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Copy-number variant

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https://www.readbyqxmd.com/read/28654678/genetic-factors-affecting-ebv-copy-number-in-lymphoblastoid-cell-lines-derived-from-the-1000-genome-project-samples
#1
Rajendra Mandage, Marco Telford, Juan Antonio Rodríguez, Xavier Farré, Hafid Layouni, Urko M Marigorta, Caitlin Cundiff, Jose Maria Heredia-Genestar, Arcadi Navarro, Gabriel Santpere
Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection...
2017: PloS One
https://www.readbyqxmd.com/read/28653806/assessment-of-large-copy-number-variants-in-patients-with-apparently-isolated-congenital-left-sided-cardiac-lesions-reveals-clinically-relevant-genomic-events
#2
Neil A Hanchard, Luis A Umana, Lisa D'Alessandro, Mahshid Azamian, Mojisola Poopola, Shaine A Morris, Susan Fernbach, Seema R Lalani, Jeffrey A Towbin, Gloria A Zender, Sara Fitzgerald-Butt, Vidu Garg, Jessica Bowman, Gladys Zapata, Patricia Hernandez, Cammon B Arrington, Dieter Furthner, Siddharth K Prakash, Neil E Bowles, Kim L McBride, John W Belmont
Congenital left-sided cardiac lesions (LSLs) are a significant contributor to the mortality and morbidity of congenital heart disease (CHD). Structural copy number variants (CNVs) have been implicated in LSL without extra-cardiac features; however, non-penetrance and variable expressivity have created uncertainty over the use of CNV analyses in such patients. High-density SNP microarray genotyping data were used to infer large, likely-pathogenic, autosomal CNVs in a cohort of 1,139 probands with LSL and their families...
June 27, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28653505/development-of-kras-mutant-lung-adenocarcinoma-in-mice-with-knockout-of-the-airway-lineage-specific-gene-gprc5a
#3
Junya Fujimoto, Sayuri Nunomura-Nakamura, Yihua Liu, Wenhua Lang, Tina McDowell, Yasminka Jakubek, Dalia Ezzeddine, Joshua Kapere Ochieng, Jason Petersen, Gareth Davies, Junya Fukuoka, Ignacio I Wistuba, Erik Ehli, Jerry Fowler, Paul Scheet, Humam Kadara
Despite the urgency for prevention and treatment of lung adenocarcinoma (LUAD), we still do not know drivers in pathogenesis of the disease. Earlier work revealed that mice with knockout of the G-protein coupled receptor Gprc5a develop late onset lung tumors including LUADs. Here, we sought to further probe the impact of Gprc5a expression on LUAD pathogenesis. We first surveyed GPRC5A expression in human tissues and found that GPRC5A was markedly elevated in human normal lung relative to other normal tissues and was consistently down-regulated in LUADs...
June 27, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28650482/the-contribution-of-rare-variants-to-risk-of-schizophrenia-in-individuals-with-and-without-intellectual-disability
#4
Tarjinder Singh, James T R Walters, Mandy Johnstone, David Curtis, Jaana Suvisaari, Minna Torniainen, Elliott Rees, Conrad Iyegbe, Douglas Blackwood, Andrew M McIntosh, Georg Kirov, Daniel Geschwind, Robin M Murray, Marta Di Forti, Elvira Bramon, Michael Gandal, Christina M Hultman, Pamela Sklar, Aarno Palotie, Patrick F Sullivan, Michael C O'Donovan, Michael J Owen, Jeffrey C Barrett
By performing a meta-analysis of rare coding variants in whole-exome sequences from 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 family trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare, damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In patients with schizophrenia who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders...
