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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/29213331/noninvasive-prenatal-diagnosis-of-fetal-aneuploidy-by-circulating-fetal-nucleated-red-blood-cells-and-extravillous-trophoblasts-using-silicon-based-nanostructured-microfluidics
#1
Chung-Er Huang, Gwo-Chin Ma, Hei-Jen Jou, Wen-Hsiang Lin, Dong-Jay Lee, Yi-Shing Lin, Norman A Ginsberg, Hsin-Fu Chen, Frank Mau-Chung Chang, Ming Chen
Background: Noninvasive prenatal testing (NIPT) based on cell-free DNA in maternal circulation has been accepted worldwide by the clinical community since 2011 but limitations, such as maternal malignancy and fetoplacental mosaicism, preclude its full replacement of invasive prenatal diagnosis. We present a novel silicon-based nanostructured microfluidics platform named as "Cell Reveal™" to demonstrate the feasibility of capturing circulating fetal nucleated red blood cells (fnRBC) and extravillous cytotrophoblasts (EVT) for cell-based noninvasive prenatal diagnosis (cbNIPD)...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29192217/decreased-mirna-expression-in-klinefelter-syndrome
#2
Laura Cimino, Michele Salemi, Rossella Cannarella, Rosita A Condorelli, Giorgio Giurato, Giovanna Marchese, Sandro La Vignera, Aldo E Calogero
The widelyvariable phenotypic spectrum and the different severity of symptoms in men with Klinefelter syndrome (KS) suggest a role for epigenetic mediators. Therefore, the aim of this study is to evaluate the possible involvement of miRNAs in the clinical manifestations of KS. To accomplish this, we performed a transcriptome analysis in peripheral blood mononuclear cells (PBMCs) of 10 non-mosaic KS patients, 10 aged-matched healthy men and 10 aged-matched healthy female controls with normal karyotype. After RNA extraction from PBMC and the preparation of RNA libraries, the samples were sequenced using next generation high-throughput sequencing technology...
November 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29191449/extent-of-chromosomal-mosaicism-influences-the-clinical-outcome-of-in%C3%A2-vitro-fertilization-treatments
#3
Francesca Spinella, Francesco Fiorentino, Anil Biricik, Sara Bono, Alessandra Ruberti, Ettore Cotroneo, Marina Baldi, Elisabetta Cursio, Maria Giulia Minasi, Ermanno Greco
OBJECTIVE: To assess whether the extent of chromosomal mosaicism can influence the success rate of IVF treatments. DESIGN: Prospective study. SETTING: Private genetic and assisted reproduction centers. PATIENT(S): The transfer of mosaic embryos was offered to 77 women for which IVF resulted in no euploid embryos available for transfer. INTERVENTION(S): All embryos were cultured to blastocyst stage; trophectoderm biopsy was performed on day 5/6 of development...
November 28, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/29186554/preclinical-validation-of-a-targeted-next-generation-sequencing-based-comprehensive-chromosome-screening-methodology-in-human-blastocysts
#4
R S Zimmerman, X Tao, D Marin, M Werner, K Hong, A Lonczak, J Landis, D Taylor, Y Zhan, R T Scott, N R Treff
STUDY QUESTION: Can a novel targeted next generation sequencing (tNGS) platform accurately detect whole chromosome aneuploidy in a trophectoderm biopsy and provide additional information to improve testing? SUMMARY ANSWER: Karyotypes obtained by tNGS were concordant with other validated platforms and SNP genotyping information obtained can be used for improved detection and quality control. WHAT IS KNOWN ALREADY: qPCR-based whole chromosome aneuploidy screening is highly accurate in comparison to other common methods and has been shown to improve IVF success in two randomized clinical trials...
November 25, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/29186371/a-recurrent-de-novo-mutation-in-tmem106b-causes-hypomyelinating-leukodystrophy
#5
Cas Simons, David Dyment, Stephen J Bent, Joanna Crawford, Marc D'Hooghe, Alfried Kohlschütter, Sunita Venkateswaran, Guy Helman, Bwee-Tien Poll-The, Christine C Makowski, Yoko Ito, Kristin Kernohan, Taila Hartley, Quinten Waisfisz, Ryan J Taft, Marjo S van der Knaap, Nicole I Wolf
Hypomyelinating leukodystrophies are a heterogeneous group of disorders with a clinical presentation that often includes early-onset nystagmus, ataxia and spasticity and a wide range of severity. Using next-generation sequencing techniques and GeneMatcher, we identified four unrelated patients with brain hypomyelination, all with the same recurrent dominant mutation, c.754G>A p.(Asp252Asn), in TMEM106B. The mutation was confirmed as de novo in three of the cases, and the mildly affected father of the fourth affected individual was confirmed as mosaic for this variant...
