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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/28433368/chromosomal-mosaicism-detected-during-preimplantation-genetic-screening-results-of-a-worldwide-web-based-survey
#1
REVIEW
Ariel Weissman, Gon Shoham, Zeev Shoham, Simon Fishel, Milton Leong, Yuval Yaron
Embryonic mosaicism, the presence of more than one distinct cell line within an embryo, has recently become the focus of growing attention and controversy in the context of preimplantation genetic screening (PGS). To evaluate the extent of mosaic aneuploidy in clinical practice and to gain insight on the practices and views regarding this issue, we conducted a survey using a prospective, 20-item Web-based questionnaire with questions related to practices and views regarding mosaicism in PGS. A total of 102 in vitro fertilization (IVF) units from 32 countries that performed 108,900 IVF cycles annually responded to the survey...
April 19, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28393271/analysis-of-implantation-and-ongoing-pregnancy-rates-following-the-transfer-of-mosaic-diploid-aneuploid-blastocysts
#2
Elpida Fragouli, Samer Alfarawati, Katharina Spath, Dhruti Babariya, Nicoletta Tarozzi, Andrea Borini, Dagan Wells
Preimplantation genetic testing for aneuploidy (PGT-A) is widely used in IVF and aims to improve outcomes by avoiding aneuploid embryo transfers. Chromosomal mosaicism is extremely common in early development and could affect the efficacy of PGT-A by causing incorrect embryo classification. Recent innovations have allowed accurate mosaicism detection in trophectoderm samples taken from blastocysts. However, there is little data concerning the impact of mosaicism on viability, and the optimal clinical pathway for such embryos is unclear...
April 9, 2017: Human Genetics
https://www.readbyqxmd.com/read/28390692/detection-of-mosaicism-at-blastocyst-stage-with-the-use-of-high-resolution-next-generation-sequencing
#3
REVIEW
Santiago Munné, Dagan Wells
A significant proportion of human preimplantation embryos produced during the course of in vitro fertilization (IVF) treatments contain two or more cytogenetically distinct cell lines. This phenomenon, known as chromosomal mosaicism, can involve the presence of cells with different types of aneuploidy in the absence of any normal cells or a mixture of euploid and abnormal cells. Although a high prevalence of mosaicism at the cleavage and blastocyst stages has been appreciated for two decades, the precise frequency of the phenomenon and its consequences for embryo viability have been difficult to quantify...
April 6, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28367155/biotechnological-advancements-and-begomovirus-management-in-okra-abelmoschus-esculentus-l-status-and-perspectives
#4
REVIEW
Gyan P Mishra, Bijendra Singh, Tania Seth, Achuit K Singh, Jaydeep Halder, Nagendran Krishnan, Shailesh K Tiwari, Prabhakar M Singh
Despite the importance of okra, as one of the important vegetable crop, very little attention has been paid to its genetic improvement using advanced biotechnological tools. The exploitation of marker assisted breeding in okra is often limited due to the availability of a few molecular markers, the absence of molecular genetic-map(s), and other molecular tools. Chromosome linkage-groups were not yet constructed for this crop and reports on marker development are very scanty and mostly hovering around cultivar characterization...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#5
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28276293/prenatal-detection-of-pik3ca-related-overgrowth-spectrum-in-cultured-amniocytes-using-long-range-pcr-and-next-generation-sequencing
#6
Elizabeth Quinlan-Jones, Denise Williams, Charlotte Bell, Claire Miller, Carolyn Gokhale, Mark D Kilby
Mutations in PIK3CA are associated with overgrowth spectrum disorders including excessive growth in some areas of the body and the central nervous system. Alterations in PIK3CA occur as somatic, postzygotic events and confer a mosaic genotype with variability in phenotypic expression being commonly observed. We describe the second reported prenatal diagnosis of a PIK3CA-related overgrowth spectrum disorder. The prenatal ultrasound features in this case enabled the presumptive, prospective diagnosis to be made which was then confirmed by genetic testing...
