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Anirban Roychowdhury, Sudip Samadder, Pijush Das, Sapan Mandloi, Sankar Addya, Chandraditya Chakraborty, Partha Sarathi Basu, Ranajit Mondal, Anup Roy, Saikat Chakrabarti, Susanta Roychoudhury, Chinmay Kumar Panda
BACKGROUND: CSCC is one of the most common cancer affecting women globally. Though it is caused by the infection of hrHPV but long latency period for malignant outcome in only a subset of hrHPV infected women indicates involvement of additional alterations, primarily CNVs. Here, we showed how CNVs played a crucial role in development of advanced tumors (stage III/IV) in Indian patients. METHODS: Initially, high-resolution CGH-SNP microarray analysis pointed out frequent CNVs followed by significantly altered genes...
September 15, 2016: Biochimica et Biophysica Acta
Egle Preiksaitiene, Eglė Benušienė, Zivile Ciuladaite, Vytautas Šliužas, Violeta Mikštienė, Vaidutis Kučinskas
OBJECTIVE: Neural tube defects belong to the second most common group of congenital anomalies, after heart defects, which can be diagnosed by prenatal ultrasonography. Rarely, neural tube defects can be associated with chromosomal abnormalities, including full and partial aneuploidies. We report a familial fetal case with syndromic spina bifida and discuss its association with partial 3q duplication and partial 5p deletion. MATERIALS AND METHODS: Clinical findings of three affected family members in two generations and two carriers of the balanced translocation are described...
June 2016: Taiwanese Journal of Obstetrics & Gynecology
Annely Richardson, Gerard T Berry, Cheryl Garganta, Mary-Alice Abbott
Hydroxysteroid 17-beta dehydrogenase type 10 (HSD10) deficiency (HSD10 disease) is a rare X-linked neurodegenerative condition caused by abnormalities in the HSD17B10 gene. A total of 10 mutations have been reported in the literature since 2000. Described phenotypes include a severe neonatal or progressive infantile form with hypotonia, choreoathetosis, seizures, cardiomyopathy, neurodegeneration, and death, as well as an attenuated form with variable regression. Here we present the second report of a c.194T>C (p...
June 14, 2016: JIMD Reports
J Perez-Escuredo, A Lopez-Hernandez, M Costales, F Lopez, S P Ares, B Vivanco, J L Llorente, M A Hermsen
BACKGROUND: Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumour related to occupational wood dust exposure. Few studies have described recurrent genetic changes on a genome-wide scale. The aim of this study was to obtain a high resolution map of recurrent genetic alterations in ITAC. MATERIAL AND METHODS: Copy number alterations were evaluated by microarray CGH and MLPA in 37 primary tumours. The results were correlated with pathological characteristics and clinical outcome...
September 2016: Rhinology
Kaihui Zhang, Fengling Song, Dongdong Zhang, Yong Liu, Haiyan Zhang, Ying Wang, Rui Dong, Yufeng Zhang, Yi Liu, Zhongtao Gai
Ring chromosome 3, r(3), is an extremely rare cytogenetic abnormality with clinical heterogeneity and only 12 cases reported in the literature. Here, we report a 1-year-old girl presenting distinctive facial features, developmental delay, and congenital heart defects with r(3) and a ∼10-Mb deletion of chromosome 3pterp25.3 (61,891-9,979,408) involving 42 known genes which was detected using G-banding karyotyping and CytoScan 750K-Array. The breakpoints in r(3) were mapped at 3p25.3 and 3q29. We also analyzed the available information on the clinical features of the reported cases with r(3) and 3p deletion syndrome in order to provide more valuable information of genotype-phenotype correlations...
2016: Cytogenetic and Genome Research
Karina S Cunha, Milena Simioni, Tarsis P Vieira, Vera L Gil-da-Silva-Lopes, Maria B Puzzi, Carlos E Steiner
Pigmentary mosaicism of Ito (PMI) is a skin abnormality often characterized by hypopigmentation of skin, following, in most cases, the Blaschko lines, usually associated with extracutaneous abnormalities, especially abnormalities of the central nervous system (CNS). It is suggested that this pattern arises from the presence and migration of two cell lineages in the ectoderm layer during the embryonic period and embryonic cell migration, with different gene expression profiles associated with pigmentation. Several types of chromosomal aberrations, with or without mosaicism, have been associated with this disorder...
