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https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#1
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#2
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#3
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327142/exome-sequencing-identified-rare-variants-in-genes-hspg2-and-atp2b4-in-a-family-segregating-developmental-dysplasia-of-the-hip
#4
Sulman Basit, Alia M Albalawi, Essa Alharby, Khalid I Khoshhal
BACKGROUND: Developmental dysplasia of the hip (DDH) is a common pathological condition of the musculoskeletal system in infants which results in a congenital and developmental malformation of the hip joint. DDH is a spectrum of pathologies affecting the infant hip ranging from asymptomatic subtle radiographic signs through mild instability to frank dislocations with acetabular dysplasia. A Saudi family with three affected individuals with DDH was identified and genetic analysis was performed to detect the possible genetic defect(s) underlying DDH in the affected members of the family...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28325361/warthin-like-papillary-renal-cell-carcinoma-clinicopathologic-morphologic-immunohistochemical-and-molecular-genetic-analysis-of-11-cases
#5
Faruk Skenderi, Monika Ulamec, Tomas Vanecek, Petr Martinek, Reza Alaghehbandan, Maria Pane Foix, Iva Babankova, Delia Perez Montiel, Isabel Alvarado-Cabrero, Marian Svajdler, Pavol Dubinský, Dana Cempirkova, Michal Pavlovsky, Semir Vranic, Ondrej Daum, Ondrej Ondic, Kristyna Pivovarcikova, Kvetoslava Michalova, Milan Hora, Pavla Rotterova, Adela Stehlikova, Martin Dusek, Michal Michal, Ondrej Hes
Oncocytic papillary renal cell carcinoma (PRCC) is a distinct subtype of PRCC, listed as a possible new variant of PRCC in the 2016 WHO classification. It is composed of papillae aligned by large single-layered eosinophilic cells showing linearly arranged oncocytoma-like nuclei. We analyzed clinicopathologic, morphologic, immunohistochemical and molecular-genetic characteristics of 11 oncocytic PRCCs with prominent tumor lymphocytic infiltrate, morphologically resembling Warthin's tumor. The patients were predominantly males (8/11, 73%), with an average age of 59years (range 14-76), and a mean tumor size of 7cm (range 1-22cm)...
April 2017: Annals of Diagnostic Pathology
https://www.readbyqxmd.com/read/28324114/novel-25-kb-deletion-of-mertk-causes-retinitis-pigmentosa-with-severe-progression
#6
Daniel R Evans, Jane S Green, Gordon J Johnson, Jeremy Schwartzentruber, Jacek Majewski, Chandree L Beaulieu, Wen Qin, Christian R Marshall, Tara A Paton, Nicole M Roslin, Andrew D Paterson, Somayyeh Fahiminiya, Justin French, Kym M Boycott, Michael O Woods
Purpose: Retinitis pigmentosa (RP) describes a complex group of inherited retinal dystrophies with almost 300 reported genes and loci. We investigated the genetic etiology of autosomal recessive RP (arRP) in a large kindred with 5 affected family members, who reside on the island of Newfoundland, Canada. Methods: Genetic linkage analysis was performed on 12 family members (Infinium HumanOmni2.5-8 BeadChip). Whole exome sequencing analysis (Illumina HiSeq) was performed on one affected individual...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28322272/neuroanatomic-epigenetic-and-genetic-differences-in-monozygotic-twins-discordant-for-attention-deficit-hyperactivity-disorder
#7
Y-C Chen, G Sudre, W Sharp, F Donovan, S C Chandrasekharappa, N Hansen, L Elnitski, P Shaw
The study of monozygotic twins discordant for attention deficit hyperactivity disorder can elucidate mechanisms that contribute to the disorder, which affects ~7% of children. First, using in vivo neuroanatomic imaging on 14 pairs of monozygotic twins (mean age 9.7, s.d. 1.9 years), we found that discordance for the disorder is mirrored by differing dimensions of deep brain structures (the striatum and cerebellum), but not the cerebral cortex. Next, using whole-blood DNA from the same twins, we found a significant enrichment of epigenetic differences in genes expressed in these 'discordant' brain structures...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28320919/pan-cancer-analysis-distinguishes-transcriptional-changes-of-aneuploidy-from-proliferation
#8
Christopher Buccitelli, Lorena Salgueiro, Konstantina Rowald, Rocio Sotillo, Balca R Mardin, Jan O Korbel
Patterns of gene expression in tumors can arise as a consequence of or result in genomic instability, characterized by the accumulation of somatic copy number alterations (SCNAs) and point mutations (PMs). Expression signatures have been widely used as markers for genomic instability, and both SCNAs and PMs could be thought to associate with distinct signatures given their different formation mechanisms. Here we test this notion by systematically investigating SCNA, PM, and transcriptome data from 2660 cancer patients representing 11 tumor types...
March 20, 2017: Genome Research
https://www.readbyqxmd.com/read/28315673/chromosomal-microarray-detection-of-constitutional-copy-number-variation-using-saliva-dna
#9
Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A Scott
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2...
