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https://www.readbyqxmd.com/read/27925267/genetic-variation-and-gene-conversions-within-the-bovine-nk-lysin-gene-family
#1
J Chen, M O Lee, J E Womack
In contrast to a single copy of the NK-lysin gene in humans and many other mammals, we previously identified a family of four expressed NK-lysin genes arising by tandem duplications on cattle chromosome 11. Here, we report two genetic variants in the bovine NK-lysin complex with potential importance in the bovine innate immune system. The first one is a 9-bp deletion causing a three-amino-acid deletion in the pro-region of the NK1 gene product. The second is a deletion of NK2B in some Holstein cattle, resulting in copy number variation that is in disequilibrium with a SNP from the bovine 770K HD SNP array...
December 7, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27924152/molecular-characterization-of-a-rare-analphoid-supernumerary-marker-chromosome-derived-from-7q35%C3%A2-%C3%A2-%C3%A2-qter-a-case-report
#2
Bárbara Marques, Cristina Ferreira, Filomena Brito, Sónia Pedro, Cristina Alves, Teresa Lourenço, Marta Amorim, Hildeberto Correia
BACKGROUND: Analphoid supernumerary marker chromosomes (aSMC) constitute one of the smallest groups of SMC, and are characterized by a centromeric constriction but no detectable alpha-satellite DNA. These marker chromosomes cannot be properly identified by conventional banding techniques alone, and molecular cytogenetic methods are necessary for a detailed characterization. Analphoid SMC derived from chromosome 7 are extremely rare, with only five cases reported so far. CASE PRESENTATION: In this work we report an aSMC involving the terminal long arm of chromosome 7 in a 10-year-old boy with multiple dysmorphic features and severe development delay...
2016: Molecular Cytogenetics
https://www.readbyqxmd.com/read/27923841/biological-and-clinical-relevance-of-associated-genomic-alterations-in-myd88-l265p-and-non-l265p-mutated-diffuse-large-b-cell-lymphoma-analysis-of-361-cases
#3
Sydney Dubois, Pierre-Julien Viailly, Elodie Bohers, Philippe Bertrand, Philippe Ruminy, Vinciane Marchand, Catherine Maingonnat, Sylvain Mareschal, Jean-Michel Picquenot, Dominique Penther, Jean-Philippe Jais, Bruno Tesson, Pauline Peyrouze, Martin Figeac, Fabienne Desmots, Thierry Fest, Corinne Haioun, Thierry Lamy, Christiane Copie-Bergman, Bettina Fabiani, Richard Delarue, Frederic Peyrade, Marc André, Nicolas Ketterer, Karen Leroy, Gilles Salles, Thierry J Molina, Herve Tilly, Fabrice Jardin
PURPOSE: MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of Activated B-Cell like (ABC) Diffuse Large B Cell Lymphoma (DLBCL), leading to constitutive NFkB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88 mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants. EXPERIMENTAL DESIGN: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next generation sequencing (NGS) focusing on 34 genes in order to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses...
December 6, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27921396/frequency-and-type-of-inheritable-mutations-induced-by-%C3%AE-rays-in-rice-as-revealed-by-whole-genome-sequencing
#4
Shan Li, Yun-Chao Zheng, Hai-Rui Cui, Hao-Wei Fu, Qing-Yao Shu, Jian-Zhong Huang
Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M2 plant, resulting in genome coverage of >45 times for each plant...
2016: Journal of Zhejiang University. Science. B
https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#5
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27918584/the-ace-1-locus-is-amplified-in-all-resistant-anopheles-gambiae-mosquitoes-fitness-consequences-of-homogeneous-and-heterogeneous-duplications
#6
Benoît S Assogba, Pascal Milesi, Luc S Djogbénou, Arnaud Berthomieu, Patrick Makoundou, Lamine S Baba-Moussa, Anna-Sophie Fiston-Lavier, Khalid Belkhir, Pierrick Labbé, Mylène Weill
Gene copy-number variations are widespread in natural populations, but investigating their phenotypic consequences requires contemporary duplications under selection. Such duplications have been found at the ace-1 locus (encoding the organophosphate and carbamate insecticides' target) in the mosquito Anopheles gambiae (the major malaria vector); recent studies have revealed their intriguing complexity, consistent with the involvement of various numbers and types (susceptible or resistant to insecticide) of copies...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27917406/genomics-of-colorectal-cancer-in-african-americans
#7
Hassan Brim, Hassan Ashktorab
Genome-wide studies are increasingly becoming a must, especially for complex diseases such as cancer where multiple genes and diverse molecular mechanisms are known to be involved in genes' function alteration. In this review, we report our latest genomic and epigenomic findings in African-American colorectal cancer patients. This population suffers a higher burden of the disease and most investigators in this field are looking for the underlying genetic and epigenetic targets that might be responsible for this disparity...