March 2016: Genetics and Molecular Biology
Megan R Glassford, Jill A Rosenfeld, Alexa A Freedman, Michael E Zwick, Jennifer G Mulle
3q29 deletion syndrome is caused by a recurrent, typically de novo heterozygous 1.6 Mb deletion, but because incidence of the deletion is rare (1 in 30,000 births) the phenotype is not well described. To characterize the range of phenotypic manifestations associated with 3q29 deletion syndrome, we have developed an online registry ( for ascertainment of study subjects and phenotypic data collection via Internet-based survey instruments. We report here on data collected during the first 18 months of registry operation, from 44 patients...
April 2016: American Journal of Medical Genetics. Part A
Elisa Biamino, Eleonora Di Gregorio, Elga Fabia Belligni, Roberto Keller, Evelise Riberi, Marina Gandione, Alessandro Calcia, Cecilia Mancini, Elisa Giorgio, Simona Cavalieri, Patrizia Pappi, Flavia Talarico, Antonio M Fea, Silvia De Rubeis, Margherita Cirillo Silengo, Giovanni Battista Ferrero, Alfredo Brusco
Copy number variation (CNV) has been associated with a variety of neuropsychiatric disorders, including intellectual disability/developmental delay (ID/DD), autism spectrum disorder (ASD), and schizophrenia (SCZ). Often, individuals carrying the same pathogenic CNV display high clinical variability. By array-CGH analysis, we identified a novel familial 3q29 deletion (1.36 Mb), centromeric to the 3q29 deletion region, which manifests with variable expressivity. The deletion was identified in a 3-year-old girl diagnosed with ID/DD and autism and segregated in six family members, all affected by severe psychiatric disorders including schizophrenia, major depression, anxiety disorder, and personality disorder...
March 2016: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
Fátima Torres, Mafalda Barbosa, Patrícia Maciel
Neurodevelopmental disorders (NDs) encompass a spectrum of neuropsychiatric manifestations. Chromosomal regions 1q21.1, 3q29, 15q11.2, 15q13.3, 16p11.2, 16p13.1 and 22q11 harbour rare but recurrent CNVs that have been uncovered as being important risk factors for several of these disorders. These rearrangements may underlie a broad phenotypical spectrum, ranging from normal development, to learning problems, intellectual disability (ID), epilepsy and psychiatric diseases, such as autism spectrum disorders (ASDs) and schizophrenia (SZ)...
February 2016: Journal of Medical Genetics
Alex V Kotlar, Kristina B Mercer, Michael E Zwick, Jennifer G Mulle
Schizophrenia research has undergone a recent transformation. By leveraging large sample sizes, genome-wide association studies of common genetic variants have approximately tripled the number of candidate genetic loci. Rare variant studies have identified copy number variants that are schizophrenia risk loci. Among these, the 3q29 microdeletion is now known to be the single largest schizophrenia risk factor. Next-generation sequencing studies are increasingly used for rare variant association testing, and have already facilitated identification of large effect alleles...
December 2015: European Journal of Medical Genetics
Debopam Samanta
No abstract text is available yet for this article.
September 2016: Acta Neurologica Belgica
A Uezato, N Yamamoto, Y Iwayama, S Hiraoka, E Hiraaki, A Umino, E Haramo, M Umino, T Yoshikawa, T Nishikawa
The human discs, large homolog 1 gene (DLG1) is mapped to the schizophrenia-susceptibility locus 3q29, and it encodes a scaffold protein that interacts with the N-methyl-D-aspartate receptor presumably dysregulated in schizophrenia. In the current study, we have newly identified a splicing variant of DLG1, which is transcribed from an unreported 95-base-pair exon (exon 3b) and is labeled 3b(+). We investigated the mRNA expression of 3b(+) in the post-mortem dorsolateral prefrontal cortices of patients with psychiatric disorders, obtained from The Stanley Medical Research Institute, and examined the potential association of the expression with the genotype of the single-nucleotide polymorphism (SNP) rs3915512 located within exon 3b...
