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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/29052058/complete-genome-sequence-of-maize-yellow-striate-virus-a-new-cytorhabdovirus-infecting-maize-and-wheat-crops-in-argentina
#1
Fernanda Maurino, Analía D Dumón, Gabriela Llauger, Vanina Alemandri, Luis A de Haro, M Fernanda Mattio, Mariana Del Vas, Irma Graciela Laguna, María de la Paz Giménez Pecci
A rhabdovirus infecting maize and wheat crops in Argentina was molecularly characterized. Through next-generation sequencing (NGS) of symptomatic leaf samples, the complete genome was obtained of two isolates of maize yellow striate virus (MYSV), a putative new rhabdovirus, differing by only 0.4% at the nucleotide level. The MYSV genome consists of 12,654 nucleotides for maize and wheat virus isolates, and shares 71% nucleotide sequence identity with the complete genome of barley yellow striate mosaic virus (BYSMV, NC028244)...
October 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29045639/a-new-perspective-on-polyploid-fragaria-strawberry-genome-composition-based-on-large-scale-multi-locus-phylogenetic-analysis
#2
Yilong Yang, Thomas M Davis
The subgenomic compositions of the octoploid (2n=8x=56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next generation sequencing (NGS) technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large scale phylogenetic analyses of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform...
October 16, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29044468/matchmaker-exchange
#3
Nara L M Sobreira, Harindra Arachchi, Orion J Buske, Jessica X Chong, Ben Hutton, Julia Foreman, François Schiettecatte, Tudor Groza, Julius O B Jacobsen, Melissa A Haendel, Kym M Boycott, Ada Hamosh, Heidi L Rehm
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29025599/constitutional-mosaicism-of-a-de-novo-tp53-mutation-in-a-patient-with-bilateral-choroid-plexus-carcinoma
#4
Joanna Trubicka, Iwona Filipek, Iwanowski Piotr, Małgorzata Rydzanicz, Wiesława Grajkowska, Dorota Piekutowska-Abramczuk, Krystyna Chrzanowska, Agnieszka Karkucińska-Więckowska, Katarzyna Iwanicka-Pronicka, Maciej Pronicki, Maria Łastowska, Rafał Płoski, Bożenna Dembowska-Bagińska
Choroid plexus tumors (CPT) constitute 2%-5% of all pediatric brain tumors and include high grade choroid plexus carcinoma (CPC). About 40% of CPC patients harbor germline TP53 mutations, associated with diminished survival rates. However, the number of TP53 carriers might be underestimated due to suboptimal ability of Sanger sequencing to identify mosaicism. We describe an 18-month-old boy with ultra-rare, bilateral disseminated CPC and negative family history of cancer. Next generation sequencing (NGS) revealed constitutional mosaicism of de novo TP53 mutation, which was barely detectable by Sanger sequencing...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29018314/experimental-infection-of-different-tomato-genotypes-with-tomato-mosaic-virus-led-to-a-low-viral-population-heterogeneity-in-the-capsid-protein-encoding-region
#5
Nina Sihelská, Zuzana Vozárová, Lukáš Predajňa, Katarína Šoltys, Martina Hudcovicová, Daniel Mihálik, Ján Kraic, Michaela Mrkvová, Otakar Kúdela, Miroslav Glasa
The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semi-quantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology...
October 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28973384/characterization-of-breakpoint-regions-of-large-structural-autosomal-mosaic-events
#6
Mitchell J Machiela, Lea Jessop, Weiyin Zhou, Meredith Yeager, Stephen J Chanock
Recent studies have reported a higher than anticipated frequency of large clonal autosomal mosaic events >2 Mb in size in the aging population. Mosaic events are detected from analyses of intensity parameters of linear stretches with deviations in heterozygous probes of single nucleotide polymorphism (SNP) microarrays. The non-random distribution of detected mosaic events throughout the genome suggests common mechanisms could influence the formation of mosaic events. Here we use publicly available data tracks from the University of California Santa Cruz Genome Browser to investigate the genomic characteristics of the regions at the terminal ends of two frequent types of large structural mosaic events: telomeric neutral events and interstitial losses...
August 16, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28956000/accurate-clinical-genetic-testing-for-autoinflammatory-diseases-using-the-next-generation-sequencing-platform-miseq
#7
Manabu Nakayama, Hirotsugu Oda, Kenji Nakagawa, Takahiro Yasumi, Tomoki Kawai, Kazushi Izawa, Ryuta Nishikomori, Toshio Heike, Osamu Ohara
Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA), also known as neonatal-onset multisystem inflammatory disease (NOMID). In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses...