June 26, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28649662/the-contribution-of-pathogenic-variants-in-breast-cancer-susceptibility-genes-to-familial-breast-cancer-risk
#5
Thomas P Slavin, Kara N Maxwell, Jenna Lilyquist, Joseph Vijai, Susan L Neuhausen, Steven N Hart, Vignesh Ravichandran, Tinu Thomas, Ann Maria, Danylo Villano, Kasmintan A Schrader, Raymond Moore, Chunling Hu, Bradley Wubbenhorst, Brandon M Wenz, Kurt D'Andrea, Mark E Robson, Paolo Peterlongo, Bernardo Bonanni, James M Ford, Judy E Garber, Susan M Domchek, Csilla Szabo, Kenneth Offit, Katherine L Nathanson, Jeffrey N Weitzel, Fergus J Couch
Understanding the gene-specific risks for development of breast cancer will lead to improved clinical care for those carrying germline mutations in cancer predisposition genes. We sought to detail the spectrum of mutations and refine risk estimates for known and proposed breast cancer susceptibility genes. Targeted massively-parallel sequencing was performed to identify mutations and copy number variants in 26 known or proposed breast cancer susceptibility genes in 2134 BRCA1/2-negative women with familial breast cancer (proband with breast cancer and a family history of breast or ovarian cancer) from a largely European-Caucasian multi-institutional cohort...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28649445/variable-phenotype-expression-in-a-family-segregating-microdeletions-of-the-nrxn1-and-mbd5-autism-spectrum-disorder-susceptibility-genes
#6
Marc Woodbury-Smith, Rob Nicolson, Mehdi Zarrei, Ryan K C Yuen, Susan Walker, Jennifer Howe, Mohammed Uddin, Ny Hoang, Janet A Buchanan, Christina Chrysler, Ann Thompson, Peter Szatmari, Stephen W Scherer
Autism Spectrum Disorder (ASD) is a developmental condition of early childhood onset, which impacts socio-communicative functioning and is principally genetic in etiology. Currently, more than 50 genomic loci are deemed to be associated with susceptibility to ASD, showing de novo and inherited unbalanced copy number variants (CNVs) and smaller insertions and deletions (indels), more complex structural variants (SVs), as well as single nucleotide variants (SNVs) deemed of pathological significance. However, the phenotypes associated with many of these genes are variable, and penetrance is largely unelaborated in clinical descriptions...
May 3, 2017: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28645800/high-throughput-sequencing-of-the-entire-genomic-regions-of-ccm1-krit1-ccm2-and-ccm3-pdcd10-to-search-for-pathogenic-deep-intronic-splice-mutations-in-cerebral-cavernous-malformations
#7
Matthias Rath, Sönke E Jenssen, Konrad Schwefel, Stefanie Spiegler, Dana Kleimeier, Christian Sperling, Lars Kaderali, Ute Felbor
Cerebral cavernous malformations (CCM) are vascular lesions of the central nervous system that can cause headaches, seizures and hemorrhagic stroke. Disease-associated mutations have been identified in three genes: CCM1/KRIT1, CCM2 and CCM3/PDCD10. The precise proportion of deep-intronic variants in these genes and their clinical relevance is yet unknown. Here, a long-range PCR (LR-PCR) approach for target enrichment of the entire genomic regions of the three genes was combined with next generation sequencing (NGS) to screen for coding and non-coding variants...
June 20, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28645778/whole-genome-sequencing-of-monozygotic-twins-discordant-for-schizophrenia-indicates-multiple-genetic-risk-factors-for-schizophrenia
#8
Jinsong Tang, Yu Fan, Hong Li, Qun Xiang, Deng-Feng Zhang, Zongchang Li, Ying He, Yanhui Liao, Ya Wang, Fan He, Fengyu Zhang, Yin Yao Shugart, Chunyu Liu, Yanqing Tang, Raymond C K Chan, Chuan-Yue Wang, Yong-Gang Yao, Xiaogang Chen
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight nonsynonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p...
June 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28645357/appreciating-the-population-wide-impact-of-copy-number-variants-on-cognition
#9
Joon-Yong An, Stephan J Sanders
No abstract text is available yet for this article.
