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https://www.readbyqxmd.com/read/29156722/whole-exome-sequencing-reveals-novel-mutations-and-epigenetic-regulation-in-hypopharyngeal-carcinoma
#1
Ping Wu, Honglong Wu, Yaoyun Tang, Shi Luo, Xing Fang, Chubo Xie, Jian He, Suping Zhao, Xiaofeng Wang, Jiajia Xu, Xi Chen, Dongfang Li, Huanming Yang, Jian Wang
Hypopharyngeal cancer (HPC) frequently presents at an advanced stage, resulting in poor prognosis. Although combined surgical therapy and chemoradiotherapy have improved the survival for patients with HPC over the past 3 decades, the mortality rate in late-stage diagnosis of HPC is unsatisfactory. In this study, we performed whole-exome sequencing (WES) of 23 hypopharyngeal tumor and paired adjacent normal tissue to identify novel candidate driver genes associated with hypopharyngeal carcinoma. We identified several copy number variants (CNVs) and 15 somatic mutation genes that were associated with hypopharyngeal carcinoma...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156220/the-epilepsy-phenotype-in-adult-patients-with-intellectual-disability-and-pathogenic-copy-number-variants
#2
Giuseppe d'Orsi, Tommaso Martino, Orazio Palumbo, Maria Grazia Pascarella, Pietro Palumbo, Maria Teresa Di Claudio, Carlo Avolio, Massimo Carella
PURPOSE: To characterize the electroclinical features of epilepsy associated with intellectual disability and pathogenic copy number variations (CNVs) METHODS: we prospectively investigated 61 adult patients with epilepsy and intellectual disability or other neurodevelopmental disorders. We performed high resolution SNP-Array analysis in order to detect clinical relevant chromosomal microdeletions and microduplications. An ordinal logistic regression model was fitted with 34 demographic, clinical and EEG-related variables in order to identify the epilepsy phenotype of patients with pathogenic CNVs...
November 14, 2017: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/29155328/mitochondrial-trna-leu-uur-c3275t-trna-gln-t4363c-and-trna-lys-a8343g-mutations-may-be-associated-with-pcos-and-metabolic-syndrome
#3
Yu Ding, Bo-Hou Xia, Cai-Juan Zhang, Guang-Chao Zhuo
Polycystic ovary syndrome (PCOS) is a very prevalent endocrine disease affecting reproductive women. Clinically, patients with this disorder are more vulnerable to develop type 2 diabetes mellitus (T2DM), cardiovascular events, as well as metabolic syndrome (MetS). To date, the molecular mechanism underlying PCOS remains largely unknown. Previously, we showed that mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) mutation was an important cause for PCOS. In the current study, we described the clinical and biochemical features of a three-generation pedigree with maternally transmitted MetS, combined with PCOS...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29147671/distal-22q11-2-microduplication-case-report-and-review-of-the-literature
#4
Elana Pinchefsky, Laurence Laneuville, Myriam Srour
Distal chromosome 22q11.2 microduplications are associated with a wide range of phenotypes and unclear pathogenicity. The authors report on a 3-year-old girl with global developmental delay harboring a de novo 1.24 Mb distal chromosome 22q11.2 microduplication and a paternally inherited 0.25 Mb chromosome 4p14 microduplication. The authors review clinical features of 30 reported cases of distal 22q11.2 duplications. Common features include developmental delay (93%), neuropsychiatric features (26%), and nonspecific facial dysmorphisms (74%)...