September 2016: Next Generation, Sequencing & Applications
https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#8
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910023/array-based-comparative-genomic-hybridization-acgh
#9
Chengsheng Zhang, Eliza Cerveira, Mallory Romanovitch, Qihui Zhu
Copy number variations (CNVs) in the genomes have been suggested to play important roles in human evolution, genetic diversity, and disease susceptibility. A number of assays have been developed for the detection of CNVs, including fluorescent in situ hybridization (FISH), array-based comparative genomic hybridization (aCGH), PCR-based assays, and next-generation sequencing (NGS). In this chapter, we describe a microarray method that has been used for the detection of genome-wide CNVs, loss of heterozygosity (LOH), and uniparental disomy (UPD) associated with constitutional and neoplastic disorders...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910017/fluorescence-in-situ-hybridization-probe-preparation
#10
Doron Tolomeo, Roscoe R Stanyon, Mariano Rocchi
The public human genome sequencing project utilized a hierarchical approach. A large number of BAC/PAC clones, with an insert size approximate from 50 kb to 300 kb, were identified and finely mapped with respect to the Sequence Tagged Site (STS) physical map and with respect to each other. A "golden path" of BACs, covering the entire human genome, was then selected and each clone was fully sequenced. The large number of remaining BACs was not fully sequenced, but the availability of the end sequence (~800-1000 bp) at each end allowed them to be very precisely mapped on the human genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27906673/multiplex-ligation-dependent-probe-amplification-assay-identifies-additional-copy-number-changes-compared-with-r-band-karyotype-and-provide-more-accuracy-prognostic-information-in-myelodysplastic-syndromes
#11
Jingya Wang, Xiaofei Ai, Tiejun Qin, Zefeng Xu, Yue Zhang, Jinqin Liu, Bing Li, Liwei Fang, Hongli Zhang, Lijuan Pan, Naibo Hu, Shiqiang Qu, Wenyu Cai, Kun Ru, Yujiao Jia, Gang Huang, Zhijian Xiao
Cytogenetic analysis provides important diagnostic and prognostic information for patients with Myelodysplastic syndromes (MDS) and plays an essential role in the International Prognostic Scoring System (IPSS) and the revised International Prognostic Scoring System (IPSS-R). Multiplex ligation-dependent probe amplification (MLPA) assay is a recently developed technique to identify targeted cytogenetic aberrations in MDS patients. In the present study, we evaluated the results obtained using an MLPA assay in 437 patients with MDS to determine the efficacy of MLPA analysis...
November 29, 2016: Oncotarget
https://www.readbyqxmd.com/read/27906459/integrative-genomic-analysis-identifies-ancestry-related-expression-quantitative-trait-loci-on-dna-polymerase-%C3%AE-and-supports-the-association-of-genetic-ancestry-with-survival-disparities-in-head-and-neck-squamous-cell-carcinoma
#12
Meganathan P Ramakodi, Karthik Devarajan, Elizabeth Blackman, Denise Gibbs, Danièle Luce, Jacqueline Deloumeaux, Suzy Duflo, Jeffrey C Liu, Ranee Mehra, Rob J Kulathinal, Camille C Ragin
BACKGROUND: African Americans with head and neck squamous cell carcinoma (HNSCC) have a lower survival rate than whites. This study investigated the functional importance of ancestry-informative single-nucleotide polymorphisms (SNPs) in HNSCC and also examined the effect of functionally important genetic elements on racial disparities in HNSCC survival. METHODS: Ancestry-informative SNPs, RNA sequencing, methylation, and copy number variation data for 316 oral cavity and laryngeal cancer patients were analyzed across 178 DNA repair genes...
