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Mosaicism next generation sequencing

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27667122/deletions-overlapping-vcan-exon-8-are-new-molecular-defects-for-wagner-disease
#15
Cyril Burin-des-Roziers, Pierre-Raphael Rothschild, Valérie Layet, Jian-Min Chen, Tiffany Ghiotti, Céline Leroux, Frans P M Cremers, Antoine P Brézin, Sophie Valleix
Wagner disease is a rare nonsyndromic autosomal-dominant vitreoretinopathy, associated with splice mutations specifically targeting VCAN exon 8. We report the extensive genetic analysis of two Wagner probands, previously found negative for disease-associated splice mutations. Next-generation sequencing (NGS), quantitative real-time PCR, and long-range PCR identified two deletions (3.4 and 10.5 kb) removing at least one exon-intron boundary of exon 8, and both correlating with an imbalance of VCAN mRNA isoforms...
January 2017: Human Mutation
https://www.readbyqxmd.com/read/27650192/rapid-identification-of-qtls-underlying-resistance-to-cucumber-mosaic-virus-in-pepper-capsicum-frutescens
#16
Guangjun Guo, Shubin Wang, Jinbing Liu, Baogui Pan, Weiping Diao, Wei Ge, Changzhou Gao, John C Snyder
Next-generation sequencing enabled a fast discovery of QTLs controlling CMV resistant in pepper. The gene CA02g19570 as a possible candidate gene of qCmr2.1 was identified for resistance to CMV in pepper. Cucumber mosaic virus (CMV) is one of the most important viruses infecting pepper, but the genetic basis of CMV resistance in pepper is elusive. In this study, we identified a candidate gene for CMV resistance QTL, qCmr2.1 through SLAF-seq. Segregation analysis in F2, BC1 and F2:3 populations derived from a cross between two inbred lines 'PBC688' (CMV-resistant) and 'G29' (CMV-susceptible) suggested quantitative inheritance of resistance to CMV in pepper...
September 20, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27631024/pik3ca-associated-developmental-disorders-exhibit-distinct-classes-of-mutations-with-variable-expression-and-tissue-distribution
#17
Ghayda Mirzaa, Andrew E Timms, Valerio Conti, Evan August Boyle, Katta M Girisha, Beth Martin, Martin Kircher, Carissa Olds, Jane Juusola, Sarah Collins, Kaylee Park, Melissa Carter, Ian Glass, Inge Krägeloh-Mann, David Chitayat, Aditi Shah Parikh, Rachael Bradshaw, Erin Torti, Stephen Braddock, Leah Burke, Sondhya Ghedia, Mark Stephan, Fiona Stewart, Chitra Prasad, Melanie Napier, Sulagna Saitta, Rachel Straussberg, Michael Gabbett, Bridget C O'Connor, Catherine E Keegan, Lim Jiin Yin, Angeline Hwei Meeng Lai, Nicole Martin, Margaret McKinnon, Marie-Claude Addor, Luigi Boccuto, Charles E Schwartz, Agustina Lanoel, Robert L Conway, Koenraad Devriendt, Katrina Tatton-Brown, Mary Ella Pierpont, Michael Painter, Lisa Worgan, James Reggin, Raoul Hennekam, Karen Tsuchiya, Colin C Pritchard, Mariana Aracena, Karen W Gripp, Maria Cordisco, Hilde Van Esch, Livia Garavelli, Cynthia Curry, Anne Goriely, Hulya Kayserilli, Jay Shendure, John Graham, Renzo Guerrini, William B Dobyns
Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals...
June 16, 2016: JCI Insight
https://www.readbyqxmd.com/read/27617123/next-generation-sequencing-in-intellectual-disability
#18
REVIEW
Gemma L Carvill, Heather C Mefford
Next-generation sequencing technologies have revolutionized gene discovery in patients with intellectual disability (ID) and led to an unprecedented expansion in the number of genes implicated in this disorder. We discuss the strategies that have been used to identify these novel genes for both syndromic and nonsyndromic ID and highlight the phenotypic and genetic heterogeneity that underpin this condition. Finally, we discuss the future of defining the genetic etiology of ID, including the role of whole-genome sequencing, mosaicism, and the importance of diagnostic testing in ID...
September 2015: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/27616633/evidence-for-feasibility-of-fetal-trophoblastic-cell-based-noninvasive-prenatal-testing
#19
Amy M Breman, Jennifer C Chow, Lance U'Ren, Elizabeth A Normand, Sadeem Qdaisat, Li Zhao, David M Henke, Rui Chen, Chad A Shaw, Laird Jackson, Yaping Yang, Liesbeth Vossaert, Rachel H V Needham, Elizabeth J Chang, Daniel Campton, Jeffrey L Werbin, Ron C Seubert, Ignatia B Van den Veyver, Jackie L Stilwell, Eric P Kaldjian, Arthur L Beaudet
OBJECTIVE: The goal was to develop methods for detection of chromosomal and subchromosomal abnormalities in fetal cells in the mother's circulation at 10-16 weeks' gestation using analysis by array comparative genomic hybridization (CGH) and/or next-generation sequencing (NGS). METHOD: Nucleated cells from 30 mL of blood collected at 10-16 weeks' gestation were separated from red cells by density fractionation and then immunostained to identify cytokeratin positive and CD45 negative trophoblasts...
November 2016: Prenatal Diagnosis
https://www.readbyqxmd.com/read/27587336/drivers-of-bacterial-genomes-plasticity-and-roles-they-play-in-pathogen-virulence-persistence-and-drug-resistance
#20
REVIEW
Seema Patel
Despite the advent of next-generation sequencing (NGS) technologies, sophisticated data analysis and drug development efforts, bacterial drug resistance persists and is escalating in magnitude. To better control the pathogens, a thorough understanding of their genomic architecture and dynamics is vital. Bacterial genome is extremely complex, a mosaic of numerous co-operating and antagonizing components, altruistic and self-interested entities, behavior of which are predictable and conserved to some extent, yet largely dictated by an array of variables...
August 30, 2016: Infection, Genetics and Evolution
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