January 2017: Child neurology open
https://www.readbyqxmd.com/read/29146900/the-genomic-landscape-of-pediatric-myelodysplastic-syndromes
#5
Jason R Schwartz, Jing Ma, Tamara Lamprecht, Michael Walsh, Shuoguo Wang, Victoria Bryant, Guangchun Song, Gang Wu, John Easton, Chimene Kesserwan, Kim E Nichols, Charles G Mullighan, Raul C Ribeiro, Jeffery M Klco
Myelodysplastic syndromes (MDS) are uncommon in children and have a poor prognosis. In contrast to adult MDS, little is known about the genomic landscape of pediatric MDS. Here, we describe the somatic and germline changes of pediatric MDS using whole exome sequencing, targeted amplicon sequencing, and/or RNA-sequencing of 46 pediatric primary MDS patients. Our data show that, in contrast to adult MDS, Ras/MAPK pathway mutations are common in pediatric MDS (45% of primary cohort), while mutations in RNA splicing genes are rare (2% of primary cohort)...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29146387/dilemmas-in-genetic-counseling-for-low-penetrance-neuro-susceptibility-loci-detected-on-prenatal-chromosomal-microarray-analysis
#6
Dana Brabbing-Goldstein, Adi Reches, Ran Svirsky, Anat Bar-Shira, Yuval Yaron
BACKGROUND: Chromosomal microarray analysis is standard of care in fetuses with malformations, detecting clinically significant copy number variants in 5-7% of cases over conventional karyotyping. However, it also detects variants of uncertain significance in 1.6% - 4.2% of the cases, some of which are low-penetrance neuro-susceptibility loci. The interpretation of these variants in pregnancy is particularly challenging, because the significance is often unclear and the clinical implications may be difficult to predict...
November 13, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29145200/the-role-of-copy-number-variants-in-disorders-of-sex-development
#7
Brittany Croft, Thomas Ohnesorg, Andrew H Sinclair
Despite considerable research effort and significant advances in sequencing technologies, the majority of disorders of sex development (DSD) cases still lack a molecular genetic diagnosis. While coding variants have been discovered in known and candidate DSD genes, comparatively little is known about copy number variations (CNVs) affecting both coding and noncoding regions. Due to rapidly falling costs of whole genome sequencing, many more CNVs in individuals with DSD will be identified. These CNVs may explain a significant number of hitherto undiagnosed cases of DSD...
November 17, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/29144225/prevalence-of-genetic-disorders-and-glut1-deficiency-in-a-ketogenic-diet-clinic
#8
Stacy Hewson, Ledia Brunga, Matilde Fernandez Ojeda, Elizabeth Imhof, Jaina Patel, Maria Zak, Elizabeth J Donner, Jeff Kobayashi, Gajja S Salomons, Saadet Mercimek-Andrews
Between July of 2012 and December of 2014, 39 patients were enrolled prospectively to investigate the prevalence of glucose transporter 1 (GLUT1) deficiency in a ketogenic diet clinic. None of them had GLUT1 deficiency. All patients seen in the same clinic within the same period were reviewed retrospectively. A total of 18 of these 85 patients had a genetic diagnosis, including GLUT1 deficiency, pathogenic copy number variants, congenital disorder of glycosylation, neuronal ceroid lipofuscinosis type II, mitochondrial disorders, tuberous sclerosis, lissencephaly, and SCN1A-, SCN8A-, and STXBP1-associated epileptic encephalopathies...
November 16, 2017: Canadian Journal of Neurological Sciences. le Journal Canadien des Sciences Neurologiques
https://www.readbyqxmd.com/read/29141989/analysis-of-copy-number-variants-on-chromosome-21-in-down-syndrome-associated-congenital-heart-defects
#9
Benjamin L Rambo-Martin, Jennifer G Mulle, David J Cutler, Lora J H Bean, Tracie C Rosser, Kenneth J Dooley, Clifford Cua, George Capone, Cheryl L Maslen, Roger H Reeves, Stephanie L Sherman, Michael E Zwick
One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2,000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: 1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and 2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold...
November 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29141672/a-novel-git2-braf-fusion-in-pilocytic-astrocytoma
#10
Jeffrey Helgager, Hart G Lidov, Navin R Mahadevan, Mark W Kieran, Keith L Ligon, Sanda Alexandrescu
BACKGROUND: KIAA1549-BRAF fusion is the most common genetic event in pilocytic astrocytoma (PA), and leads to activation of the mitogen activated protein kinase (MAPK) signaling pathway. Fusions of BRAF with other partner genes, as well as other genetic alterations not involving BRAF but also leading to MAPK pathway activation have been described rarely. CASE PRESENTATION: We present a new fusion partner in the low-grade glioma of a 10-year-old male, who presented with headaches and recent episodes of seizures...