March 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/28953922/germline-and-somatic-mutations-in-cortical-malformations-molecular-defects-in-argentinean-patients-with-neuronal-migration-disorders
#8
Dolores González-Morón, Sebastián Vishnopolska, Damián Consalvo, Nancy Medina, Marcelo Marti, Marta Córdoba, Cecilia Vazquez-Dusefante, Santiago Claverie, Sergio Alejandro Rodríguez-Quiroga, Patricia Vega, Walter Silva, Silvia Kochen, Marcelo Andrés Kauffman
Neuronal migration disorders are a clinically and genetically heterogeneous group of malformations of cortical development, frequently responsible for severe disability. Despite the increasing knowledge of the molecular mechanisms underlying this group of diseases, their genetic diagnosis remains unattainable in a high proportion of cases. Here, we present the results of 38 patients with lissencephaly, periventricular heterotopia and subcortical band heterotopia from Argentina. We performed Sanger and Next Generation Sequencing (NGS) of DCX, FLNA and ARX and searched for copy number variations by MLPA in PAFAH1B1, DCX, POMT1, and POMGNT1...
2017: PloS One
https://www.readbyqxmd.com/read/28916543/cryopyrin-associated-periodic-syndromes-in-italian-patients-evaluation-of-the-rate-of-somatic-nlrp3-mosaicism-and-phenotypic-characterization
#9
Denise Lasigliè, Anna Mensa-Vilaro, Denise Ferrera, Roberta Caorsi, Federica Penco, Giuseppe Santamaria, Marco Di Duca, Giulia Amico, Kenji Nakagawa, Francesca Antonini, Alberto Tommasini, Rita Consolini, Antonella Insalaco, Marco Cattalini, Laura Obici, Romina Gallizzi, Francesca Santarelli, Genny Del Zotto, Mariasavina Severino, Anna Rubartelli, Roberto Ravazzolo, Alberto Martini, Isabella Ceccherini, Ryuta Nishikomori, Marco Gattorno, Juan I Arostegui, Silvia Borghini
OBJECTIVE: To evaluate the rate of somatic NLRP3 mosaicism in an Italian cohort of mutation-negative patients with cryopyrin-associated periodic syndrome (CAPS). METHODS: The study enrolled 14 patients with a clinical phenotype consistent with CAPS in whom Sanger sequencing of the NLRP3 gene yielded negative results. Patients' DNA were subjected to amplicon-based NLRP3 deep sequencing. RESULTS: Low-level somatic NLRP3 mosaicism has been detected in 4 patients, 3 affected with chronic infantile neurological cutaneous and articular syndrome and 1 with Muckle-Wells syndrome...
September 15, 2017: Journal of Rheumatology
https://www.readbyqxmd.com/read/28877744/exome-sequences-versus-sequential-gene-testing-in-the-uk-highly-specialised-service-for-limb-girdle-muscular-dystrophy
#10
Elizabeth Harris, Ana Topf, Rita Barresi, Judith Hudson, Helen Powell, James Tellez, Debbie Hicks, Anna Porter, Marta Bertoli, Teresinha Evangelista, Chiara Marini-Betollo, Ólafur Magnússon, Monkol Lek, Daniel MacArthur, Kate Bushby, Hanns Lochmüller, Volker Straub
BACKGROUND: Limb girdle muscular dystrophies are a group of rare and genetically heterogeneous diseases that share proximal weakness as a common feature; however they are often lacking very specific phenotypic features to allow an accurate differential diagnosis based on the clinical signs only, limiting the diagnostic rate using phenotype driven genetic testing. Next generation sequencing provides an opportunity to obtain molecular diagnoses for undiagnosed patients, as well as identifying novel genetic causes of muscle diseases...
September 6, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28862265/anaplastic-sarcomas-of-the-kidney-are-characterized-by-dicer1-mutations
#11
Mona K Wu, Gordan M Vujanic, Somayyeh Fahiminiya, Noriko Watanabe, Paul S Thorner, Maureen J O'Sullivan, Marc R Fabian, William D Foulkes
Anaplastic sarcoma of the kidney is a rare tumor (≤25 reported cases) characterized by the presence of cysts, and solid areas composed of bundles of undifferentiated spindle cells, showing marked cellular anaplasia (usually accompanied by TP53 overexpression). These tumors often feature prominent areas of cartilage or chondroid material. Germline mutations in DICER1, encoding the microRNA (miRNA) processor DICER1, cause an eponymous syndrome. Recent reports suggest that anaplastic sarcoma of the kidney should be included in DICER1 syndrome as germline DICER1 mutations are associated with the occurrence of such tumors...
