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Mosaicism next generation sequencing

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
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...
September 27, 2016: Fertility and Sterility
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
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 non-syndromic 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, quantitative real-time PCR, and long-range PCR, identified two deletions (3.4 kb and 10.5 kb) removing at least one exon-intron boundary of exon 8, and both correlating with an imbalance of VCAN mRNA isoforms...
September 26, 2016: Human Mutation
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
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
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
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...
September 12, 2016: Prenatal Diagnosis
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
Sang-Yun Cho, Seungmo Lim, Hongsup Kim, Seung-In Yi, Jae Sun Moon
We report here the first complete genome sequence of Ornithogalum mosaic virus (OrMV) isolated from Taean, South Korea, in 2011, which was obtained by next-generation sequencing and Sanger sequencing. The sequence information provided here may serve as a potential reference for other OrMV isolates.
2016: Genome Announcements
Jacques Davy Ibaba, Mark D Laing, Augustine Gubba
Moroccan watermelon mosaic virus (MWMV) has been prevalent in cucurbits in the Republic of South Africa (RSA) since it was first reported in 1987. However, full genome studies of the South African isolates have never been conducted previously. The full genome of two MWMV isolates infecting cucurbits (Cucurbita pepo L.) in the province of KwaZulu-Natal, RSA, was compared with the genome of the Tunisian isolate in this communication. The genome sequences of the RSA MWMV isolates were elucidated using next-generation sequencing and Sanger sequencing...
July 23, 2016: Virus Genes
Matthew J Meier, Jason M O'Brien, Marc A Beal, Beverly Allan, Carole L Yauk, Francesco Marchetti
BACKGROUND: Mosaicism, the presence of genetically distinct cell populations within an organism, has emerged as an important contributor to disease. Mutational events occurring during embryonic development can cause mosaicism in any tissue, but the influence of environmental factors on levels of mosaicism is unclear. OBJECTIVES: We investigated whether in utero exposure to the widespread environmental mutagen benzo[a]pyrene (BaP) impacts the burden and distribution of mutations in adult mice...
July 22, 2016: Environmental Health Perspectives
Marta Cardoso, Paula Paulo, Sofia Maia, Manuel R Teixeira
Truncating activating mutations in the last exon of PPM1D have been described in patients with breast, ovarian, colorectal and non-small cell lung cancer, but recent data indicate that they may be associated with previous chemotherapy. In this study we evaluated the prevalence of PPM1D mutations in white blood cells (WBC) of 462 patients with early-onset and/or familial/hereditary prostate cancer (PrCa) by sequencing the coding region of exon 6. Two truncating mutations were found in two patients (0.4%), both treated with androgen-ablation therapy but no chemotherapy prior to blood collection...
July 12, 2016: Genes, Chromosomes & Cancer
Ahmad N Abou Tayoun, Bryan Krock, Nancy B Spinner
INTRODUCTION: The last two decades have witnessed revolutionary changes in clinical diagnostics, fueled by the Human Genome Project and advances in high throughput, Next Generation Sequencing (NGS). We review the current state of sequencing-based pediatric diagnostics, associated challenges, and future prospects. AREAS COVERED: We present an overview of genetic disease in children, review the technical aspects of Next Generation Sequencing and the strategies to make molecular diagnoses for children with genetic disease...
September 2016: Expert Review of Molecular Diagnostics
Anna Mensa-Vilaro, María Teresa Bosque, Giuliana Magri, Yoshitaka Honda, Helios Martínez-Banaclocha, Marta Casorran-Berges, Jordi Sintes, Eva González-Roca, Estibaliz Ruiz-Ortiz, Toshio Heike, Juan J Martínez-Garcia, Alberto Baroja-Mazo, Andrea Cerutti, Ryuta Nishikomori, Jordi Yagüe, Pablo Pelegrín, Concha Delgado-Beltran, Juan I Aróstegui
OBJECTIVE: Gain-of-function NLRP3 mutations cause cryopyrin-associated periodic syndromes (CAPS), with gene mosaicism playing a relevant role in their pathogenesis. This study was undertaken to characterise the genetic cause underlying a patient with late-onset but otherwise typical CAPS. METHODS: We studied a 64 years-old patient who presented with recurrent episodes of urticarial-like rash, fever, conjunctivitis, and oligoarthritis at the age of 56. DNA was extracted from both unfractionated blood, and from isolated leukocyte and CD34(+) subpopulations...
