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Mosaicism next generation sequencing

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https://www.readbyqxmd.com/read/28579407/detailed-investigation-into-the-cytogenetic-constitution-and-pregnancy-outcome-of-replacing-mosaic-blastocysts-detected-with-the-use-of-high-resolution-next-generation-sequencing
#1
Santiago Munné, Joshua Blazek, Michael Large, Pedro A Martinez-Ortiz, Haley Nisson, Emmeline Liu, Nicoletta Tarozzi, Andrea Borini, Amie Becker, John Zhang, Susan Maxwell, James Grifo, Dhruti Babariya, Dagan Wells, Elpida Fragouli
OBJECTIVE: To determine the pregnancy outcome potential of mosaic embryos, detected by means of preimplantation genetic screening (PGS) with the use of next-generation sequencing (NGS). DESIGN: Retrospective study. SETTING: Genetics laboratories. PATIENT(S): PGS cycles during which either mosaic or euploid embryos were replaced. INTERVENTION(S): Blastocysts were biopsied and processed with the use of NGS, followed by frozen embryo transfer...
June 1, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/28549997/deep-sequencing-of-atrial-fibrillation-patients-with-mitral-valve-regurgitation-shows-no-evidence-of-mosaicism-but-reveals-novel-rare-germline-variants
#2
Emilie Gregers, Gustav Ahlberg, Thea Christensen, Javad Jabbari, Kirstine O Larsen, Cecilie B Herfelt, Kristoffer M Henningsen, Laura Andreasen, Jens J Thiis, Jens Lund, Susanne Holme, Stig Haunsø, Bo H Bentzen, Nicole Schmitt, Jesper H Svendsen, Morten S Olesen
BACKGROUND: Atrial fibrillation (AF) is the most common cardiac arrhythmia. Valvular heart disease is a strong predictor, yet the underlying molecular mechanisms are unknown. OBJECTIVE: The purpose of this study was to investigate the prevalence of somatic variants in AF candidate genes in an AF patient population undergoing surgery for mitral valve regurgitation (MVR) to determine whether these patients are genetically predisposed to AF. METHODS: DNA was extracted from blood and left atrial tissue from 44 AF patients with MVR...
May 24, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28502730/overgrowth-syndromes-caused-by-somatic-variants-in-the-phosphatidylinositol-3-kinase-akt-mammalian-target-of-rapamycin-pathway
#3
REVIEW
Gozde Akgumus, Fengqi Chang, Marilyn M Li
Somatic variants have been well described in tumorigenesis; however, they are only recently appreciated in other human disorders, such as mosaic overgrowth syndromes. Although overgrowth is a manifestation in many genetic syndromes, not all overgrowth syndromes are inherited. Mosaic somatic variants have been lately described in several overgrowth disorders, such as Proteus syndrome, CLOVES (congenital, lipomatous, overgrowth, vascular malformations, epidermal nevi, and spinal/skeletal anomalies and/or scoliosis) syndrome, megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, and megalencephaly-capillary malformation-polymicrogyria syndrome...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28502725/molecular-diagnosis-of-mosaic-overgrowth-syndromes-using-a-custom-designed-next-generation-sequencing-panel
#4
Fengqi Chang, Liu Liu, Erica Fang, Guangcheng Zhang, Tiansheng Chen, Kajia Cao, Yanchun Li, Marilyn M Li
Recent studies have discovered a group of overgrowth syndromes, such as congenital lipomatous overgrowth with vascular, epidermal, and skeletal anomalies (CLOVES) syndrome, Proteus syndrome, and megalencephaly-capillary malformation-polymicrogyria (MCAP) syndrome, are caused by somatic activating variants in the genes involved in the phosphatidylinositol 3-kinase/AKT/mechanistic target of rapamycin pathway. Because of the low-abundance nature of these pathogenic variants, Sanger sequencing often yields negative results...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28497491/male-child-with-somatic-mosaic-osteopathia-striata-with-cranial-sclerosis-caused-by-a-novel-pathogenic-amer1-frameshift-mutation
#5
Jennifer Hague, Isabelle Delon, Kim Brugger, Howard Martin, Leanne Sparnon, Ingrid Simonic, Stephen Abbs, Soo-Mi Park
Osteopathia striata with cranial sclerosis (OSCS; OMIM #300373) is a rare X-linked dominant condition caused by mutations in the AMER1 gene (also known as WTX or FAM123B). It is a condition which usually affects females in whom the clinical phenotype can be extremely variable. Conversely affected males typically die in utero or during the neonatal period [Perdu et al. (); Clinical Genetics 80: 383-388; Vasiljevic et al. (); Prenatal Diagnosis 35: 302-304]. There have been a small number of reported cases of surviving males, including three patients who are somatic mosaic for the condition [Chénier, Noor, Dupuis, Stavropoulos, & Mendoza-Londono, (); American Journal of Medical Genetics Part A 158A: 2946-2952; Holman et al...
May 12, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28450889/identification-of-mosaic-and-segmental-aneuploidies-by-next-generation-sequencing-in-preimplantation-genetic-screening-can-improve-clinical-outcomes-compared-to-array-comparative-genomic-hybridization
#6
Hsing-Hua Lai, Tzu-Hsuan Chuang, Lin-Kin Wong, Meng-Ju Lee, Chia-Lin Hsieh, Huai-Lin Wang, Shee-Uan Chen
BACKGROUND: Chromosomal mosaicism is observed as the presence of both euploid and aneuploid cells in a particular blastocyst. Recent studies have reported that the implantation rate of mosaic embryo transfer is remarkably lower than the euploid embryos. The superior capability of next-generation sequencing (NGS) to detect chromosomal mosaicism in preimplantation genetic screening (PGS) remains controversial, and several data displayed similar implantation and pregnancy rates using NGS or array comparative genomic hybridization (aCGH)...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28433368/chromosomal-mosaicism-detected-during-preimplantation-genetic-screening-results-of-a-worldwide-web-based-survey
#7
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...
May 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
#8
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
#9
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
#10
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-toward-next-generation-sequencing-and-newborn-screening
#11
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in female patients and is not currently part of newborn screening (NBS). Diagnosis is often delayed, resulting in missed crucial diagnostic and therapeutic opportunities. Objectives: This study sought to determine if whole-exome sequencing (WES) as part of a potential NBS program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on blood samples from women with TS (n = 27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
May 1, 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
#12
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
#13
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
#14
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...
June 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
#15
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
#16
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
#17
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
#18
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...
June 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28107419/a-new-israeli-tobamovirus-isolate-infects-tomato-plants-harboring-tm-22-resistance-genes
#19
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
#20
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
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