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Copy number variation

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https://www.readbyqxmd.com/read/29147009/mitochondrial-uqcrb-as-a-new-molecular-prognostic-biomarker-of-human-colorectal-cancer
#1
Hyun-Chul Kim, Junghwa Chang, Hannah S Lee, Ho Jeong Kwon
Ubiquinol cytochrome c reductase binding protein (UQCRB) is important for mitochondrial complex III stability, electron transport, cellular oxygen sensing and angiogenesis. However, its potential as a prognostic marker in colorectal cancer (CRC) remains unclear. The aim of this study was to determine whether UQCRB can be used as a diagnostic molecular marker for CRC. The correlation between the expression of three genes (UQCRB, UQCRFS1 and MT-CYB) in the mitochondrial respiratory chain complex III and clinico-pathological features was determined...
November 17, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29145200/the-role-of-copy-number-variants-in-disorders-of-sex-development
#2
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/29144792/effect-of-blood-collection-tube-type-and-time-to-processing-on-the-enumeration-and-high-content-characterization-of-circulating-tumor-cells-using-the-high-definition-single-cell-assay
#3
Mariam Rodríguez-Lee, Anand Kolatkar, Madelyn McCormick, Angel D Dago, Jude Kendall, Nils Anders Carlsson, Kelly Bethel, Emily J Greenspan, Shelley E Hwang, Kathryn R Waitman, Jorge J Nieva, James Hicks, Peter Kuhn
CONTEXT: - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE: - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA)...
November 16, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29143607/features-of-ppd-b1-expression-regulation-and-their-impact-on-the-flowering-time-of-wheat-near-isogenic-lines
#4
Antonina A Kiseleva, Elena K Potokina, Elena A Salina
BACKGROUND: Photoperiod insensitive Ppd-1a alleles determine early flowering of wheat. Increased expression of homoeologous Ppd-D1a and Ppd-A1a result from deletions in the promoter region, and elevated expression of Ppd-B1a is determined by an increased copy number. RESULTS: In this study, using bread wheat cultivars Sonora and PSL2, which contrast in flowering time, and near-isogenic lines resulting from their cross, "Ppd-m" and "Ppd-w" with Ppd-B1a introgressed from Sonora, we investigated the putative factors that influence Ppd-B1a expression...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29141310/-analysis-of-gene-mutation-of-early-onset-epileptic-spasm-with-unknown-reason
#5
X Yang, G Pan, W H Li, L M Zhang, B B Wu, H J Wang, P Zhang, S Z Zhou
Objective: To summarize the gene mutation of early onset epileptic spasm with unknown reason. Method: In this prospective study, data of patients with early onset epileptic spasm with unknown reason were collected from neurological department of Children's Hospital of Fudan University between March 2016 and December 2016. Patients with known disorders such as infection, metabolic, structural, immunological problems and known genetic mutations were excluded. Patients with genetic disease that can be diagnosed by clinical manifestations and phenotypic characteristics were also excluded...
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29141226/a-pan-cancer-analysis-of-the-expression-and-clinical-relevance-of-small-nucleolar-rnas-in-human-cancer
#6
Jing Gong, Yajuan Li, Chun-Jie Liu, Yu Xiang, Chunlai Li, Youqiong Ye, Zhao Zhang, David H Hawke, Peter K Park, Lixia Diao, John A Putkey, Liuqing Yang, An-Yuan Guo, Chunru Lin, Leng Han
Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29138475/the-rises-and-falls-of-opsin-genes-in-59-ray-finned-fish-genomes-and-their-implications-for-environmental-adaptation
#7
Jinn-Jy Lin, Feng-Yu Wang, Wen-Hsiung Li, Tzi-Yuan Wang
We studied the evolution of opsin genes in 59 ray-finned fish genomes. We identified the opsin genes and adjacent genes (syntenies) in each genome. Then we inferred the changes in gene copy number (N), syntenies, and tuning sites along each phylogenetic branch during evolution. The Exorh (rod opsin) gene has been retained in 56 genomes. Rh1, the intronless rod opsin gene, first emerged in ancestral Actinopterygii, and N increased to 2 by the teleost-specific whole genome duplication, but then decreased to 1 in the ancestor of Neoteleostei fishes...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136137/copy-number-variation-and-expression-analysis-reveals-a-non-orthologous-pinta-gene-family-member-involved-in-butterfly-vision
