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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/29644724/a-novel-missense-mutation-in-grin2a-causes-a-nonepileptic-neurodevelopmental-disorder
#1
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
#2
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
#3
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...
March 28, 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
#4
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)...
March 9, 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
#5
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
#6
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
#7
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
#8
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...
February 20, 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
#9
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...
February 20, 2018: Epilepsia
https://www.readbyqxmd.com/read/29455859/heterozygous-mutations-in-oas1-cause-infantile-onset-pulmonary-alveolar-proteinosis-with-hypogammaglobulinemia
#10
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...
February 12, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29451896/hypomyelinating-disorders-in-china-the-clinical-and-genetic-heterogeneity-in-119-patients
#11
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
#12
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
#13
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
#14
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 2018: Human Genetics
https://www.readbyqxmd.com/read/29409008/targeted-next-generation-sequencing-for-differential-diagnosis-of-neurofibromatosis-type-2-schwannomatosis-and-meningiomatosis
#15
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
#16
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
#17
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-syndrome
#18
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 syndrome remain obscure, in particular, the interplay between the monoclonal protein and increased interleukin-1β (IL-1β) production, although interest in the contribution of genetic factors has been fueled by detection of somatic NLRP3 mosaicism in 2 patients with the variant-type Schnitzler syndrome. At 2 specialist UK centers, we have identified 21 patients who fulfilled diagnostic criteria for Schnitzler syndrome with urticarial rash, fever, arthralgia, and bone pain; 47% reported weight loss, 40% fatigue, and 21% lymphadenopathy...
March 1, 2018: Blood
https://www.readbyqxmd.com/read/29280016/virome-analysis-of-lily-plants-reveals-a-new-potyvirus
#19
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...
April 2018: 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
#20
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
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