hydrophobic, and they seem to be unable to form a pore in the plasma membrane. This prompted the hypothesis that rBAT and 4F2hc are subunits or modulators of the corresponding amino acid transporters...
June 1996: Amino Acids
Denise Feierabend, Jan Walter, Susanne Grube, Christian Herbold, Christian Beetz, Rolf Kalff, Christian Ewald
Gain of (proto-)oncogenes and loss or promoter hypermethylation of tumor suppressor genes (TSGs) play essential roles in tumorigenesis. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) allows simultaneous detection of both these alterations. MS-MLPA was performed on 20 medulloblastoma samples (n = 12 cryoconserved; n = 8 formalin-fixed paraffin-embedded, FFPE) in order to screen for copy number changes in 77 unselected TSGs and (proto-)oncogenes as well as for promoter hypermethylation in a subset of 33 TSGs...
January 2014: Journal of Neuro-oncology
Hannah Mary Grayton, Markus Missler, David Andrew Collier, Cathy Fernandes
BACKGROUND: Copy number variants have emerged as an important genomic cause of common, complex neurodevelopmental disorders. These usually change copy number of multiple genes, but deletions at 2p16.3, which have been associated with autism, schizophrenia and mental retardation, affect only the neurexin 1 gene, usually the alpha isoform. Previous analyses of neurexin 1α (Nrxn1α) knockout (KO) mouse as a model of these disorders have revealed impairments in synaptic transmission but failed to reveal defects in social behaviour, one of the core symptoms of autism...
2013: PloS One
Miroslava Hancarova, Martina Simandlova, Jana Drabova, Katrin Mannik, Ants Kurg, Zdenek Sedlacek
The 2p15-p16.1 microdeletion syndrome is a novel, rare disorder characterized by developmental delay, intellectual disability, microcephaly, growth retardation, facial abnormalities, and other medical problems. We report here on an 11-year-old female showing clinical features consistent with the syndrome and carrying a de novo 0.45 Mb long deletion of the paternally derived 2p16.1 allele. The deleted region contains only three protein-coding RefSeq genes, BCL11A, PAPOLG, and REL, and one long non-coding RNA gene FLJ16341...
April 2013: American Journal of Medical Genetics. Part A
Mindy Preston Dabell, Jill A Rosenfeld, Patricia Bader, Luis F Escobar, Dima El-Khechen, Stephanie E Vallee, Mary Beth Palko Dinulos, Cynthia Curry, Jamie Fisher, Raymond Tervo, Mark C Hannibal, Kiana Siefkas, Philip R Wyatt, Lauren Hughes, Rosemarie Smith, Sara Ellingwood, Yves Lacassie, Tracy Stroud, Sandra A Farrell, Pedro A Sanchez-Lara, Linda M Randolph, Dmitriy Niyazov, Cathy A Stevens, Cheri Schoonveld, David Skidmore, Sara MacKay, Judith H Miles, Manikum Moodley, Adam Huillet, Nicholas J Neill, Jay W Ellison, Blake C Ballif, Lisa G Shaffer
Deletions at 2p16.3 involving exons of NRXN1 are associated with susceptibility for autism and schizophrenia, and similar deletions have been identified in individuals with developmental delay and dysmorphic features. We have identified 34 probands with exonic NRXN1 deletions following referral for clinical microarray-based comparative genomic hybridization. To more firmly establish the full phenotypic spectrum associated with exonic NRXN1 deletions, we report the clinical features of 27 individuals with NRXN1 deletions, who represent 23 of these 34 families...
April 2013: American Journal of Medical Genetics. Part A
Karla Bermudez-Wagner, Linda J B Jeng, Anne M Slavotinek, Erica F Sanford
No abstract text is available yet for this article.
January 2013: Clinical Dysmorphology
Jennifer Edelmann, Karlheinz Holzmann, Florian Miller, Dirk Winkler, Andreas Bühler, Thorsten Zenz, Lars Bullinger, Michael W M Kühn, Andreas Gerhardinger, Johannes Bloehdorn, Ina Radtke, Xiaoping Su, Jing Ma, Stanley Pounds, Michael Hallek, Peter Lichter, Jan Korbel, Raymonde Busch, Daniel Mertens, James R Downing, Stephan Stilgenbauer, Hartmut Döhner
To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism-array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q...
December 6, 2012: Blood
Maarten J Van Den Bossche, Mandy Johnstone, Mojca Strazisar, Benjamin S Pickard, Dirk Goossens, An-Sofie Lenaerts, Sonia De Zutter, Annelie Nordin, Karl-Fredrik Norrback, Julien Mendlewicz, Daniel Souery, Peter De Rijk, Bernard G Sabbe, Rolf Adolfsson, Douglas Blackwood, Jurgen Del-Favero
From a number of genome-wide association studies it was shown that de novo and/or rare copy number variants (CNVs) are found at an increased frequency in neuropsychiatric diseases. In this study we examined the prevalence of CNVs in six genomic regions (1q21.1, 2p16.3, 3q29, 15q11.2, 15q13.3, and 16p11.2) previously implicated in neuropsychiatric diseases. Hereto, a cohort of four neuropsychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, and intellectual disability) and control individuals from three different populations was used in combination with Multilpex Amplicon Quantifiaction (MAQ) assays, capable of high resolution (kb range) and custom-tailored CNV detection...
October 2012: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
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