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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/29866057/chinese-cases-of-early-infantile-epileptic-encephalopathy-a-novel-mutation-in-the-pcdh19-gene-was-proved-in-a-mosaic-male-case-report
#1
Yuxia Tan, Mei Hou, Shaochun Ma, Peipei Liu, Shungang Xia, Yu Wang, Liping Chen, Zongbo Chen
BACKGROUND: The link between the protocadherin-19 (PCDH19) gene and epilepsy suggests that an unusual form of X-linked inheritance affects females but is transmitted through asymptomatic males. Individuals with epilepsy associated with mutations in the PCDH19 gene display generalized or focal seizures with or without fever sensitivity. The clinical manifestation of the condition ranges from mild to severe, resulting in intellectual disability and behavioural disturbance. In the present study, we assessed mutations in the PCDH19 gene and the clinical features of a group of Chinese patients with early infantile epileptic encephalopathy and aimed to provide further insight into the understanding of epilepsy and mental retardation limited to females (EFMR; MIM 300088)...
June 4, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29796631/chromosomal-mosaicism-in-human-blastocysts-the-ultimate-challenge-of-preimplantation-genetic-testing
#2
M Popovic, A Dheedene, C Christodoulou, J Taelman, L Dhaenens, F Van Nieuwerburgh, D Deforce, E Van den Abbeel, P De Sutter, B Menten, B Heindryckx
STUDY QUESTION: To what extent does a trophectoderm (TE) biopsy reliably reflect the chromosomal constitution of the inner cell mass (ICM) in human blastocysts? SUMMARY ANSWER: Concordance between TE and ICM was established in 62.1% of the embryos analysed. WHAT IS KNOWN ALREADY: Next generation sequencing (NGS) platforms have recently been optimised for preimplantation genetic testing for aneuploidies (PGT-A). However, higher sensitivity has led to an increase in reports of chromosomal mosaicism within a single TE biopsy...
May 23, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29792207/metagenomic-analysis-of-viruses-associated-with-maize-lethal-necrosis-in-kenya
#3
Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A Holton, Bramwel W Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia-Ruiz
BACKGROUND: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA...
May 23, 2018: Virology Journal
https://www.readbyqxmd.com/read/29778385/frequencies-of-chromosome-specific-mosaicisms-in-trophoectoderm-biopsies-detected-by-next-generation-sequencing
#4
Gary Nakhuda, Chen Jing, Rachel Butler, Colleen Guimond, Jason Hitkari, Elizabeth Taylor, Niamh Tallon, Albert Yuzpe
OBJECTIVE: To examine the chromosome-specific frequencies of mosaicism detected by next-generation sequencing (NGS) compared with constitutional aneuploidy. DESIGN: Retrospective cross-sectional review of NGS results from trophectoderm biopsies analyzed by per-chromosome prevalence of mosaicism and constitutional aneuploidy. SETTING: Private fertility clinic. PATIENT(S): A total of 378 patients who underwent preimplantation genetic screening by NGS for routine clinical indications from February 2016 to April 2017...
May 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29753892/next-generation-sequencing-reveals-packaging-of-host-rnas-by-brome-mosaic-virus
#5
N Shrestha, P H Weber, S V Burke, W Wysocki, M R Duvall, J J Bujarski
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol...
May 10, 2018: Virus Research
https://www.readbyqxmd.com/read/29687187/complete-sequence-and-diversity-of-a-maize-associated-polerovirus-in-east-africa
#6
Deogracious P Massawe, Lucy R Stewart, Jovia Kamatenesi, Theodore Asiimwe, Margaret G Redinbaugh
Since 2011-2012, Maize lethal necrosis (MLN) has emerged in East Africa, causing massive yield loss and propelling research to identify viruses and virus populations present in maize. As expected, next generation sequencing (NGS) has revealed diverse and abundant viruses from the family Potyviridae, primarily sugarcane mosaic virus (SCMV), and maize chlorotic mottle virus (MCMV) (Tombusviridae), which are known to cause MLN by synergistic co-infection. In addition to these expected viruses, we identified a virus in the genus Polerovirus (family Luteoviridae) in 104/172 samples selected for MLN or other potential virus symptoms from Kenya, Uganda, Rwanda, and Tanzania...
June 2018: Virus Genes
https://www.readbyqxmd.com/read/29681099/2016-children-s-tumor-foundation-conference-on-neurofibromatosis-type-1-neurofibromatosis-type-2-and-schwannomatosis
#7
Michael J Fisher, Allan J Belzberg, Peter de Blank, Thomas De Raedt, Florent Elefteriou, Rosalie E Ferner, Marco Giovannini, Gordon J Harris, Michel Kalamarides, Matthias A Karajannis, AeRang Kim, Conxi Lázaro, Lu Q Le, Wei Li, Robert Listernick, Staci Martin, Helen Morrison, Eric Pasmant, Nancy Ratner, Elisabeth Schorry, Nicole J Ullrich, David Viskochil, Brian Weiss, Brigitte C Widemann, Yuan Zhu, Annette Bakker, Eduard Serra
Organized and hosted by the Children's Tumor Foundation (CTF), the Neurofibromatosis (NF) conference is the premier annual gathering for clinicians and researchers interested in neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2), and schwannomatosis (SWN). The 2016 edition constituted a blend of clinical and basic aspects of NF research that helped in clarifying different advances in the field. The incorporation of next generation sequencing is changing the way genetic diagnostics is performed for NF and related disorders, providing solutions to problems like genetic heterogeneity, overlapping clinical manifestations, or the presence of mosaicism...