2015: Translational Psychiatry
Stephan J Sanders, Xin He, A Jeremy Willsey, A Gulhan Ercan-Sencicek, Kaitlin E Samocha, A Ercument Cicek, Michael T Murtha, Vanessa H Bal, Somer L Bishop, Shan Dong, Arthur P Goldberg, Cai Jinlu, John F Keaney, Lambertus Klei, Jeffrey D Mandell, Daniel Moreno-De-Luca, Christopher S Poultney, Elise B Robinson, Louw Smith, Tor Solli-Nowlan, Mack Y Su, Nicole A Teran, Michael F Walker, Donna M Werling, Arthur L Beaudet, Rita M Cantor, Eric Fombonne, Daniel H Geschwind, Dorothy E Grice, Catherine Lord, Jennifer K Lowe, Shrikant M Mane, Donna M Martin, Eric M Morrow, Michael E Talkowski, James S Sutcliffe, Christopher A Walsh, Timothy W Yu, David H Ledbetter, Christa Lese Martin, Edwin H Cook, Joseph D Buxbaum, Mark J Daly, Bernie Devlin, Kathryn Roeder, Matthew W State
Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing...
September 23, 2015: Neuron
I Quintela, F Barros-Angueira, L Perez-Gay, D Dacruz, M Castro-Gago, A Carracedo, J Eiris-Punal
INTRODUCTION: The 3q29 microdeletion and microduplication syndromes are characterised by a marked phenotypic heterogeneity, and delayed development and a mild-moderate degree of intellectual disability are the most frequent clinical manifestations. CASE REPORTS: Two patients with reciprocal chromosomal aberrations in the 3q29 region. The patient with 3q29 microdeletion presented learning disabilities, borderline microcephaly, mild facial dysmorphism, attentional deficit and impulsiveness, and anxious and obsessive traits...
September 16, 2015: Revista de Neurologia
A J Novak, Y W Asmann, M J Maurer, C Wang, S L Slager, L S Hodge, M Manske, T Price-Troska, Z-Z Yang, M T Zimmermann, G S Nowakowski, S M Ansell, T E Witzig, E McPhail, R Ketterling, A L Feldman, A Dogan, B K Link, T M Habermann, J R Cerhan
Lack of remission or early relapse remains a major clinical issue in diffuse large B-cell lymphoma (DLBCL), with 30% of patients failing standard of care. Although clinical factors and molecular signatures can partially predict DLBCL outcome, additional information is needed to identify high-risk patients, particularly biologic factors that might ultimately be amenable to intervention. Using whole-exome sequencing data from 51 newly diagnosed and immunochemotherapy-treated DLBCL patients, we evaluated the association of somatic genomic alterations with patient outcome, defined as failure to achieve event-free survival at 24 months after diagnosis (EFS24)...
2015: Blood Cancer Journal
David Nauen, Lisa Haley, Ming-Tseh Lin, Arie Perry, Caterina Giannini, Peter C Burger, Fausto J Rodriguez
Oligodendroglioma represents a distinctive neoplasm in adults but similar neoplasms occur rarely in children. We studied 20 cases of pediatric oligodendroglioma by SNP array (median age 9 years, range 1-19; 15 grade II and 5 grade III). Cytogenetic abnormalities were present in 8 (53%) grade II and all five anaplastic oligodendrogliomas. Most changes were in the form of deletion and copy neutral loss of heterozygosity (LOH). The most common abnormality was 1p deletion (n = 5). Whole arm 1p19q co-deletion was present in three cases from adolescent patients and 9p loss in 3, including one low-grade oligodendroglioma with CDKN2A homozygous deletion...
March 2016: Brain Pathology
George Kirov
Over the last few years at least 11 copy number variations (CNVs) have been shown convincingly to increase risk to developing schizophrenia: deletions at 1q21.1, NRXN1, 3q29, 15q11.2, 15q13.3 and 22q11.2, and duplications at 1q21.1, 7q11.23, 15q11.2-q13.1, 16p13.1 and proximal 16p11.2. They are very rare, found cumulatively in 2.4% of patients with schizophrenia and in only 0.5% of controls. They all increase risk for other neurodevelopmental disorders, such as developmental delay and autism spectrum disorders, where they are found at higher rates (3...