December 1, 2016: Cancer
https://www.readbyqxmd.com/read/27904779/generation-characterization-and-maintenance-of-trastuzumab-resistant-her2-breast-cancer-cell-lines
#13
Sandra Zazo, Paula González-Alonso, Ester Martín-Aparicio, Cristina Chamizo, Ion Cristóbal, Oriol Arpí, Ana Rovira, Joan Albanell, Pilar Eroles, Ana Lluch, Juan Madoz-Gúrpide, Federico Rojo
Trastuzumab became the therapy of choice for patients with HER2-positive breast cancer in 1998, and it has provided clinical benefit ever since. However, a significant percentage of patients show primary resistance to trastuzumab at diagnosis, and most patients with metastatic disease that initially respond to trastuzumab eventually progress (acquired resistance). Consequently, there is an urgent need to improve our knowledge of the mechanisms governing resistance, so that specific therapeutic strategies can be developed to provide improved efficacy...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#14
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902797/self-fertility-in-a-cultivated-diploid-potato-population-examined-with-the-infinium-8303-potato-single-nucleotide-polymorphism-array
#15
Brenda A Peterson, Sarah H Holt, F Parker E Laimbeer, Andreas G Doulis, Joseph Coombs, David S Douches, Michael A Hardigan, C Robin Buell, Richard E Veilleux
Within a population of F hybrids between two genotypes ( L. Group Phureja DM 1-3 516 R44 [DM] and L. Group Tuberosum RH89-039-16 [RH]) used in the potato genome sequencing project, we observed fruit set after self-pollination on many plants. Examination of pollen tube growth in self-fertile and self-unfruitful F plants after controlled self-pollinations revealed no difference in the ability of pollen tubes to reach the ovary. To identify genomic regions linked with self-fertility, we genotyped the F population using a genome-wide single-nucleotide polymorphism (SNP) array...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27899115/characterizing-the-impact-of-sustained-sulfadoxine-pyrimethamine-use-upon-the-plasmodium-falciparum-population-in-malawi
#16
Matt Ravenhall, Ernest Diez Benavente, Mwapatsa Mipando, Anja T R Jensen, Colin J Sutherland, Cally Roper, Nuno Sepúlveda, Dominic P Kwiatkowski, Jacqui Montgomery, Kamija S Phiri, Anja Terlouw, Alister Craig, Susana Campino, Harold Ocholla, Taane G Clark
BACKGROUND: Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population. METHODS: Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used...
November 29, 2016: Malaria Journal
https://www.readbyqxmd.com/read/27896996/cerna-search-method-identified-a-met-activated-subgroup-among-egfr-dna-amplified-lung-adenocarcinoma-patients
#17
Halla Kabat, Leo Tunkle, Inhan Lee
Given the diverse molecular pathways involved in tumorigenesis, identifying subgroups among cancer patients is crucial in precision medicine. While most targeted therapies rely on DNA mutation status in tumors, responses to such therapies vary due to the many molecular processes involved in propagating DNA changes to proteins (which constitute the usual drug targets). Though RNA expressions have been extensively used to categorize tumors, identifying clinically important subgroups remains challenging given the difficulty of discerning subgroups within all possible RNA-RNA networks...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896964/integrative-analysis-for-lung-adenocarcinoma-predicts-morphological-features-associated-with-genetic-variations
#18
Chao Wang, Hai Su, Lin Yang, Kun Huang
Lung cancer is one of the most deadly cancers and lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. However, LUAD is highly heterogeneous due to genetic difference as well as phenotypic differences such as cellular and tissue morphology. In this paper, we systematically examine the relationships between histological features and gene transcription. Specifically, we calculated 283 morphological features from histology images for 201 LUAD patients from TCGA project and identified the morphological feature with strong correlation with patient outcome...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896456/dna-copy-number-profiling-in-microsatellite-stable-and-microsatellite-unstable-hereditary-non-polyposis-colorectal-cancers-by-targeted-cnv-array
#19
Weixiang Chen, Jun Ding, Long Jiang, Zebing Liu, Xiaoyan Zhou, Daren Shi
About half of hereditary non-polyposis colorectal cancers (HNPCCs) fulfilling the Amsterdam criteria (AC) do not display evidence of mismatch repair defects, and the difference between microsatellite-stable (MSS) and microsatellite-unstable HNPCC remains poorly understood. The study was to compare overall copy number variation (CNV) and loss of heterozygosity (LOH) of the entire genome in HNPCCs with MSS and microsatellite-instability (MSI) using the Cytoscan HD Array. This was a study carried out in samples from 20 patients with MSS HNPCC and four patients with MSI HNPCC from the Fudan University Shanghai Cancer Center (China)...
November 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27896429/copy-number-variability-in-parkinson-s-disease-assembling-the-puzzle-through-a-systems-biology-approach
#20
REVIEW
Valentina La Cognata, Giovanna Morello, Velia D'Agata, Sebastiano Cavallaro
Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs)...
November 28, 2016: Human Genetics
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