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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/29451896/hypomyelinating-disorders-in-china-the-clinical-and-genetic-heterogeneity-in-119-patients
#1
Haoran Ji, Dongxiao Li, Ye Wu, Quanli Zhang, Qiang Gu, Han Xie, Taoyun Ji, Huifang Wang, Lu Zhao, Haijuan Zhao, Yanling Yang, Hongchun Feng, Hui Xiong, Jinhua Ji, Zhixian Yang, Liping Kou, Ming Li, Xinhua Bao, Xingzhi Chang, Yuehua Zhang, Li Li, Huijuan Li, Zhengping Niu, Xiru Wu, Jiangxi Xiao, Yuwu Jiang, Jingmin Wang
OBJECTIVE: Hypomyelinating disorders are a group of clinically and genetically heterogeneous diseases characterized by neurological deterioration with hypomyelination visible on brain MRI scans. This study was aimed to clarify the clinical and genetic features of HMDs in Chinese population. METHODS: 119 patients with hypomyelinating disorders in Chinese population were enrolled and evaluated based on their history, clinical manifestation, laboratory examinations, series of brain MRI with follow-up, genetic etiological tests including chromosomal analysis, multiplex ligation probe amplification, Sanger sequencing, targeted enrichment-based next-generation sequencing and whole exome sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29429120/a-local-strain-of-paprika-mild-mottle-virus-breaks-l3-resistance-in-peppers-and-is-accelerated-in-tomato-brown-rugose-fruit-virus-infected-tm-22-resistant-tomatoes
#2
Neta Luria, Elisheva Smith, Noa Sela, Oded Lachman, Ilana Bekelman, Amnon Koren, Aviv Dombrovsky
During October 2014, unfamiliar mild mosaic and mottling symptoms were identified on leaves of pepper (Capsicum chinense cv. Habanero) seedlings grown in the Arava valley in Israel 2-3 weeks post planting. Symptomatic plants were tested positive by ELISA using laboratory-produced antisera for tobamovirus species. Typical tobamovirus rod-shaped morphology was observed by transmission electron microscopy (TEM) analysis of purified virion preparation that was used for mechanical inoculation of laboratory test plants for the completion of Koch's postulates...
February 10, 2018: Virus Genes
https://www.readbyqxmd.com/read/29419890/genetic-and-clinical-findings-in-a-chinese-cohort-of-patients-with-collagen-vi-related-myopathies
#3
Y Fan, A Liu, C Wei, H Yang, X Chang, S Wang, Y Yuan, C Bonnemann, Q Wu, X Wu, H Xiong
Collagen VI-related myopathy, caused by pathogenic variants in the genes encoding collagen VI, represents a clinical continuum from Ullrich congenital muscular dystrophy (UCMD) to Bethlem myopathy (BM). Clinical data of 60 probands and their family members were collected and muscle biopsies of 26 patients were analyzed. COL6A1, COL6A2 and COL6A3 exons were analyzed by direct sequencing or next generation sequencing (NGS). Sixty patients were characterized by delayed motor milestones, muscle weakness, skin and joint changes with forty UCMD and twenty BM...
February 8, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29417219/robust-identification-of-mosaic-variants-in-congenital-heart-disease
#4
Kathryn B Manheimer, Felix Richter, Lisa J Edelmann, Sunita L D'Souza, Lisong Shi, Yufeng Shen, Jason Homsy, Marko T Boskovski, Angela C Tai, Joshua Gorham, Christopher Yasso, Elizabeth Goldmuntz, Martina Brueckner, Richard P Lifton, Wendy K Chung, Christine E Seidman, J G Seidman, Bruce D Gelb
Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (n = 715) and a cohort of healthy individuals (n = 416)...
February 7, 2018: Human Genetics
https://www.readbyqxmd.com/read/29409008/targeted-next-generation-sequencing-for-differential-diagnosis-of-neurofibromatosis-type-2-schwannomatosis-and-meningiomatosis
#5
Camille Louvrier, Eric Pasmant, Audrey Briand-Suleau, Joëlle Cohen, Patrick Nitschké, Juliette Nectoux, Lucie Orhant, Cécile Zordan, Cyril Goizet, Stéphane Goutagny, Dominique Lallemand, Michel Vidaud, Dominique Vidaud, Michel Kalamarides, Béatrice Parfait
Background: Clinical overlap between neurofibromatosis type 2 (NF2), schwannomatosis, and meningiomatosis can make clinical diagnosis difficult. Hence, molecular investigation of germline and tumor tissues may improve the diagnosis. Methods: We present the targeted next generation sequencing (NGS) of NF2, SMARCB1, LZTR1, SMARCE1, and SUFU tumor suppressor genes, using an amplicon-based approach. We analyzed blood DNA from a cohort of 196 patients, including patients with: NF2 (N=79), schwannomatosis (N=40), meningiomatosis (N=12), and no clearly established diagnosis (N=65)...