November 27, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/29182661/classical-and-next-generation-sequencing-approaches-unravel-bymovirus-diversity-in-barley-crops-in-france
#6
Mathieu Rolland, Julie Villemot, Armelle Marais, Sébastien Theil, Chantal Faure, Valérie Cadot, Romain Valade, Cindy Vitry, Frank Rabenstein, Thierry Candresse
Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease...
2017: PloS One
https://www.readbyqxmd.com/read/29179772/recurrent-de-novo-mutations-in-neurodevelopmental-disorders-properties-and-clinical-implications
#7
REVIEW
Amy B Wilfert, Arvis Sulovari, Tychele N Turner, Bradley P Coe, Evan E Eichler
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs...
November 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29174369/-analyzing-the-genetic-spectrum-of-vascular-anomalies-with-overgrowth-via-cancer-genomics
#8
Dawn H Siegel, Catherine E Cottrell, Jenna L Streicher, Kala F Schilter, Donald G Basel, Eulalia Baselga, Patricia E Burrows, Heather M Ciliberto, Katinka A Vigh-Conrad, Lawrence F Eichenfield, Kristen E Holland, Marcia Hogeling, John N Jensen, Michael E Kelly, Wendy Kim, David M King, Catherine McCuaig, Katherine A Mueller, Elena Pope, Julie Powell, Harper Price, Jack E Steiner, Ilona J Frieden, Megha M Tollefson, Beth A Drolet
Vascular anomalies are variably associated with overgrowth, skeletal anomalies, and abnormalities of the brain, leptomeninges, and eye. We assembled a 16-institution network to determine the range of genetic variants associated with a spectrum of vascular anomalies with overgrowth, ranging from mild to severe. Due to overlap between cancer-associated variants and previously described somatic variants in vascular overgrowth syndromes, we employed tumor genetic profiling via high-depth next generation sequencing using a panel to assay affected tissue from a diverse cohort of subjects with vascular anomalies with overgrowth...
November 22, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29163631/prenatal-diagnosis-of-fragile-x-can-a-full-mutation-allele-in-the-fmr1-gene-contract-to-a-normal-size
#9
Esther Manor, Azhar Jabareen, Nurit Magal, Arei Kofman, Randi J Hagerman, Flora Tassone
Here we describe a case of a prenatal diagnosis of a male fetus that inherited the unstable allele from his full mutation mosaic mother (29, 160, >200 CGG repeats) reduced to a normal size range (19 CGG repeats). Haplotype analysis showed that the fetus 19 CGG repeats allele derived from the maternal unstable allele which was inherited from his maternal grandmother. No size mosaicism was detected by testing the DNA from in vitro cultured samples, including seventh passage culture as well as from two amniocentesis samples...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29160035/mosaic-uniparental-disomy-results-in-gm1-gangliosidosis-with-normal-enzyme-assay
#10
Kenneth A Myers, Mark F Bennett, Chung W Chow, Susan M Carden, Simone A Mandelstam, Melanie Bahlo, Ingrid E Scheffer
Inherited metabolic disorders are traditionally diagnosed using broad and expensive panels of screening tests, often including invasive skin and muscle biopsy. Proponents of next-generation genetic sequencing have argued that replacing these screening panels with whole exome sequencing (WES) would save money. Here, we present a complex patient in whom WES allowed diagnosis of GM1 gangliosidosis, caused by homozygous GLB1 mutations, resulting in β-galactosidase deficiency. A 10-year-old girl had progressive neurologic deterioration, macular cherry-red spot, and cornea verticillata...
November 21, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29155047/novel-mosaic-variants-in-two-patients-with-cornelia-de-lange-syndrome
#11
Jelena Pozojevic, Ilaria Parenti, Luitgard Graul-Neumann, Sara Ruiz Gil, Erwan Watrin, Kerstin S Wendt, Ralf Werner, Tim M Strom, Gabriele Gillessen-Kaesbach, Frank J Kaiser
Cornelia de Lange syndrome (CdLS) is a dominantly inherited developmental disorder caused by mutations in genes that encode for either structural (SMC1A, SMC3, RAD21) or regulatory (NIPBL, HDAC8) subunits of the cohesin complex. NIPBL represents the major gene of the syndrome and heterozygous mutations can be identified in more than 65% of patients. Interestingly, large portions of these variants were described as somatic mosaicism and often escape standard molecular diagnostics using lymphocyte DNA. Here we discuss the role of somatic mosaicism in CdLS and describe two additional patients with NIPBL mosaicism detected by targeted gene panel or exome sequencing...