July 15, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#10
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641109/rare-copy-number-variants-in-nrxn1-and-cntn6-increase-risk-for-tourette-syndrome
#11
Alden Y Huang, Dongmei Yu, Lea K Davis, Jae Hoon Sul, Fotis Tsetsos, Vasily Ramensky, Ivette Zelaya, Eliana Marisa Ramos, Lisa Osiecki, Jason A Chen, Lauren M McGrath, Cornelia Illmann, Paul Sandor, Cathy L Barr, Marco Grados, Harvey S Singer, Markus M Nöthen, Johannes Hebebrand, Robert A King, Yves Dion, Guy Rouleau, Cathy L Budman, Christel Depienne, Yulia Worbe, Andreas Hartmann, Kirsten R Müller-Vahl, Manfred Stuhrmann, Harald Aschauer, Mara Stamenkovic, Monika Schloegelhofer, Anastasios Konstantinidis, Gholson J Lyon, William M McMahon, Csaba Barta, Zsanett Tarnok, Peter Nagy, James R Batterson, Renata Rizzo, Danielle C Cath, Tomasz Wolanczyk, Cheston Berlin, Irene A Malaty, Michael S Okun, Douglas W Woods, Elliott Rees, Carlos N Pato, Michele T Pato, James A Knowles, Danielle Posthuma, David L Pauls, Nancy J Cox, Benjamin M Neale, Nelson B Freimer, Peristera Paschou, Carol A Mathews, Jeremiah M Scharf, Giovanni Coppola
Tourette syndrome (TS) is a model neuropsychiatric disorder thought to arise from abnormal development and/or maintenance of cortico-striato-thalamo-cortical circuits. TS is highly heritable, but its underlying genetic causes are still elusive, and no genome-wide significant loci have been discovered to date. We analyzed a European ancestry sample of 2,434 TS cases and 4,093 ancestry-matched controls for rare (< 1% frequency) copy-number variants (CNVs) using SNP microarray data. We observed an enrichment of global CNV burden that was prominent for large (> 1 Mb), singleton events (OR = 2...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28639280/mutational-profiles-of-brenner-tumors-show-distinctive-features-uncoupling-urothelial-carcinomas-and-ovarian-carcinoma-with-transitional-cell-histology
#12
Nicole Pfarr, Silvia Darb-Esfahani, Jonas Leichsenring, Eliane Taube, Melanie Boxberg, Ioana Braicu, Moritz Jesinghaus, Roland Penzel, Volker Endris, Aurelia Noske, Wilko Weichert, Peter Schirmacher, Carsten Denkert, Albrecht Stenzinger
Brenner tumors (BT) are rare ovarian tumors encompassing benign, borderline and malignant variants. While the histopathology of BTs and their clinical course is well described, little is known about the underlying genetic defects. We employed targeted next generation sequencing to analyze the mutational landscape in a cohort of 23 BT cases (17 benign, 2 borderline, 4 malignant) and 3 ovarian carcinomas with transitional cell histology (TCC). Copy number variations (CNV) were validated by fluorescence in-situ hybridization (FISH) and quantitative PCR-based copy number assays...
June 22, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28639189/enhancing-neuronogenesis-and-counteracting-neuropathogenic-gene-haploinsufficiencies-by-rna-gene-activation
#13
Antonello Mallamaci
Small activating RNAs (saRNAs), targeting endogenous genes and stimulating their transcription, are a promising tool for implementing a variety of neurotherapeutic strategies. Among these there is the stimulation of select histogenetic subroutines for purposes of cell-based brain repair, as well as the therapeutic treatment of gene expression deficits underlying severe neurological disorders.We employed RNA activation (RNAa) to transactivate the Emx2 transcription factor gene in embryonic cortico-cerebral precursor cells...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28638988/same-day-genomic-and-epigenomic-diagnosis-of-brain-tumors-using-real-time-nanopore-sequencing
#14
Philipp Euskirchen, Franck Bielle, Karim Labreche, Wigard P Kloosterman, Shai Rosenberg, Mailys Daniau, Charlotte Schmitt, Julien Masliah-Planchon, Franck Bourdeaut, Caroline Dehais, Yannick Marie, Jean-Yves Delattre, Ahmed Idbaih
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., for 1p/19q-codeletion or IDH mutations, to make an integrated histomolecular diagnosis. However, a plethora of sophisticated technologies is currently needed to assess different genomic and epigenomic alterations and turnaround times are in the range of weeks, which makes standardized and widespread implementation difficult and hinders timely decision making...