November 15, 2017: Diagnostic Pathology
https://www.readbyqxmd.com/read/29136137/copy-number-variation-and-expression-analysis-reveals-a-non-orthologous-pinta-gene-family-member-involved-in-butterfly-vision
#11
Aide Macias-Muñoz, Kyle J McCulloch, Adriana D Briscoe
Vertebrate (CRALBP) and Drosophila (PINTA) proteins with a CRAL-TRIO domain transport retinal-based chromophores that bind to opsin proteins and are necessary for phototransduction. The CRAL-TRIO domain gene family is composed of genes that encode proteins with a common N-terminal structural domain. While there is an expansion of this gene family in Lepidoptera, there is no lepidopteran ortholog of pinta. Further, the function of these genes in lepidopterans has not yet been established. Here we explored the molecular evolution and expression of CRAL-TRIO domain genes in the butterfly Heliconius melpomene in order to identify a member of this gene family as a candidate chromophore transporter...
November 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29130988/recurrent-copy-number-variants-associated-with-syndromic-short-stature-of-unknown-cause
#12
Thais K Homma, Ana C V Krepischi, Tatiane K Furuya, Rachel S Honjo, Alexsandra C Malaquias, Debora R Bertola, Silvia S Costa, Ana P Canton, Rosimeire A Roela, Bruna L Freire, Chong A Kim, Carla Rosenberg, Alexander A L Jorge
BACKGROUND/AIMS: Genetic imbalances are responsible for many cases of short stature of unknown etiology. This study aims to identify recurrent pathogenic copy number variants (CNVs) in patients with syndromic short stature of unknown cause. METHODS: We selected 229 children with short stature and dysmorphic features, developmental delay, and/or intellectual disability, but without a recognized syndrome. All patients were evaluated by chromosomal microarray (array-based comparative genomic hybridization/single nucleotide polymorphism array)...
November 9, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/29129660/microduplication-of-10q26-3-in-a-chinese-hypertriglyceridemia-patient
#13
Jing-Jing Li, Ya-Qin Chen, Liang-Liang Fan, Jie-Yuan Jin, Shuai Guo, Rong Xiang
Hypertriglyceridemia (HTG) plays an important role in the development and progression of atherosclerosis. It is inherited in an autosomal dominant pattern with a frequency of approximately 1:1,000,000 worldwide. Previous study has demonstrated that more than six genes underlie this disorder. In addition, copy number variants (CNVs) including disease-causing genes also play a crucial role in it. In this study, we have employed SNP-ARRAY chip technology to detect the pathogenic CNVs in a HTG patient who carried no meaningful mutations in HTG candidate genes...
November 9, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/29129316/functional-consequences-of-chrna7-copy-number-alterations-in-induced-pluripotent-stem-cells-and-neural-progenitor-cells
#14
Madelyn A Gillentine, Jiani Yin, Aleksandar Bajic, Ping Zhang, Steven Cummock, Jean J Kim, Christian P Schaaf
Copy-number variants (CNVs) of chromosome 15q13.3 manifest clinically as neuropsychiatric disorders with variable expressivity. CHRNA7, encoding for the α7 nicotinic acetylcholine receptor (nAChR), has been suggested as a candidate gene for the phenotypes observed. Here, we used induced pluripotent stem cells (iPSCs) and neural progenitor cells (NPCs) derived from individuals with heterozygous 15q13.3 deletions and heterozygous 15q13.3 duplications to investigate the CHRNA7-dependent molecular consequences of the respective CNVs...
November 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29128521/prenatal-chromosomal-microarray-analysis-in-fetuses-with-congenital-heart-disease-a-prospective-cohort-study
#15
Yan Wang, Li Cao, Dong Liang, Lulu Meng, Yun Wu, Fengchang Qiao, Xiuqing Ji, Chunyu Luo, Jingjing Zhang, Tianhui Xu, Bin Yu, Leilei Wang, Ting Wang, Qiong Pan, Dingyuan Ma, Ping Hu, Zhengfeng Xu
BACKGROUD: Currently, chromosomal microarray analysis is considered as the first-tier test in pediatric care and prenatal diagnosis. However, the diagnostic yield of CMA for prenatal diagnosis of congenital heart disease has not been evaluated based on a large cohort. OBJECTIVE: Our aim was to evaluate the clinical utility of chromosomal microarray as the first-tier test for chromosomal abnormalities in fetuses with congenital heart disease. STUDY DESIGN: In this prospective study, 602 prenatal cases of congenital heart disease were investigated using SNP array over a 5-year period...