June 6, 2016: Arthritis & Rheumatology
Marc-Manuel Hahn, Lilian Vreede, Sonja A S A Bemelmans, Erica van der Looij, Ad Geurts van Kessel, Hans K Schackert, Marjolijn J L Ligtenberg, Nicoline Hoogerbrugge, Roland P Kuiper, Richarda M de Voer
Germline mutations in BUB1B, encoding BUBR1, one of the crucial components of the spindle assembly checkpoint (SAC), have been shown to cause variable phenotypes, including the recessive mosaic variegated aneuploidy (MVA) syndrome, which predisposes to cancer. Reduced levels of the wild-type BUBR1 protein have been linked to the development of gastrointestinal neoplasms. To determine whether mutations in BUB1B are enriched in individuals with colorectal cancer (CRC), we performed amplicon-based targeted next-generation sequencing of BUB1B on germline DNA of 192 individuals with early-onset CRC (≤50 years)...
November 2016: Genes, Chromosomes & Cancer
J D Ibaba, M D Laing, A Gubba
Zucchini shoestring virus (ZSSV) has been proposed to be a putative potyvirus in the papaya ringspot virus (PRSV) cluster, based on the sequence similarity of its coat protein to those of related potyviruses. ZSSV has been associated with the outbreak of a damaging disease of baby marrow (Cucurbita pepo L.) that had been observed throughout the province of KwaZulu-Natal, in the Republic of South Africa (RSA). We report the genome sequence of ZSSV, determined by next-generation sequencing of total RNA extracted from an infected baby marrow (Cucurbita pepo L...
August 2016: Archives of Virology
Wenke Zhang, Ying Liu, Li Wang, Hui Wang, Minyue Ma, Mengnan Xu, Xiaofei Xu, ZhiYing Gao, Jinliang Duan, David S Cram, Yuanqing Yao
PURPOSE: The purpose of this study was to apply next-generation sequencing (NGS) technology to identify chromosomally normal embryos for transfer in preimplantation genetic diagnosis (PGD) cycles for translocations. METHODS: A total of 21 translocation couples with a history of infertility and repeated miscarriage presented at our PGD clinic for 24-chromosome embryo testing using copy number variation sequencing (CNV-Seq). RESULTS: Testing of 98 embryo samples identified 68 aneuploid (69...
July 2016: Journal of Assisted Reproduction and Genetics
Wenhui L Li, Jonathan Buckley, Pedro A Sanchez-Lara, Dennis T Maglinte, Lucy Viduetsky, Tatiana V Tatarinova, Jennifer G Aparicio, Jonathan W Kim, Margaret Au, Dejerianne Ostrow, Thomas C Lee, Maurice O'Gorman, Alexander Judkins, David Cobrinik, Timothy J Triche
Retinoblastoma is a childhood eye malignancy that can lead to the loss of vision, eye(s), and sometimes life. The tumors are initiated by inactivating mutations in both alleles of the tumor-suppressor gene, RB1, or, rarely, by MYCN amplification. Timely identification of a germline RB1 mutation in blood samples or either somatic RB1 mutation or MYCN amplification in tumors is important for effective care and management of retinoblastoma patients and their families. However, current procedures to thoroughly test RB1 mutations are complicated and lengthy...
July 2016: Journal of Molecular Diagnostics: JMD
H Tuhan, A Anik, G Catli, H Onay, A Aykut, A Abaci, E Bober
Steroidogenic factor-1 (SF-1), also known as nuclear receptor subfamily 5 group A member 1 (NR5A1), is a member of orphan receptor subfamily and located on chromosome 9 (9q33). In 46, XY individuals with mutation of SF-1 gene, adrenal failure, testis dysgenesis, androgen synthesis defects, hypospadias and anorchia with microphallus, infertility can occur from severe to mild. We report a case of a 20-day-old male who is admitted to our clinic due to ambiguous genitalia. In this report, we describe a novel heterozygous c...
May 2, 2016: Andrologia
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