September 1, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28855261/detection-of-structural-mosaicism-from-targeted-and-whole-genome-sequencing-data
#12
Daniel A King, Alejandro Sifrim, Tomas W Fitzgerald, Raheleh Rahbari, Emma Hobson, Tessa Homfray, Sahar Mansour, Sarju G Mehta, Mohammed Shehla, Susan E Tomkins, Pradeep C Vasudevan, Matthew E Hurles
Structural mosaic abnormalities are large post-zygotic mutations present in a subset of cells and have been implicated in developmental disorders and cancer. Such mutations have been conventionally assessed in clinical diagnostics using cytogenetic or microarray testing. Modern disease studies rely heavily on exome sequencing, yet an adequate method for the detection of structural mosaicism using targeted sequencing data is lacking. Here, we present a method, called MrMosaic, to detect structural mosaic abnormalities using deviations in allele fraction and read coverage from next-generation sequencing data...
October 2017: Genome Research
https://www.readbyqxmd.com/read/28854270/hypermethylation-of-the-non-imprinted-maternal-meg3-and-paternal-mest-alleles-is-highly-variable-among-normal-individuals
#13
Larissa Haertle, Anna Maierhofer, Julia Böck, Harald Lehnen, Yvonne Böttcher, Matthias Blüher, Martin Schorsch, Ramya Potabattula, Nady El Hajj, Silke Appenzeller, Thomas Haaf
Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28845532/mutational-analysis-using-sanger-and-next-generation-sequencing-in-sporadic-spindle-cell-hemangiomas-a-study-of-19-cases
#14
Roel W Ten Broek, Elise M Bekers, Wendy W J de Leng, Eric Strengman, Bastiaan B J Tops, Heinz Kutzner, Jan Willem Leeuwis, Joost M van Gorp, David H Creytens, Thomas Mentzel, Paul J van Diest, Astrid Eijkelenboom, Uta Flucke
Spindle cell hemangioma (SCH) is a distinct vascular soft-tissue lesion characterized by cavernous blood vessels and a spindle cell component mainly occurring in the distal extremities of young adults. The majority of cases harbor heterozygous mutations in IDH1/2 sporadically or rarely in association with Maffucci syndrome. However, based on mosaicism and accordingly a low percentage of lesional cells harboring a mutant allele, detection can be challenging. We tested 19 sporadic SCHs by Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), conventional next generation sequencing (NGS), and NGS using a single molecule molecular inversion probes (smMIP)-based library preparation to compare their diagnostic value...
August 28, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28837158/high-frequency-of-mosaic-pathogenic-variants-in-genes-causing-epilepsy-related-neurodevelopmental-disorders
#15
Mary Beth Stosser, Amanda S Lindy, Elizabeth Butler, Kyle Retterer, Caitlin M Piccirillo-Stosser, Gabriele Richard, Dianalee A McKnight
PurposeMosaicism probably represents an underreported cause of genetic disorders due to detection challenges during routine molecular diagnostics. The purpose of this study was to evaluate the frequency of mosaicism detected by next-generation sequencing in genes associated with epilepsy-related neurodevelopmental disorders.MethodsWe conducted a retrospective analysis of 893 probands with epilepsy who had a multigene epilepsy panel or whole-exome sequencing performed in a clinical diagnostic laboratory and were positive for a pathogenic or likely pathogenic variant in one of nine genes (CDKL5, GABRA1, GABRG2, GRIN2B, KCNQ2, MECP2, PCDH19, SCN1A, or SCN2A)...
August 24, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28803391/mutational-analysis-of-the-rb1-gene-and-the-inheritance-patterns-of-retinoblastoma-in-jordan
#16
Yacoub A Yousef, Abdelghani Tbakhi, Maysa Al-Hussaini, Ibrahim AlNawaiseh, Ala Saab, Amal Afifi, Maysa Naji, Mona Mohammad, Rasha Deebajah, Imad Jaradat, Iyad Sultan, Mustafa Mehyar
Retinoblastoma (RB) is a childhood cancer developing in the retina due to RB1 pathologic variant. Herein we are evaluating the oncogenic mutations in the RB1 gene and the inheritance patterns of RB in the Jordanian patients. In this prospective study, the peripheral blood of 50 retinoblastoma patients was collected, genomic DNA was extracted, mutations were identified using Quantitative multiplex PCR (QM-PCR), Allele-specific PCR, Next Generation Sequencing analysis, and Sanger sequencing. In this cohort of 50 patients, 20(40%) patients had unilateral RB and 30(60%) were males...