March 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28314689/dna-methylation-based-classification-and-grading-system-for-meningioma-a-multicentre-retrospective-analysis
#10
Felix Sahm, Daniel Schrimpf, Damian Stichel, David T W Jones, Thomas Hielscher, Sebastian Schefzyk, Konstantin Okonechnikov, Christian Koelsche, David E Reuss, David Capper, Dominik Sturm, Hans-Georg Wirsching, Anna Sophie Berghoff, Peter Baumgarten, Annekathrin Kratz, Kristin Huang, Annika K Wefers, Volker Hovestadt, Martin Sill, Hayley P Ellis, Kathreena M Kurian, Ali Fuat Okuducu, Christine Jungk, Katharina Drueschler, Matthias Schick, Melanie Bewerunge-Hudler, Christian Mawrin, Marcel Seiz-Rosenhagen, Ralf Ketter, Matthias Simon, Manfred Westphal, Katrin Lamszus, Albert Becker, Arend Koch, Jens Schittenhelm, Elisabeth J Rushing, V Peter Collins, Stefanie Brehmer, Lukas Chavez, Michael Platten, Daniel Hänggi, Andreas Unterberg, Werner Paulus, Wolfgang Wick, Stefan M Pfister, Michel Mittelbronn, Matthias Preusser, Christel Herold-Mende, Michael Weller, Andreas von Deimling
BACKGROUND: The WHO classification of brain tumours describes 15 subtypes of meningioma. Nine of these subtypes are allotted to WHO grade I, and three each to grade II and grade III. Grading is based solely on histology, with an absence of molecular markers. Although the existing classification and grading approach is of prognostic value, it harbours shortcomings such as ill-defined parameters for subtypes and grading criteria prone to arbitrary judgment. In this study, we aimed for a comprehensive characterisation of the entire molecular genetic landscape of meningioma to identify biologically and clinically relevant subgroups...
March 14, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28304131/copy-number-variation-in-19-italian-multiplex-families-with-autism-spectrum-disorder-importance-of-synaptic-and-neurite-elongation-genes
#11
Carla Lintas, Chiara Picinelli, Ignazio Stefano Piras, Roberto Sacco, Claudia Brogna, Antonio M Persico
Autism Spectrum Disorder (ASD) is endowed with impressive heritability estimates and high recurrence rates. Its genetic underpinnings are nonetheless very heterogeneous, with common, and rare contributing variants located in hundreds of different loci, each characterized by variable levels of penetrance. Multiplex families from single ethnic groups represent a useful means to reduce heterogeneity and enhance genetic load. We screened 19 Italian ASD multiplex families (3 triplets and 16 duplets, total N = 41 ASD subjects), using array-CGH (Agilent 180 K)...
March 17, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28302160/increased-genomic-burden-of-germline-copy-number-variants-is-associated-with-early-onset-breast-cancer-australian-breast-cancer-family-registry
#12
Logan C Walker, John F Pearson, George A R Wiggins, Graham G Giles, John L Hopper, Melissa C Southey
BACKGROUND: Women with breast cancer who have multiple affected relatives are more likely to have inherited genetic risk factors for the disease. All the currently known genetic risk factors for breast cancer account for less than half of the average familial risk. Furthermore, the genetic factor(s) underlying an increased cancer risk for many women from multiple-case families remain unknown. Rare genomic duplications and deletions, known as copy number variants (CNVs), cover more than 10% of a human genome, are often not assessed in studies of genetic predisposition, and could account for some of the so-called "missing heritability"...
March 16, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28301526/novel-copy-number-variation-of-the-tgf%C3%AE-3-gene-is-associated-with-tgf%C3%AE-3-gene-expression-and-duration-of-fertility-traits-in-hens
#13
Lantao Gu, Chenghao Sun, Yangzhang Gong, Mei Yu, Shijun Li
Improvements in the duration of fertility (DF) could increase the interval between successive artificial inseminations, thereby decreasing the cost associated with production of hatching eggs. The molecular mechanisms involved in DF in hens remains under-explored. In this study, expression levels of the transforming growth factor-β genes (TGFβs: TGFβ1, TGFβ2, TGFβ3) were investigated in utero-vaginal junctions (UVJs) of hens with long DF (Group L, n = 10) and short DF (Group S, n = 10). TGFβ1 and 2 tended to exhibit higher expression levels in UVJs from Group L hens...
2017: PloS One
https://www.readbyqxmd.com/read/28295514/intragenic-copy-number-variation-in-the-filaggrin-gene-in-ethiopian-patients-with-atopic-dermatitis
#14
Kerstin Fernandez, Samina Asad, Fulya Taylan, Carl-Fredrik Wahlgren, Kassahun D Bilcha, Magnus Nordenskjöld, Mårten C G Winge, Maria Bradley
Genetic variants in filaggrin (FLG) involving truncating mutations or intragenic copy number variation are strongly associated with the risk of developing atopic dermatitis (AD) in European and Asian populations. Few loss-of-function mutations have been identified in Africans, although an association between FLG copy number variation and AD severity in a small African American cohort has been proposed. We studied the association between FLG copy number and AD in 132 Ethiopians and found no association between AD severity and FLG copy number, suggesting that other, still unidentified genetic factors are of more importance in predisposing Ethiopians to AD...