May 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29644724/a-novel-missense-mutation-in-grin2a-causes-a-nonepileptic-neurodevelopmental-disorder
#8
Ana Fernández-Marmiesse, Hirofumi Kusumoto, Saray Rekarte, Iria Roca, Jin Zhang, Scott J Myers, Stephen F Traynelis, Mª Luz Couce, Luis Gutierrez-Solana, Hongjie Yuan
BACKGROUND: Mutations in the GRIN2A gene, which encodes the GluN2A (glutamate [NMDA] receptor subunit epsilon-1) subunit of the N-methyl-d-aspartate receptor, have been identified in patients with epilepsy-aphasia spectrum disorders, idiopathic focal epilepsies with centrotemporal spikes, and epileptic encephalopathies with severe developmental delay. However, thus far, mutations in this gene have not been associated with a nonepileptic neurodevelopmental disorder with dystonia. OBJECTIVES: The objective of this study was to identify the disease-causing gene in 2 siblings with neurodevelopmental and movement disorders with no epileptiform abnormalities...
April 11, 2018: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/29618827/niptmer-rapid-k-mer-based-software-package-for-detection-of-fetal-aneuploidies
#9
Martin Sauk, Olga Žilina, Ants Kurg, Eva-Liina Ustav, Maire Peters, Priit Paluoja, Anne Mari Roost, Hindrek Teder, Priit Palta, Nathalie Brison, Joris R Vermeesch, Kaarel Krjutškov, Andres Salumets, Lauris Kaplinski
Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29605407/next-generation-sequencing-for-preimplantation-genetic-screening-improves-pregnancy-outcomes-compared-with-array-comparative-genomic-hybridization-in-single-thawed-euploid-embryo-transfer-cycles
#10
Jenna Friedenthal, Susan M Maxwell, Santiago Munné, Yael Kramer, David H McCulloh, Caroline McCaffrey, James A Grifo
OBJECTIVE: To evaluate whether the use of next generation sequencing (NGS) for preimplantation genetic screening (PGS) in single thawed euploid embryo transfer (STEET) cycles improves pregnancy outcomes compared with array comparative genomic hybridization (aCGH). DESIGN: Retrospective cohort study. SETTING: Single university-based fertility center. PATIENT(S): A total of 916 STEET cycles from January 2014 to December 2016 were identified...
April 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29547808/evaluation-of-preimplantation-genetic-testing-for-chromosomal-structural-rearrangement-by-a-commonly-used-next-generation-sequencing-workflow
#11
Judy F C Chow, William S B Yeung, Vivian C Y Lee, Estella Y L Lau, Ernest H Y Ng
OBJECTIVES: To evaluate the applicability of a commonly used next generation sequencing workflow in detecting unbalanced meiotic segregation products for reciprocal translocation and inversion carriers. STUDY DESIGN: All preimplantation genetic testing treatment cycles performed for reciprocal translocation or inversion carriers from 2012 to April 2017 were included. Three hundreds and forty-two archived whole genome amplified DNA, which had previously analyzed by array comparative genomic hybridization (aCGH), were retrospectively analyzed by next generation sequencing (NGS)...
May 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/29545304/genome-sequence-of-a-tomato-infecting-tomato-mosaic-virus-isolate-from-zimbabwe
#12
Charles Karavina, Jacques D Ibaba, Augustine Gubba
A tomato-infecting tomato mosaic virus (ToMV) isolate was detected in Zimbabwe using lateral flow kits and double-antibody sandwich enzyme-linked immunosorbent assay. Next-generation sequencing and de novo assembly were subsequently performed to determine its genome sequence. The ToMV genome of the Zimbabwe isolate is the second to be reported in Africa.
March 15, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29510240/expanding-the-phenotypic-spectrum-associated-with-ophn1-mutations-report-of-17-individuals-with-intellectual-disability-but-no-cerebellar-hypoplasia
#13
REVIEW
Stéphanie Moortgat, Damien Lederer, Marie Deprez, Marga Buzatu, Philippe Clapuyt, Sébastien Boulanger, Valérie Benoit, Sandrine Mary, Agnès Guichet, Alban Ziegler, Estelle Colin, Dominique Bonneau, Isabelle Maystadt
Mutations in the oligophrenin 1 gene (OPHN1) have been identified in patients with X-linked intellectual disability (XLID) associated with cerebellar hypoplasia and ventriculomegaly, suggesting it could be a recognizable syndromic intellectual disability (ID). Affected individuals share additional clinical features including speech delay, seizures, strabismus, behavioral difficulties, and slight facial dysmorphism. OPHN1 is located in Xq12 and encodes a Rho-GTPase-activating protein involved in the regulation of the G-protein cycle...