January 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28261977/tissue-specific-mosaicism-for-a-lethal-osteogenesis-imperfecta-col1a1-mutation-causes-mild-oi-eds-overlap-syndrome
#7
Sofie Symoens, Wouter Steyaert, Lynn Demuynck, Anne De Paepe, Karin E M Diderich, Fransiska Malfait, Paul J Coucke
Type I collagen is the predominant protein of connective tissues such as skin and bone. Mutations in the type I collagen genes (COL1A1 and COL1A2) mainly cause osteogenesis imperfecta (OI). We describe a patient with clinical signs of Ehlers-Danlos syndrome (EDS), including fragile skin, easy bruising, recurrent luxations, and fractures resembling mild OI. Biochemical collagen analysis of the patients' dermal fibroblasts showed faint overmodification of the type I collagen bands, a finding specific for structural defects in type I collagen...
March 6, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28247096/next-generation-sequencing-and-molecular-analysis-of-artichoke-italian-latent-virus
#8
Toufic Elbeaino, Imen Belghacem, Tiziana Mascia, Donato Gallitelli, Michele Digiaro
Next-generation sequencing (NGS) allowed the assembly of the complete RNA-1 and RNA-2 sequences of a grapevine isolate of artichoke Italian latent virus (AILV). RNA-1 and RNA-2 are 7,338 and 4,630 nucleotides in length excluding the 3' terminal poly(A) tail, and encode two putative polyproteins of 255.8 kDa (p1) and 149.6 kDa (p2), respectively. All conserved motifs and predicted cleavage sites, typical for nepovirus polyproteins, were found in p1 and p2. AILV p1 and p2 share high amino acid identity with their homologues in beet ringspot virus (p1, 81% and p2, 71%), tomato black ring virus (p1, 79% and p2, 63%), grapevine Anatolian ringspot virus (p1, 65% and p2, 63%), and grapevine chrome mosaic virus (p1, 60% and p2, 54%), and to a lesser extent with other grapevine nepoviruses of subgroup A and C...
February 28, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28202009/development-of-intron-targeting-it-markers-specific-for-chromosome-arm-4vs-of-haynaldia-villosa-by-chromosome-sorting-and-next-generation-sequencing
#9
Haiyan Wang, Keli Dai, Jin Xiao, Chunxia Yuan, Renhui Zhao, Jaroslav Doležel, Yufeng Wu, Aizhong Cao, Peidu Chen, Shouzhong Zhang, Xiue Wang
BACKGROUND: Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28173822/an-example-of-the-utility-of-genomic-analysis-for-fast-and-accurate-clinical-diagnosis-of-complex-rare-phenotypes
#10
Polona Le Quesne Stabej, Chela James, Louise Ocaka, Mehmet Tekman, Stephanie Grunewald, Emma Clement, Horia C Stanescu, Robert Kleta, Deborah Morrogh, Alistair Calder, Hywel J Williams, Maria Bitner-Glindzicz
BACKGROUND: We describe molecular diagnosis in a complex consanguineous family: four offspring presented with combinations of three distinctive phenotypes; non-syndromic hearing loss (NSHL), an unusual skeletal phenotype comprising multiple fractures, cranial abnormalities and diaphyseal expansion, and significant developmental delay with microcephaly. We performed Chromosomal Microarray Analysis on the offspring with either the skeletal or developmental delay phenotypes, and linkage analysis and whole exome sequencing (WES) on all four children, parents and maternal aunt...
February 7, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28151489/molecular-diagnosis-of-pik3ca-related-overgrowth-spectrum-pros-in-162-patients-and-recommendations-for-genetic-testing
#11
Paul Kuentz, Judith St-Onge, Yannis Duffourd, Jean-Benoît Courcet, Virginie Carmignac, Thibaud Jouan, Arthur Sorlin, Claire Abasq-Thomas, Juliette Albuisson, Jeanne Amiel, Daniel Amram, Stéphanie Arpin, Tania Attie-Bitach, Nadia Bahi-Buisson, Sébastien Barbarot, Geneviève Baujat, Didier Bessis, Olivia Boccara, Maryse Bonnière, Odile Boute, Anne-Claire Bursztejn, Christine Chiaverini, Valérie Cormier-Daire, Christine Coubes, Bruno Delobel, Patrick Edery, Salima El Chehadeh, Christine Francannet, David Geneviève, Alice Goldenberg, Damien Haye, Bertrand Isidor, Marie-Line Jacquemont, Philippe Khau Van Kien, Didier Lacombe, Ludovic Martin, Jelena Martinovic, Annabel Maruani, Michèle Mathieu-Dramard, Juliette Mazereeuw-Hautier, Caroline Michot, Cyril Mignot, Juliette Miquel, Fanny Morice-Picard, Florence Petit, Alice Phan, Massimiliano Rossi, Renaud Touraine, Alain Verloes, Marie Vincent, Catherine Vincent-Delorme, Sandra Whalen, Marjolaine Willems, Nathalie Marle, Daphné Lehalle, Julien Thevenon, Christel Thauvin-Robinet, Smaïl Hadj-Rabia, Laurence Faivre, Pierre Vabres, Jean-Baptiste Rivière
PURPOSE: Postzygotic activating mutations of PIK3CA cause a wide range of mosaic disorders collectively referred to as PIK3CA-related overgrowth spectrum (PROS). We describe the diagnostic yield and characteristics of PIK3CA sequencing in PROS. METHODS: We performed ultradeep next-generation sequencing (NGS) of PIK3CA in various tissues from 162 patients referred to our clinical laboratory and assessed diagnostic yield by phenotype and tissue tested. RESULTS: We identified disease-causing mutations in 66...