February 2, 2018: Neuro-oncology
https://www.readbyqxmd.com/read/29373974/degree-of-mosaicism-in-trophectoderm-does-not-predict-pregnancy-potential-a-corrected-analysis-of-pregnancy-outcomes-following-transfer-of-mosaic-embryos
#6
Vitaly A Kushnir, Sarah K Darmon, David H Barad, Norbert Gleicher
BACKGROUND: Preimplantation genetic screening (PGS) is increasingly utilized as an adjunct procedure to IVF. Recently healthy euploid live birth were reported following transfer of mosaic embryos. Several recent publications have surmised that the degree of trophectoderm (TE) mosaicism in transferred embryos is predictive of ongoing pregnancy and miscarriage rates. METHODS: This is a corrected analysis of previously published retrospective data on vitro fertilization (IVF) cycle outcomes involving replacement of 143 mosaic and 1045 euploid embryos tested by PGS, utilizing high-resolution next-generation sequencing (NGS) of TE and determination of percentages of mosaicism...
January 26, 2018: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/29348353/next-generation-sequencing-reveals-the-first-complete-genome-sequence-of-cowpea-aphid-borne-mosaic-virus-from-uganda
#7
E K Mbeyagala, P Tukamuhabwa, J Bisikwa, T Holton, S B Mukasa
We present here the first complete genome sequence of Cowpea aphid-borne mosaic virus (CABMV) isolated from cowpea in Uganda and compare it with five CABMV complete genome sequences from Brazil (2), India (2), and Zimbabwe (1). It most resembled the genomes of two Brazilian isolates (MG-Avr and BR1) and one Indian isolate (RR3).
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29284595/molecular-genetic-investigation-clinical-features-and-response-to-treatment-in-21-patients-with-schnitzler-s-syndrome
#8
Dorota M Rowczenio, Shelly Pathak, Juan I Arostegui, Anna Mensa-Vilaro, Ebun Omoyinmi, Paul Brogan, Dan Lipsker, Thomas Scambler, Roger Owen, Hadija Trojer, Anna Baginska, Julian D Gillmore, Ashutosh D Wechalekar, Thirusha Lane, Rene Williams, Taryn Youngstein, Philip N Hawkins, Sinisa Savic, Helen J Lachmann
To date, the pathogenic mechanisms underlying Schnitzler's syndrome remain obscure, in particular the interplay between the monoclonal protein and increased IL-1beta production, although interest in the contribution of genetic factors has been fuelled by detection of somatic NLRP3 mosaicism in two patients with the variant-type Schnitzler's syndrome. At two specialist UK centres we have identified 21 patients, who fulfilled diagnostic criteria for Schnitzler's syndrome with urticarial rash, fever, arthralgia and bone pain; 47% reported weight loss, 40% fatigue and 21% lymphadenopathy...
December 28, 2017: Blood
https://www.readbyqxmd.com/read/29280016/virome-analysis-of-lily-plants-reveals-a-new-potyvirus
#9
Yongqiang Li, Anning Jia, Yan Qiao, Jun Xiang, Yongjiang Zhang, Wenhe Wang
Lily plants exhibiting virus-like symptoms of leaf yellowing, twisting and brownish necrotic spots were collected, and next-generation sequencing of small RNAs was conducted to identify the associated viruses. Cucumber mosaic virus, lily symptomless virus and a hitherto unrecorded potyvirus, tentatively named "lily yellow mosaic virus" (LYMV), were detected. The genomic RNA of LYMV was 9811 nt in length, encoding a large polyprotein of 3,124 amino acids with a predicted Mr of 353.3 kDa. BLAST analysis showed that LYMV shared a high degree of amino acid sequence identity with Thunberg fritillary mosaic virus (55%), bean yellow mosaic virus (52%), clover yellow vein virus (51%), leek yellow stripe virus (51%), and lily mottle virus (52%), and these viruses clustered together in a phylogenetic tree...
December 26, 2017: Archives of Virology
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
#10
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
#11
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-vitro-fertilization-treatments
#12
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...
January 2018: 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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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