November 8, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29126171/copy-number-variant-in-the-region-of-adenosine-kinase-adk-and-its-possible-contribution-to-schizophrenia-susceptibility
#16
Hiroki Kimura, Itaru Kushima, Akira Yohimi, Branko Aleksic, Norio Ozaki
Background: Adenosine kinase (ADK) is supposed to be a schizophrenia (SCZ) susceptibility gene based on the findings that ADK is an enzyme that catalyzes transfer of the gamma-phosphate from ATP to adenosine, which interacts with dopamine and glutamate, neurotransmitters. However, no reports of SCZ cases with loss of function variants in the ADK region have been published. In our previous study investigating copy number variants (CNV) in SCZ, we detected a CNV in the ADK region in one of 1699 SCZ patients...
November 6, 2017: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29116104/germline-copy-number-variations-are-associated-with-breast-cancer-risk-and-prognosis
#17
Mahalakshmi Kumaran, Carol E Cass, Kathryn Graham, John R Mackey, Roland Hubaux, Wan Lam, Yutaka Yasui, Sambasivarao Damaraju
Breast cancer is one of the most common cancers among women, and susceptibility is explained by genetic, lifestyle and environmental components. Copy Number Variants (CNVs) are structural DNA variations that contribute to diverse phenotypes via gene-dosage effects or cis-regulation. In this study, we aimed to identify germline CNVs associated with breast cancer susceptibility and their relevance to prognosis. We performed whole genome CNV genotyping in 422 cases and 348 controls using Human Affymetrix SNP 6 array...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29114042/deletion-variants-of-cfhr1-and-cfhr3-associate-with-mesangial-immune-deposits-but-not-with-progression-of-iga-nephropathy
#18
Perrine Jullien, Blandine Laurent, Guillaume Claisse, Ingrid Masson, Miriana Dinic, Damien Thibaudin, Francois Berthoux, Eric Alamartine, Christophe Mariat, Nicolas Maillard
Activation of complement through the alternative pathway has a key role in the pathogenesis of IgA nephropathy (IgAN). Large, international, genome-wide association studies have shown that deletion of complement factor H-related genes 1 and 3 (CFHR3,1Δ) is associated with a reduced risk of developing IgAN, although the prognostic value of these deletions in IgAN remains unknown. Here, we compared the renal outcomes of patients with IgAN according to their CFHR3,1Δ genotype. This retrospective, monocentric cohort study included 639 white patients with biopsy-proven IgAN since 1979 (mean age at diagnosis, 40...
November 7, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29112706/nanostringnormcnv-pre-processing-of-nanostring-cnv-data
#19
Dorota H Sendorek, Emilie Lalonde, Cindy Q Yao, Veronica Y Sabelnykova, Robert G Bristow, Paul C Boutros
Summary: The NanoString System is a well-established technology for measuring RNA and DNA abundance. Although it can estimate copy number variation, relatively few tools support analysis of these data. To address this gap, we created NanoStringNormCNV, an R package for pre-processing and copy number variant calling from NanoString data. This package implements algorithms for pre-processing, quality-control, normalization and copy number variation detection. A series of reporting and data visualization methods support exploratory analyses...
November 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29108269/microarray-analyses-reveal-genes-related-to-progression-and-prognosis-of-esophageal-squamous-cell-carcinoma
#20
Mao Qixing, Dong Gaochao, Xia Wenjie, Wang Anpeng, Chen Bing, Ma Weidong, Xu Lin, Jiang Feng
Esophageal squamous cell carcinoma is a high morbidity and mortality cancer in China. Here are few biomarkers and therapeutic targets. Our study was aimed to identify candidate genes correlated to ESCC. Oncomine, The Cancer Genome Atlas, Gene Expression Omnibus were retrieved for eligible ESCC data. Deregulated genes were identified by meta-analysis and validated by an independent dataset. Survival analyses and bioinformatics analyses were used to explore potential mechanisms. Copy number variant analyses identified upstream mechanisms of candidate genes...
October 3, 2017: Oncotarget
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