November 15, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29135076/a-heterozygous-mutation-in-rpgr-associated-with-x-linked-retinitis-pigmentosa-in-a-patient-with-turner-syndrome-mosaicism-45-x-46-xx
#12
Qi Zhou, Fengxia Yao, Feng Wang, Hui Li, Rui Chen, Ruifang Sui
Turner syndrome with retinitis pigmentosa (RP) is rare, with only three cases reported based on clinical examination alone. We summarized the 4-year follow-up and molecular findings in a 28-year-old patient with Turner syndrome and the typical features of short stature and neck webbing, who also had X-linked RP. Her main complaints were night blindness and progressive loss of vision since the age of 9 years. Ophthalmologic examination, optical coherent tomographic imaging, and visual electrophysiology tests showed classic manifestations of RP...
November 14, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29094240/complete-genome-sequence-of-a-novel-bromovirus-infecting-elderberry-sambucus-nigra-l-in-the-czech-republic
#13
Dana Šafářová, Thierry Candresse, Milan Navrátil
The genus Bromovirus currently contains six species whose members have relatively narrow host ranges. In the present work, a new bromovirus infecting elderberry (Sambucus nigra L.) is reported. dsRNA was purified and sequenced by next-generation sequencing, and with minimal additional completion by Sanger sequencing, the full tripartite genome was obtained. RNA1 is 3241 nt long and contains ORF1 (1a protein), RNA2 is 2810 nt long and contains ORF2 (2a protein), and RNA3 is 2244 nt long and contains ORF3a (movement protein) and ORF3b (coat protein, CP), separated by an intercistronic poly(A) stretch...
November 1, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29070607/contribution-of-de-novo-and-mosaic-tp53-mutations-to-li-fraumeni-syndrome
#14
Mariette Renaux-Petel, Françoise Charbonnier, Jean-Christophe Théry, Pierre Fermey, Gwendoline Lienard, Jacqueline Bou, Sophie Coutant, Myriam Vezain, Edwige Kasper, Steeve Fourneaux, Sandrine Manase, Maud Blanluet, Bruno Leheup, Ludovic Mansuy, Jacqueline Champigneulle, Céline Chappé, Michel Longy, Nicolas Sévenet, Brigitte Bressac-de Paillerets, Léa Guerrini-Rousseau, Laurence Brugières, Olivier Caron, Jean-Christophe Sabourin, Isabelle Tournier, Stéphanie Baert-Desurmont, Thierry Frébourg, Gaëlle Bougeard
BACKGROUND: Development of tumours such as adrenocortical carcinomas (ACC), choroid plexus tumours (CPT) or female breast cancers before age 31 or multiple primary cancers belonging to the Li-Fraumeni (LFS) spectrum is, independently of the familial history, highly suggestive of a germline TP53 mutation. The aim of this study was to determine the contribution of de novo and mosaic mutations to LFS. METHODS AND RESULTS: Among 328 unrelated patients harbouring a germline TP53 mutation identified by Sanger sequencing and/or QMPSF, we could show that the mutations had occurred de novo in 40 cases, without detectable parental age effect...
October 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29055690/application-of-digital-pcr-with-chip-in-a-tube-format-to-analyze-adenomatous-polyposis-coli-apc-somatic-mosaicism
#15
Tomoaki Kahyo, Moriya Iwaizumi, Hidetaka Yamada, Hong Tao, Kiyotaka Kurachi, Haruhiko Sugimura
BACKGROUND: Over the past decade, digital PCR (dPCR) technology has significantly improved, and its application in clinical diagnostics is rapidly advancing. The Clarity™ dPCR platform, which employs the chip-in-a-tube format to broaden its range of applications, has been used to determine gene copy number. However, detection of mutations in human samples, the most demanding task in clinical practice, has not yet been reported using this platform. METHODS: The Clarity™ dPCR platform was used to detect somatic Adenomatous polyposis coli mosaicism c...
October 18, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29052058/complete-genome-sequence-of-maize-yellow-striate-virus-a-new-cytorhabdovirus-infecting-maize-and-wheat-crops-in-argentina
#16
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
#17
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
#18
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
#19
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
#20
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
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