March 10, 2017: Pediatric Dermatology
https://www.readbyqxmd.com/read/28295210/cnvs-analysis-in-a-cohort-of-isolated-and-syndromic-dd-id-reveals-novel-genomic-disorders-position-effects-and-candidate-disease-genes
#15
Eleonora Di Gregorio, Evelise Riberi, Elga Fabia Belligni, Elisa Biamino, Malte Spielmann, Ugo Ala, Alessandro Calcia, Irene Bagnasco, Diana Carli, Giorgia Gai, Mara Giordano, Andrea Guala, Roberto Keller, Giorgia Mandrile, Carlo Arduino, Antonella Maffè, Valeria Giorgia Naretto, Fabio Sirchia, Lorena Sorasio, Silvana Ungari, Andrea Zonta, Giulia Zacchetti, Flavia Talarico, Patrizia Pappi, Simona Cavalieri, Elisa Giorgio, Cecilia Mancini, Marta Ferrero, Alessandro Brussino, Elisa Savin, Marina Gandione, Alessandra Pelle, Daniela Francesca Giachino, Mario De Marchi, Gabriella Restagno, Paolo Provero, Margherita Cirillo Silengo, Enrico Grosso, Joseph D Buxbaum, Barbara Pasini, Silvia De Rubeis, Alfredo Brusco, Giovanni Battista Ferrero
Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect Copy Number Variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes...
March 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28292787/extensive-copy-number-variation-in-fermentation-related-genes-among-saccharomyces-cerevisiae-wine-strains
#16
Jacob Steenwyk, Antonis Rokas
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S...
March 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#17
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
March 13, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28287554/detection-of-copy-number-alterations-using-single-cell-sequencing
#18
Kristin A Knouse, Jie Wu, Austin Hendricks
Detection of genomic changes at single cell resolution is important for characterizing genetic heterogeneity and evolution in normal tissues, cancers, and microbial populations. Traditional methods for assessing genetic heterogeneity have been limited by low resolution, low sensitivity, and/or low specificity. Single cell sequencing has emerged as a powerful tool for detecting genetic heterogeneity with high resolution, high sensitivity and, when appropriately analyzed, high specificity. Here we provide a protocol for the isolation, whole genome amplification, sequencing, and analysis of single cells...
February 17, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28287497/role-of-genetics-in-the-etiology-of-autistic-spectrum-disorder-towards-a-hierarchical-diagnostic-strategy
#19
REVIEW
Cyrille Robert, Laurent Pasquier, David Cohen, Mélanie Fradin, Roberto Canitano, Léna Damaj, Sylvie Odent, Sylvie Tordjman
Progress in epidemiological, molecular and clinical genetics with the development of new techniques has improved knowledge on genetic syndromes associated with autism spectrum disorder (ASD). The objective of this article is to show the diversity of genetic disorders associated with ASD (based on an extensive review of single-gene disorders, copy number variants, and other chromosomal disorders), and consequently to propose a hierarchical diagnostic strategy with a stepwise evaluation, helping general practitioners/pediatricians and child psychiatrists to collaborate with geneticists and neuropediatricians, in order to search for genetic disorders associated with ASD...
March 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28284480/copy-number-variations-found-in-patients-with-a-corpus-callosum-abnormality-and-intellectual-disability
#20
Solveig Heide, Boris Keren, Thierry Billette de Villemeur, Sandra Chantot-Bastaraud, Christel Depienne, Caroline Nava, Cyril Mignot, Aurélia Jacquette, Eric Fonteneau, Elodie Lejeune, Corinne Mach, Isabelle Marey, Sandra Whalen, Didier Lacombe, Sophie Naudion, Caroline Rooryck, Annick Toutain, Cédric Le Caignec, Damien Haye, Laurence Olivier-Faivre, Alice Masurel-Paulet, Christel Thauvin-Robinet, Fabien Lesne, Anne Faudet, Dorothée Ville, Vincent des Portes, Damien Sanlaville, Jean-Pierre Siffroi, Marie-Laure Moutard, Delphine Héron
OBJECTIVE: To evaluate the role that chromosomal micro-rearrangements play in patients with both corpus callosum abnormality and intellectual disability, we analyzed copy number variations (CNVs) in patients with corpus callosum abnormality/intellectual disability STUDY DESIGN: We screened 149 patients with corpus callosum abnormality/intellectual disability using Illumina SNP arrays. RESULTS: In 20 patients (13%), we have identified at least 1 CNV that likely contributes to corpus callosum abnormality/intellectual disability phenotype...
March 8, 2017: Journal of Pediatrics
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