#8
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/29135520/epithelial-myoepithelial-carcinoma-frequent-morphologic-and-molecular-evidence-of-preexisting-pleomorphic-adenoma-common-hras-mutations-in-plag1-intact-and-hmga2-intact-cases-and-occasional-tp53-fbxw7-and-smarcb1-alterations-in-high-grade-cases
#9
Soufiane El Hallani, Aaron M Udager, Diana Bell, Isabel Fonseca, Lester D R Thompson, Adel Assaad, Abbas Agaimy, Alyssa M Luvison, Caitlyn Miller, Raja R Seethala, Simion Chiosea
We hypothesized that there is a relationship between the preexisting pleomorphic adenoma [PA]), histologic grade of epithelial-myoepithelial carcinomas (EMCAs), and genetic alterations. EMCAs (n=39) were analyzed for morphologic and molecular evidence of preexisting PA (PLAG1, HMGA2 status by fluorescence in situ hybridization, FISH, and FGFR1-PLAG1 fusion by next-generation sequencing, NGS). Twenty-three EMCAs were further analyzed by NGS for mutations and copy number variation in 50 cancer-related genes. On the basis of combined morphologic and molecular evidence of PA, the following subsets of EMCA emerged: (a) EMCAs with morphologic evidence of preexisting PA, but intact PLAG1 and HMGA2 (12/39, 31%), (b) Carcinomas with PLAG1 alterations (9/39, 23%), or (c) HMGA2 alterations (10/39, 26%), and (d) de novo carcinomas, without morphologic or molecular evidence of PA (8/39, 21%)...
November 9, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/29134670/altered-mitochondrial-genome-content-signals-worse-pathology-and-prognosis-in-prostate-cancer
#10
Anton M F Kalsbeek, Eva K F Chan, Judith Grogan, Desiree C Petersen, Weerachai Jaratlerdsiri, Ruta Gupta, Ruth J Lyons, Anne-Maree Haynes, Lisa G Horvath, James G Kench, Phillip D Stricker, Vanessa M Hayes
BACKGROUND: Mitochondrial genome (mtDNA) content is depleted in many cancers. In prostate cancer, there is intra-glandular as well as inter-patient mtDNA copy number variation. In this study, we determine if mtDNA content can be used as a predictor for prostate cancer staging and outcomes. METHODS: Fresh prostate cancer biopsies from 115 patients were obtained at time of surgery. All cores underwent pathological review, followed by isolation of cancer and normal tissue...
November 14, 2017: Prostate
https://www.readbyqxmd.com/read/29132549/association-of-copy-number-variations-in-complement-factor-h-related-genes-among-age-related-macular-degenerative-subjects
#11
Norshakimah Md Bakri, Vasudevan Ramachandran, Hoo Fan Kee, Visvaraja Subrayan, Hazlita Isa, Nor Fariza Ngah, Nur Afiqah Mohamad, Ching Siew Mooi, Chan Yoke Mun, Patimah Ismail, Fazliana Ismail, Erma Suryana Sukiman, Wan Alia Wan Sulaiman
Age-related macular degeneration (AMD) is the most widely recognised cause of irreversible vision loss and previous studies have suggested that the advancement of wet AMD is influenced by both modifiable and non-modifiable elements. Single nucleotide polymorphism (SNPs) and copy number of variations (CNVs) have been associated with AMD in various populations, however the results are conflicting. Our aim is to determine the CNVs of Complement Factor H-Related genes among Malaysian subjects with wet AMD. 130 patients with wet AMD and 120 healthy controls were included in this research...
December 2017: Kaohsiung Journal of Medical Sciences
https://www.readbyqxmd.com/read/29128521/prenatal-chromosomal-microarray-analysis-in-fetuses-with-congenital-heart-disease-a-prospective-cohort-study
#12
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/29125573/tailoring-nutritional-advice-for-mexicans-based-on-prevalence-profiles-of-diet-related-adaptive-gene-polymorphisms
#13
Claudia Ojeda-Granados, Arturo Panduro, Karina Gonzalez-Aldaco, Maricruz Sepulveda-Villegas, Ingrid Rivera-Iñiguez, Sonia Roman
Diet-related adaptive gene (DRAG) polymorphisms identified in specific populations are associated with chronic disorders in carriers of the adaptive alleles due to changes in dietary and lifestyle patterns in recent times. Mexico's population is comprised of Amerindians (AM) and Mestizos who have variable AM, European (EUR) and African genetic ancestry and an increased risk of nutrition-related chronic diseases. Nutritional advice based on the Mexican genome and the traditional food culture is needed to develop preventive and therapeutic strategies...