March 3, 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29500570/discovery-of-a-novel-geminivirus-associated-with-camellia-chlorotic-dwarf-disease
#14
Song Zhang, Pan Shen, Min Li, Xin Tian, Changyong Zhou, Mengji Cao
Next-generation sequencing of small RNAs and PCR amplification with two pairs of back-to-back primers, followed by cloning and sequencing, allowed identification of a novel geminivirus isolate provisionally named camellia chlorotic dwarf-associated virus (CaCDaV). The complete genome sequence of CaCDaV comprises 3,687 nucleotides (nts) and six open reading frames (ORFs). The genome and putative proteins of CaCDaV were most closely related to those of two unclassified geminiviruses: citrus chlorotic dwarf-associated virus (CCDaV, 3,640 nt) and mulberry mosaic dwarf-associated virus (MMDaV, 2,952 nt)...
March 2, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29471395/origin-and-composition-of-cell-free-dna-in-spent-medium-from-human-embryo-culture-during-preimplantation-development
#15
M Vera-Rodriguez, A Diez-Juan, J Jimenez-Almazan, S Martinez, R Navarro, V Peinado, A Mercader, M Meseguer, D Blesa, I Moreno, D Valbuena, C Rubio, C Simon
STUDY QUESTION: What is the origin and composition of cell-free DNA in human embryo spent culture media? SUMMARY ANSWER: Cell-free DNA from human embryo spent culture media represents a mix of maternal and embryonic DNA, and the mixture can be more complex for mosaic embryos. WHAT IS KNOWN ALREADY: In 2016, ~300 000 human embryos were chromosomally and/or genetically analyzed using preimplantation genetic testing for aneuploidies (PGT-A) or monogenic disorders (PGT-M) before transfer into the uterus...
April 1, 2018: Human Reproduction
https://www.readbyqxmd.com/read/29460957/mosaicism-of-de-novo-pathogenic-scn1a-variants-in-epilepsy-is-a-frequent-phenomenon-that-correlates-with-variable-phenotypes
#16
Iris M de Lange, Marco J Koudijs, Ruben van 't Slot, Boudewijn Gunning, Anja C M Sonsma, Lisette J J M van Gemert, Flip Mulder, Ellen C Carbo, Marjan J A van Kempen, Nienke E Verbeek, Isaac J Nijman, Robert F Ernst, Sanne M C Savelberg, Nine V A M Knoers, Eva H Brilstra, Bobby P C Koeleman
OBJECTIVE: Phenotypes caused by de novo SCN1A pathogenic variants are very variable, ranging from severely affected patients with Dravet syndrome to much milder genetic epilepsy febrile seizures plus cases. The most important determinant of disease severity is the type of variant, with variants that cause a complete loss of function of the SCN1A protein (α-subunit of the neuronal sodium channel Nav1.1) being detected almost exclusively in Dravet syndrome patients. However, even within Dravet syndrome disease severity ranges greatly, and consequently other disease modifiers must exist...
March 2018: Epilepsia
https://www.readbyqxmd.com/read/29455859/heterozygous-mutations-in-oas1-cause-infantile-onset-pulmonary-alveolar-proteinosis-with-hypogammaglobulinemia
#17
Kazutoshi Cho, Masafumi Yamada, Kazunaga Agematsu, Hirokazu Kanegane, Noriko Miyake, Masahiro Ueki, Takuma Akimoto, Norimoto Kobayashi, Satoru Ikemoto, Mishie Tanino, Atsushi Fujita, Itaru Hayasaka, Satoshi Miyamoto, Mari Tanaka-Kubota, Koh Nakata, Masaaki Shiina, Kazuhiro Ogata, Hisanori Minakami, Naomichi Matsumoto, Tadashi Ariga
Pulmonary alveolar proteinosis (PAP) is characterized by accumulation of a surfactant-like substance in alveolar spaces and hypoxemic respiratory failure. Genetic PAP (GPAP) is caused by mutations in genes encoding surfactant proteins or genes encoding a surfactant phospholipid transporter in alveolar type II epithelial cells. GPAP is also caused by mutations in genes whose products are implicated in surfactant catabolism in alveolar macrophages (AMs). We performed whole-exome sequence analysis in a family affected by infantile-onset PAP with hypogammaglobulinemia without causative mutations in genes associated with PAP: SFTPB, SFTPC, ABCA3, CSF2RA, CSF2RB, and GATA2...
March 1, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29451896/hypomyelinating-disorders-in-china-the-clinical-and-genetic-heterogeneity-in-119-patients
#18
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-l-3-resistance-in-peppers-and-is-accelerated-in-tomato-brown-rugose-fruit-virus-infected-tm-2-2-resistant-tomatoes
#19
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...
April 2018: Virus Genes
https://www.readbyqxmd.com/read/29419890/genetic-and-clinical-findings-in-a-chinese-cohort-of-patients-with-collagen-vi-related-myopathies
#20
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 40 UCMD and 20 BM...
February 8, 2018: Clinical Genetics
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