October 15, 2015: Human Molecular Genetics
Erica J Childs, Evelina Mocci, Daniele Campa, Paige M Bracci, Steven Gallinger, Michael Goggins, Donghui Li, Rachel E Neale, Sara H Olson, Ghislaine Scelo, Laufey T Amundadottir, William R Bamlet, Maarten F Bijlsma, Amanda Blackford, Michael Borges, Paul Brennan, Hermann Brenner, H Bas Bueno-de-Mesquita, Federico Canzian, Gabriele Capurso, Giulia M Cavestro, Kari G Chaffee, Stephen J Chanock, Sean P Cleary, Michelle Cotterchio, Lenka Foretova, Charles Fuchs, Niccola Funel, Maria Gazouli, Manal Hassan, Joseph M Herman, Ivana Holcatova, Elizabeth A Holly, Robert N Hoover, Rayjean J Hung, Vladimir Janout, Timothy J Key, Juozas Kupcinskas, Robert C Kurtz, Stefano Landi, Lingeng Lu, Ewa Malecka-Panas, Andrea Mambrini, Beatrice Mohelnikova-Duchonova, John P Neoptolemos, Ann L Oberg, Irene Orlow, Claudio Pasquali, Raffaele Pezzilli, Cosmeri Rizzato, Amethyst Saldia, Aldo Scarpa, Rachael Z Stolzenberg-Solomon, Oliver Strobel, Francesca Tavano, Yogesh K Vashist, Pavel Vodicka, Brian M Wolpin, Herbert Yu, Gloria M Petersen, Harvey A Risch, Alison P Klein
Pancreatic cancer is the fourth leading cause of cancer death in the developed world. Both inherited high-penetrance mutations in BRCA2 (ref. 2), ATM, PALB2 (ref. 4), BRCA1 (ref. 5), STK11 (ref. 6), CDKN2A and mismatch-repair genes and low-penetrance loci are associated with increased risk. To identify new risk loci, we performed a genome-wide association study on 9,925 pancreatic cancer cases and 11,569 controls, including 4,164 newly genotyped cases and 3,792 controls in 9 studies from North America, Central Europe and Australia...
August 2015: Nature Genetics
Julio Rodriguez-Lopez, Noa Carrera, Manuel Arrojo, Jorge Amigo, Beatriz Sobrino, Mario Páramo, Eduardo Paz, Santiago Agra, Ramón Ramos-Ríos, Julio Brenlla, Ángel Carracedo, Javier Costas
Several recurrent copy number variants (CNVs) increasing risk to neuropsychiatric diseases have been identified in recent years. They show variable clinical expressivity, being associated with different disorders, and incomplete penetrance. However, due to its very low frequency, the full variety of clinical outcomes associated with each one of these CNVs is unknown. Current methods for detection of CNVs are labor intensive, expensive or not suitable for high throughput analysis. Quantitative interspecies competitive PCR linked to variant minisequencing and detection by mass-spectrometry may overcome these limitations...
May 20, 2015: Clinica Chimica Acta; International Journal of Clinical Chemistry
Valentina Guida, Lorenzo Sinibaldi, Mario Pagnoni, Laura Bernardini, Sara Loddo, Katia Margiotti, Maria Cristina Digilio, Maria Teresa Fadda, Bruno Dallapiccola, Giorgio Iannetti, De Luca Alessandro
Oculo auriculo vertebral spectrum (OAVS; OMIM 164210) is a clinically and genetically heterogeneous disorder originating from an abnormal development of the first and second branchial arches. Main clinical characteristics include defects of the aural, oral, mandibular, and vertebral development. Anomalies of the cardiac, pulmonary, renal, skeletal, and central nervous systems have also been described. We report on a 25-year-old male showing a spectrum of clinical manifestations fitting the OAVS diagnosis: hemifacial microsomia, asymmetric mandibular hypoplasia, preauricular pits and tags, unilateral absence of the auditory meatus, dysgenesis of the inner ear and unilateral microphthalmia...
April 2015: American Journal of Medical Genetics. Part A
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