August 12, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28765789/deep-sequencing-reveals-variations-in-somatic-cell-mosaic-mutations-between-monozygotic-twins-with-discordant-psychiatric-disease
#17
Yoshiro Morimoto, Shinji Ono, Akira Imamura, Yuji Okazaki, Akira Kinoshita, Hiroyuki Mishima, Hideyuki Nakane, Hiroki Ozawa, Koh-Ichiro Yoshiura, Naohiro Kurotaki
Monozygotic (MZ) twins have been thought to be genetically identical. However, recent studies have shown discordant variants between them. We performed whole-exome sequencing (WES) in five MZ twin pairs with discordant neurodevelopmental disorders and one healthy control MZ twin to detect discordant variants. We identified three discordant variants confirmed by deep sequencing after analysis by personalized next-generation sequencing (NGS). Three mutations in FBXO38 (chr5:147774428;T>G), SMOC2 (chr6:169051385;A>G) and TDRP (chr8:442616;A>G), were detected with low allele frequency of mutant alleles on deep sequencing, suggesting that these loci are mosaic due to somatic mutations in a developmental stage...
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28760337/somatic-mosaicism-represents-an-underestimated-event-underlying-collagen-6-related-disorders
#18
Adele D'Amico, Fabiana Fattori, Giorgio Tasca, Stefania Petrini, Francesca Gualandi, Alessandro Bruselles, Valentina D'Oria, Margherita Verardo, Rosalba Carrozzo, Marcello Niceta, Bjarne Udd, Alessandra Ferlini, Marco Tartaglia, Enrico Bertini
BACKGROUND: Collagen VI-related disorders (COL6-RD) are a group of heterogenous muscular diseases due to mutations in the COL6A1, COL6A2 and COL6A3 genes, encoding for collagen VI, a critical component of the extracellular matrix. Ullrich congenital muscle disorder and Bethlem myopathy represent the ends of a clinical spectrum that includes intermediate phenotypes of variable severity. UCMD are caused by recessive loss of function mutations or de-novo dominant-negative mutations. The intermediate phenotype and BM are more commonly caused by dominantly acting mutations, and less commonly by recessive mutations...
July 22, 2017: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/28750028/clinical-impact-of-a-targeted-next-generation-sequencing-gene-panel-for-autoinflammation-and-vasculitis
#19
Ebun Omoyinmi, Ariane Standing, Annette Keylock, Fiona Price-Kuehne, Sonia Melo Gomes, Dorota Rowczenio, Sira Nanthapisal, Thomas Cullup, Rodney Nyanhete, Emma Ashton, Claire Murphy, Megan Clarke, Helena Ahlfors, Lucy Jenkins, Kimberly Gilmour, Despina Eleftheriou, Helen J Lachmann, Philip N Hawkins, Nigel Klein, Paul A Brogan
BACKGROUND: Monogenic autoinflammatory diseases (AID) are a rapidly expanding group of genetically diverse but phenotypically overlapping systemic inflammatory disorders associated with dysregulated innate immunity. They cause significant morbidity, mortality and economic burden. Here, we aimed to develop and evaluate the clinical impact of a NGS targeted gene panel, the "Vasculitis and Inflammation Panel" (VIP) for AID and vasculitis. METHODS: The Agilent SureDesign tool was used to design 2 versions of VIP; VIP1 targeting 113 genes, and a later version, VIP2, targeting 166 genes...
2017: PloS One
https://www.readbyqxmd.com/read/28724316/molecular-diagnosis-of-autosomal-dominant-polycystic-kidney-disease
#20
Xuewen Song, Amirreza Haghighi, Ioan-Andrei Iliuta, York Pei
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease that accounts for 5-10% of end-stage renal disease in developed countries. Mutations in PKD1 and PKD2 account for a majority of cases. Mutation screening of PKD1 is technically challenging largely due to the complexity resulting from duplication of its first 33 exons in six highly homologous pseudogenes (i.e. PKD1P1-P6). Protocol using locus-specific long-range and nested PCR has enabled comprehensive PKD1 mutation screening but is labor-intensive and costly...
October 2017: Expert Review of Molecular Diagnostics
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