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https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27896277/prediction-of-bacillus-calmette-guerin-response-in-patients-with-bladder-cancer-after-transurethral-resection-of-bladder-tumor-by-using-genetic-variation-based-on-genomic-studies
#14
REVIEW
Ning Zhang, Guangliang Jiang, Xu Liu, Rong Na, Xiang Wang, Jianfeng Xu
Purpose. We aimed to comprehensively review contemporary literature on genetic and epigenetic biomarkers associated with the prediction of Bacillus Calmette-Guerin (BCG) response after the transurethral resection of a bladder tumor and to discuss the application of these biomarkers in precision cancer care for bladder cancer. Method. We performed a systematic review of published literatures in the databases PubMed and Embase by using the following key words: bladder cancer, BCG, gene, and methylation. Studies associated with cell lines, animal models, and muscle invasive bladder cancer were excluded...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27894409/the-effects-of-mitochondrial-dna-deletion-and-copy-number-variations-on-different-exercise-intensities-in-highly-trained-swimmers
#15
O Baykara, S K Sahin, F Akbas, M Guven, I Onaran
It has been suggested that heavy exercise might increase oxidative stress, causing mitochondrial DNA (mtDNA) mutations as well as DNA mutations and changes in the mtDNA copy number in cells. mtDNA4977 deletion is one of the most common deletions seen on mitochondria. We hypothesize association between exercise induced oxidative stress and mtDNA damage in peripheral blood lymphocytes (PBLs) of highly trained swimmers. Therefore we studied the mtDNA4977 deletion level, mtDNA copy number and their relationship with cellular ATP and oxidative stress status in PBLs of swimmers...
October 31, 2016: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/27893852/a-comparative-study-of-smn-protein-and-mrna-in-blood-and-fibroblasts-in-patients-with-spinal-muscular-atrophy-and-healthy-controls
#16
Renske I Wadman, Marloes Stam, Marc D Jansen, Yana van der Weegen, Camiel A Wijngaarde, Oliver Harschnitz, Peter Sodaar, Kees P J Braun, Dennis Dooijes, Henny H Lemmink, Leonard H van den Berg, W Ludo van der Pol
BACKGROUND: Clinical trials to test safety and efficacy of drugs for patients with spinal muscular atrophy (SMA) are currently underway. Biomarkers that document treatment-induced effects are needed because disease progression in childhood forms of SMA is slow and clinical outcome measures may lack sensitivity to detect meaningful changes in motor function in the period of 1-2 years of follow-up during randomized clinical trials. OBJECTIVE: To determine and compare SMN protein and mRNA levels in two cell types (i...
2016: PloS One
https://www.readbyqxmd.com/read/27884178/patterns-of-ribosomal-protein-expression-specify-normal-and-malignant-human-cells
#17
Joao C Guimaraes, Mihaela Zavolan
BACKGROUND: Ribosomes are highly conserved molecular machines whose core composition has traditionally been regarded as invariant. However, recent studies have reported intriguing differences in the expression of some ribosomal proteins (RPs) across tissues and highly specific effects on the translation of individual mRNAs. RESULTS: To determine whether RPs are more generally linked to cell identity, we analyze the heterogeneity of RP expression in a large set of human tissues, primary cells, and tumors...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884122/assessment-of-copy-number-variations-in-120-patients-with-poland-syndrome
#18
Carlotta Maria Vaccari, Elisa Tassano, Michele Torre, Stefania Gimelli, Maria Teresa Divizia, Maria Victoria Romanini, Simone Bossi, Ilaria Musante, Maura Valle, Filippo Senes, Nunzio Catena, Maria Francesca Bedeschi, Anwar Baban, Maria Grazia Calevo, Massimo Acquaviva, Margherita Lerone, Roberto Ravazzolo, Aldamaria Puliti
BACKGROUND: Poland Syndrome (PS) is a rare congenital disorder presenting with agenesis/hypoplasia of the pectoralis major muscle variably associated with thoracic and/or upper limb anomalies. Most cases are sporadic, but familial recurrence, with different inheritance patterns, has been observed. The genetic etiology of PS remains unknown. Karyotyping and array-comparative genomic hybridization (CGH) analyses can identify genomic imbalances that can clarify the genetic etiology of congenital and neurodevelopmental disorders...
November 25, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27883173/clinical-application-of-snp-array-analysis-in-first-trimester-pregnancy-loss-a-prospective-study
#19
Yan Wang, Qing Cheng, Lulu Meng, Chunyu Luo, Huanran Hu, Jingjing Zhang, Jian Cheng, Tianhui Xu, Tao Jiang, Dong Liang, Ping Hu, Zhengfeng Xu
Chromosomal microarray analysis (CMA) has been used routinely in pediatric and prenatal genetic diagnosis in clinical practice, but it has rarely been applied to miscarriage analysis. In this study, we conducted a prospective study to evaluate the feasibility of CMA for genetic diagnosis of first-trimester miscarriage specimens. We successfully analyzed 551 fresh miscarriage specimens using SNP array. Among the specimens, 2.9% (16/551) had significant maternal cell contamination and were excluded from the study...
November 24, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27882129/whole-genome-resequencing-of-100-healthy-individuals-using-dna-pooling
#20
Xiaobin Wang, Weiguo Sui, Weiqing Wu, Xianliang Hou, Minglin Ou, Yueying Xiang, Yong Dai
With the advent of next-generation sequencing technology, the cost of sequencing has significantly decreased. However, sequencing costs remain high for large-scale studies. In the present study, DNA pooling was applied as a cost-effective strategy for sequencing. The sequencing results for 100 healthy individuals obtained via whole-genome resequencing and using DNA pooling are presented in the present study. In order to minimise the likelihood of systematic bias in sampling, paired-end libraries with an insert size of 500 bp were prepared for all samples and then subjected to whole-genome sequencing using four lanes for each library and resulting in at least a 30-fold haploid coverage for each sample...
November 2016: Experimental and Therapeutic Medicine
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