November 10, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29124819/limited-role-of-differential-fractionation-in-genome-content-variation-and-function-in-maize-zea-mays-l-inbred-lines
#14
Alex B Brohammer, Thomas Jy Kono, Nathan M Springer, Suzanne E McGaugh, Candice N Hirsch
Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207...
November 10, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29122641/regularities-in-zebra-finch-song-beyond-the-repeated-motif
#15
Julia Hyland Bruno, Ofer Tchernichovski
The proliferation of birdsong research into the neural mechanisms of vocal learning is indebted to the remarkable stereotypy of the zebra finch's song motif. Motifs are composed of several copied syllables, which birds learn to produce in a fixed order. But at a higher level of organization-the bout-zebra finch song is no longer stereotyped. Song bouts include several repetitions of the motif, which are often linked by a variable number of short "connector" vocalizations. In this conceptual methods paper, we show that combinatorial analysis alone yields an incomplete description of this bout-level structure...
November 6, 2017: Behavioural Processes
https://www.readbyqxmd.com/read/29118396/engineering-saccharomyces-cerevisiae-for-geranylgeraniol-overproduction-by-combinatorial-design
#16
Tian-Qing Song, Ming-Zhu Ding, Fang Zhai, Duo Liu, Hong Liu, Wen-Hai Xiao, Ying-Jin Yuan
Combinatorial design is an effective strategy to acquire the optimal solution in complex systems. In this study, the combined effects of pathway combination, promoters' strength fine-tuning, copy numbers and integration locus variations caused by δ-integration were explored in Saccharomyces cerevisiae using geranylgeraniol (GGOH) production as an example. Two GGOH biosynthetic pathway branches were constructed. In branch 1, GGOH was converted from isopentenyl pyrophosphate (IPP) and farnesyl diphosphate (FPP)...
November 8, 2017: Scientific Reports
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/29113949/dysregulated-expression-of-the-microrna-mir-137-and-its-target-yb-1-contribute-to-the-invasive-characteristics-of-malignant-pleural-mesothelioma
#18
Thomas G Johnson, Karin Schelch, Yuen Y Cheng, Marissa Williams, Kadir H Sarun, Michaela B Kirschner, Steven Kao, Anthony Linton, Sonja Klebe, Brian C McCaughan, Ruby Cy Lin, Christine Pirker, Walter Berger, Annette Lasham, Nico van Zandwijk, Glen Reid
BACKGROUND: Malignant pleural mesothelioma (MPM) is an aggressive malignancy linked to asbestos exposure. On a genomic level, MPM is characterised by frequent chromosomal deletions of tumour suppressors, including microRNAs. MiR-137 plays a tumour suppressor role in other cancers, so the aim of this study was to characterise it and its target Y-box binding protein-1 (YB-1) in MPM. BASIC PROCEDURES: Expression, methylation and copy number status of miR-137 and its host gene MIR137HG were assessed by PCR...
November 4, 2017: Journal of Thoracic Oncology
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/29109420/passage-dependent-accumulation-of-somatic-mutations-in-mesenchymal-stromal-cells-during-in-vitro-culture-revealed-by-whole-genome-sequencing
#20
Myungshin Kim, Je-Keun Rhee, Hayoung Choi, Ahlm Kwon, Jiyeon Kim, Gun Dong Lee, Dong Wook Jekarl, Seungok Lee, Yonggoo Kim, Tae-Min Kim
Human mesenchymal stromal cells (MSCs) have served as a major cellular resource for cell-based immunomodulatory and regenerative therapies. However, genomic instability may accumulate during ex vivo expansion of MSCs, thereby increasing the potential of malignant transformation. Here, we performed whole genome sequencing of two peripheral blood-derived MSC lines (MSC1 and MSC2) at various passages (passage 1 [P1] to P9). The majority of single-nucleotide variations (SNVs) occurred in later passages; specifically, 90% and 70% of all SNVs in MSC1 and MSC2 were observed in P9 and P7/P9, respectively...
November 6, 2017: Scientific Reports
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