February 2, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28132024/mosaichunter-accurate-detection-of-postzygotic-single-nucleotide-mosaicism-through-next-generation-sequencing-of-unpaired-trio-and-paired-samples
#12
August Yue Huang, Zheng Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Xiaoxu Yang, Yuehua Zhang, Liping Wei
Genomic mosaicism arising from postzygotic mutations has long been associated with cancer and more recently with non-cancer diseases. It has also been detected in healthy individuals including healthy parents of children affected with genetic disorders, highlighting its critical role in the origin of genetic mutations. However, most existing software for the genome-wide identification of single-nucleotide mosaicisms (SNMs) requires a paired control tissue obtained from the same individual which is often unavailable for non-cancer individuals and sometimes missing in cancer studies...
January 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28107419/a-new-israeli-tobamovirus-isolate-infects-tomato-plants-harboring-tm-22-resistance-genes
#13
Neta Luria, Elisheva Smith, Victoria Reingold, Ilana Bekelman, Moshe Lapidot, Ilan Levin, Nadav Elad, Yehudit Tam, Noa Sela, Ahmad Abu-Ras, Nadav Ezra, Ami Haberman, Liron Yitzhak, Oded Lachman, Aviv Dombrovsky
An outbreak of a new disease infecting tomatoes occurred in October-November 2014 at the Ohad village in Southern Israel. Symptomatic plants showed a mosaic pattern on leaves accompanied occasionally by narrowing of leaves and yellow spotted fruit. The disease spread mechanically and rapidly reminiscent of tobamovirus infection. Epidemiological studies showed the spread of the disease in various growing areas, in the South and towards the Southeast and Northern parts of the country within a year. Transmission electron microscope (TEM) analysis showed a single rod-like form characteristic to the Tobamovirus genus...
2017: PloS One
https://www.readbyqxmd.com/read/28106558/validation-of-suspected-somatic-single-nucleotide-variations-in-the-brain-of-alzheimer-s-disease-patients
#14
Alberto Gomez-Ramos, Angel J Picher, Esther García, Patricia Garrido, Felix Hernandez, Eduardo Soriano, Jesús Avila
Next-generation sequencing techniques and genome-wide association study analyses have provided a huge amount of data, thereby enabling the identification of DNA variations and mutations related to disease pathogenesis. New techniques and software tools have been developed to improve the accuracy and reliability of this identification. Most of these tools have been designed to discover and validate single nucleotide variants (SNVs). However, in addition to germ-line mutations, human tissues bear genomic mosaicism, which implies that somatic events are present only in low percentages of cells within a given tissue, thereby hindering the validation of these variations using standard genetic tools...
January 19, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28077634/characterization-of-hepatitis-c-virus-hcv-envelope-diversification-from-acute-to-chronic-infection-within-a-sexually-transmitted-hcv-cluster-by-using-single-molecule-real-time-sequencing
#15
Cynthia K Y Ho, Jayna Raghwani, Sylvie Koekkoek, Richard H Liang, Jan T M Van der Meer, Marc Van Der Valk, Menno De Jong, Oliver G Pybus, Janke Schinkel, Richard Molenkamp
In contrast to other available next-generation sequencing platforms, PacBio single-molecule, real-time (SMRT) sequencing has the advantage of generating long reads albeit with a relatively higher error rate in unprocessed data. Using this platform, we longitudinally sampled and sequenced the hepatitis C virus (HCV) envelope genome region (1,680 nucleotides [nt]) from individuals belonging to a cluster of sexually transmitted cases. All five subjects were coinfected with HIV-1 and a closely related strain of HCV genotype 4d...
