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Mosaicism next generation sequencing

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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-hcv-envelope-diversification-from-acute-to-chronic-infection-using-smrt-sequencing-within-a-sexually-transmitted-hepatitis-c-virus-cluster
#7
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 (1680 nt) from individuals belonging to a cluster of sexually-transmitted cases. All five subjects were HIV-1 coinfected and infected with a closely related strain of HCV genotype 4d...
January 11, 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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27868338/incomplete-timothy-syndrome-secondary-to-a-mosaic-mutation-of-the-cacna1c-gene-diagnosed-using-next-generation-sequencing
#13
Amandine Baurand, Sylvie Falcon-Eicher, Gabriel Laurent, Elisabeth Villain, Caroline Bonnet, Christel Thauvin-Robinet, Caroline Jacquot, Jean-Christophe Eicher, Jean-Baptiste Gourraud, Sébastien Schmitt, Stéphane Bézieau, Mathilde Giraud, Solenne Dumont, Paul Kuentz, Vincent Probst, Antoine Burguet, Florence Kyndt, Laurence Faivre
Autosomal dominant genetic diseases can occur de novo and in the form of somatic mosaicism, which can give rise to a less severe phenotype, and make diagnosis more difficult given the sensitivity limits of the methods used. We report the case of female child with a history of surgery for syndactyly of the hands and feet, who was admitted at 6 years of age to a pediatric intensive care unit following cardiac arrest. The electrocardiogram (ECG) showed a long QT interval that on occasions reached 500 ms. Despite the absence of facial dysmorphism and the presence of normal psychomotor development, a diagnosis of Timothy syndrome was made given the association of syndactyly and the ECG features...
February 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27861560/a-genetic-algorithm-for-diploid-genome-reconstruction-using-paired-end-sequencing
#14
Chuan-Kang Ting, Choun-Sea Lin, Ming-Tsai Chan, Jian-Wei Chen, Sheng-Yu Chuang, Yao-Ting Huang
The genome of many species in the biosphere is a diploid consisting of paternal and maternal haplotypes. The differences between these two haplotypes range from single nucleotide polymorphisms (SNPs) to large-scale structural variations (SVs). Existing genome assemblers for next-generation sequencing platforms attempt to reconstruct one consensus sequence, which is a mosaic of two parental haplotypes. Reconstructing paternal and maternal haplotypes is an important task in linkage analysis and association studies...
2016: PloS One
https://www.readbyqxmd.com/read/27842993/diagnosis-and-clinical-management-of-embryonic-mosaicism
#15
REVIEW
Nidhee M Sachdev, Susan M Maxwell, Andria G Besser, James A Grifo
Embryonic mosaicism occurs when two or more cell populations with different genotypes are present within the same embryo. New diagnostic techniques for preimplantation genetic screening (PGS), such as next-generation sequencing, have led to increased reporting of mosaicism. The interpretation of mosaicism is complicated because the transfer of some mosaic embryos has resulted in live births. Mosaic embryos may represent a third category between normal (euploidy) and abnormal (aneuploidy). This category of mosaic embryos may be characterized by decreased implantation and pregnancy potential as well as increased risk of genetic abnormalities and adverse pregnancy outcomes...
January 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/27814723/ecogenomic-survey-of-plant-viruses-infecting-tobacco-by-next-generation-sequencing
#16
Ibukun A Akinyemi, Fang Wang, Benguo Zhou, Shuishui Qi, Qingfa Wu
BACKGROUND: The invasion of plant by viruses cause major damage to plants and reduces crop yield and integrity. Devastating plant virus infection has been experienced at different times all over the world, which are attributed to different events of mutation, re-assortment and recombination occurring in the viruses. Strategies for proper virus management has been mostly limited to eradicating the vectors that spreads the plant viruses. However, development of prompt and effective diagnostic methods are required to monitor emerging and re-emerging diseases that may be symptomatic or asymptomatic in the plant as well as the genetic variation and evolution in the plant viruses...
November 4, 2016: Virology Journal
https://www.readbyqxmd.com/read/27796712/female-x-linked-alport-syndrome-with-somatic-mosaicism
#17
Kana Yokota, Kandai Nozu, Shogo Minamikawa, Tomohiko Yamamura, Keita Nakanishi, Hisashi Kaneda, Riku Hamada, Yoshimi Nozu, Akemi Shono, Takeshi Ninchoji, Naoya Morisada, Shingo Ishimori, Junya Fujimura, Tomoko Horinouchi, Hiroshi Kaito, Koichi Nakanishi, Ichiro Morioka, Mariko Taniguchi-Ikeda, Kazumoto Iijima
BACKGROUND: X-linked Alport syndrome (XLAS) is a progressive, hereditary nephropathy. Although males with XLAS usually develop end-stage renal disease before 30 years of age, some men show a milder phenotype and possess somatic mosaic variants of the type IV collagen α5 gene (COL4A5), with severity depending on variant frequencies. In females, somatic mosaic variants are rarely reported in XLAS, and it is not clear what determines severity. METHODS: Two females with somatic mosaic mutations in COL4A5 with variant frequencies of 17...
October 31, 2016: Clinical and Experimental Nephrology
https://www.readbyqxmd.com/read/27720647/sanger-confirmation-is-required-to-achieve-optimal-sensitivity-and-specificity-in-next-generation-sequencing-panel-testing
#18
Wenbo Mu, Hsiao-Mei Lu, Jefferey Chen, Shuwei Li, Aaron M Elliott
Next-generation sequencing (NGS) has rapidly replaced Sanger sequencing as the method of choice for diagnostic gene-panel testing. For hereditary-cancer testing, the technical sensitivity and specificity of the assay are paramount as clinicians use results to make important clinical management and treatment decisions. There is significant debate within the diagnostics community regarding the necessity of confirming NGS variant calls by Sanger sequencing, considering that numerous laboratories report having 100% specificity from the NGS data alone...
October 4, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/27692437/why-do-euploid-embryos-miscarry-a-case-control-study-comparing-the-rate-of-aneuploidy-within-presumed-euploid-embryos-that-resulted-in-miscarriage-or-live-birth-using-next-generation-sequencing
#19
Susan M Maxwell, Pere Colls, Brooke Hodes-Wertz, David H McCulloh, Caroline McCaffrey, Dagan Wells, Santiago Munné, James A Grifo
OBJECTIVE: To determine whether undetected aneuploidy contributes to pregnancy loss after transfer of euploid embryos that have undergone array comparative genomic hybridization (aCGH). DESIGN: Case-control study. SETTING: University-based fertility center. PATIENT(S): Cases included 38 patients who underwent frozen euploid ET as determined by aCGH, resulting in miscarriage. Controls included 38 patients who underwent frozen euploid ET as determined by aCGH, resulting in a live birth...
November 2016: Fertility and Sterility
https://www.readbyqxmd.com/read/27681629/early-somatic-mosaicism-is-a-rare-cause-of-long-qt-syndrome
#20
James Rush Priest, Charles Gawad, Kristopher M Kahlig, Joseph K Yu, Thomas O'Hara, Patrick M Boyle, Sridharan Rajamani, Michael J Clark, Sarah T K Garcia, Scott Ceresnak, Jason Harris, Sean Boyle, Frederick E Dewey, Lindsey Malloy-Walton, Kyla Dunn, Megan Grove, Marco V Perez, Norma F Neff, Richard Chen, Katsuhide Maeda, Anne Dubin, Luiz Belardinelli, John West, Christian Antolik, Daniela Macaya, Thomas Quertermous, Natalia A Trayanova, Stephen R Quake, Euan A Ashley
Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel NaV1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
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