June 21, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28631888/the-importance-of-phase-analysis-in-multiexon-copy-number-variation-detected-by-acgh-in-autosomal-recessive-disorder-loci
#15
Madelyn A Gillentine, Christian P Schaaf, Ankita Patel
Cohen Syndrome (CS) is a rare autosomal recessive disorder caused by homozygous or compound heterozygous pathogenic variants in VPS13B, also known as COH1. Over 100 pathogenic variants in VSP13B, primarily truncations, and copy number variants, have been found in patients with CS. Here, we present an 11-month-old girl with CS caused by two multi-exonic small deletions in VSP13B in trans. Array comparative genomic hybridization has revolutionized the field of genome copy number analysis down to the exonic level, however it has its limitations...
June 20, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28630456/rare-disruptive-variants-in-the-disc1-interactome-and-regulome-association-with-cognitive-ability-and-schizophrenia
#16
S Teng, P A Thomson, S McCarthy, M Kramer, S Muller, J Lihm, S Morris, D C Soares, W Hennah, S Harris, L M Camargo, V Malkov, A M McIntosh, J K Millar, D H Blackwood, K L Evans, I J Deary, D J Porteous, W R McCombie
Schizophrenia (SCZ), bipolar disorder (BD) and recurrent major depressive disorder (rMDD) are common psychiatric illnesses. All have been associated with lower cognitive ability, and show evidence of genetic overlap and substantial evidence of pleiotropy with cognitive function and neuroticism. Disrupted in schizophrenia 1 (DISC1) protein directly interacts with a large set of proteins (DISC1 Interactome) that are involved in brain development and signaling. Modulation of DISC1 expression alters the expression of a circumscribed set of genes (DISC1 Regulome) that are also implicated in brain biology and disorder...
June 20, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28629877/the-effect-of-a-genetic-variant-on-quantitative-real-time-pcr-in-a-case-of-disseminated-adenovirus-infection
#17
Thomas J Gniadek, Michael T Forman, Isabella Martin, Ravit Arav-Boger, Alexandra Valsamakis
A patient developed disseminated adenovirus infection following bone marrow transplant. TaqMan real-time PCR showed reduced maximum fluorescence in the amplification curve from all plasma samples. Sequencing revealed three single nucleotide mismatches between the TaqMan probe and probe binding region. Real-time PCR with probe matching the isolate sequence showed normal amplification and a higher copy number result.
June 1, 2017: Diagnostic Microbiology and Infectious Disease
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#18
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28626423/ubiquitin-proteasome-collagen-cup-pathway-in-preterm-premature-rupture-of-fetal-membranes
#19
Xinliang Zhao, Xiaoyan Dong, Xiucui Luo, Jing Pan, Weina Ju, Meijiao Zhang, Peirong Wang, Mei Zhong, Yanhong Yu, W Ted Brown, Nanbert Zhong
Spontaneous preterm birth (sPTB) occurs before 37 gestational weeks, with preterm premature rupture of the membranes (PPROM) and spontaneous preterm labor (sPTL) as the predominant adverse outcomes. Previously, we identified altered expression of long non-coding RNAs (lncRNAs) and message RNAs (mRNAs) related to the ubiquitin proteasome system (UPS) in human placentas following pregnancy loss and PTB. We therefore hypothesized that similar mechanisms might underlie PPROM. In the current study, nine pairs of ubiquitin-proteasome-collagen (CUP) pathway-related mRNAs and associated lncRNAs were found to be differentially expressed in PPROM and sPTL...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28618053/association-of-aberrant-right-subclavian-artery-with-abnormal-karyotype-and-microarray-results
#20
Ran Svirsky, Adi Reches, Dana Brabbing-Goldstein, Anat Bar Shira, Yuval Yaron
OBJECTIVES: to evaluate the incidence of chromosomal aberration (both microscopic and sub-microscopic) in fetuses with an aberrant right subclavian artery (ARSA) detected by ultrasonographic anomaly scan. METHODS: The study included 62 pregnant women whose fetuses were diagnosed with ARSA who were referred for genetic counseling. Of these, 55 patients underwent amniocentesis and 7 declined invasive testing. All 55 amniocentesis samples were tested by standard G-banding and chromosomal microarray (CMA), except for 2 samples for which only karyotype and FISH for 22q11...
June 15, 2017: Prenatal Diagnosis
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