March 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28063088/mosaicism-for-a-pathogenic-mfn2-mutation-causes-minimal-clinical-features-of-cmt2a-in-the-parent-of-a-severely-affected-child
#16
Katherine Schon, Olivera Spasic-Boskovic, Kim Brugger, Tracey D Graves, Stephen Abbs, Soo-Mi Park, Gautam Ambegaonkar, Ruth Armstrong
Charcot-Marie-Tooth disease (CMT) refers to a genetically heterogeneous group of disorders which cause a peripheral motor and sensory neuropathy. The overall prevalence is 1 in 2500 individuals. Mutations in the MFN2 gene are the commonest cause for the axonal (CMT2) type. We describe a Caucasian 5-year old girl affected by CMT2A since the age of 2 years. She presented with unsteady gait, in-turning of the feet and progressive foot deformities. Nerve conduction studies suggested an axonal neuropathy and molecular testing identified a previously reported pathogenic variant c...
January 2017: Neurogenetics
https://www.readbyqxmd.com/read/28049534/case-report-maternal-mosaicism-resulting-in-inheritance-of-a-novel-gata6-mutation-causing-pancreatic-agenesis-and-neonatal-diabetes-mellitus
#17
Daphne Yau, Elisa De Franco, Sarah E Flanagan, Sian Ellard, Miriam Blumenkrantz, John J Mitchell
BACKGROUND: Haploinsufficiency of the GATA6 transcription factor gene was recently found to be the most common cause of pancreatic agenesis, a rare cause of neonatal diabetes mellitus. Although most cases are de novo, we describe three siblings with inherited GATA6 haploinsufficiency and the rare finding of parental mosaicism. CASE PRESENTATION: The proband was born at term with severe intrauterine growth restriction, the first child of non-consanguineous parents...
January 3, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/28040094/introduction-subchromosomal-abnormalities-in-preimplantation-embryonic-aneuploidy-screening
#18
Richard T Scott
The application of next generation sequencing platforms for embryonic aneuploidy screening provides enhanced resolution that allows routine evaluation of subchromosomal copy number abnormalities and mosaicism. Approximately 20% of embryos that would be designated as euploid using the conventional 24-chromosome aneuploidy screening will have evidence of a subchromosomal abnormality or mosaicism. This new information brings many challenges. Understanding the impact of these abnormalities on implantation and delivery rates is key to optimizing clinical counseling and management...
January 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/27977123/profiling-protease-specificity-combining-yeast-er-sequestration-screening-yess-with-next-generation-sequencing
#19
Qing Li, Li Yi, Kam Hon Hoi, Peter Marek, George Georgiou, Brent L Iverson
An enzyme engineering technology involving yeast endoplasmic reticulum (ER) sequestration screening (YESS) has been recently developed. Here, a new method is established, in which the YESS platform is combined with NextGen sequencing (NGS) to enable a comprehensive survey of protease specificity. In this approach, a combinatorial substrate library is targeted to the yeast ER and transported through the secretory pathway, interacting with any protease(s) residing in the ER. Multicolor FACS screening is used to isolate cells labeled with fluorophore-conjugated antibodies, followed by NGS to profile the cleaved substrates...
January 3, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/27943641/genomic-variants-genes-and-pathways-of-alzheimer-s-disease-an-overview
#20
REVIEW
Adam C Naj, Gerard D Schellenberg
Alzheimer's disease (AD) (MIM: 104300) is a highly heritable disease with great complexity in its genetic contributors, and represents the most common form of dementia. With the gradual aging of the world's population, leading to increased prevalence of AD, and the substantial cost of care for those afflicted, identifying the genetic causes of disease represents a critical effort in identifying therapeutic targets. Here we provide a comprehensive review of genomic studies of AD, from the earliest linkage studies identifying monogenic contributors to early-onset forms of AD to the genome-wide and rare variant association studies of recent years that are being used to characterize the mosaic of genetic contributors to late-onset AD (LOAD), and which have identified approximately ∼20 genes with common variants contributing to LOAD risk...
January 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
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