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Pan Genome

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https://www.readbyqxmd.com/read/27904700/detection-of-gene-copy-number-alterations-in-dcis-and-invasive-breast-cancer-by-qm-fish
#1
Aifeng Pan, Yawei Zhou, Kun Mu, Yansong Liu, Feifei Sun, Peng Li, Li Li
The exact roles of copy number alteration (CNA) in initiation, progression and immunotherapy of breast cancer and the genomic alterations behind progression from ductal carcinoma in situ (DCIS) to invasive carcinoma remain unknown. Quantitative multi-gene fluorescence in situ hybridization (QM-FISH) opens a possibility of large scale genomic analysis of specific deletions and amplifications with high-resolution at one cell level. We detected CNAs of 30 genes using QM-FISH and analyzed their association with clinicopathological parameters and patients' outcomes in 66 breast cancers with synchronous invasive carcinoma and DCIS...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27903973/association-of-a-cytarabine-chemosensitivity-related-gene-expression-signature-with-survival-in-cytogenetically-normal-acute-myeloid-leukemia
#2
Han Yan, Lu Wen, Dan Tan, Pan Xie, Feng-Mei Pang, Hong-Hao Zhou, Wei Zhang, Zhao-Qian Liu, Jie Tang, Xi Li, Xiao-Ping Chen
The prognosis of cytogenetically normal acute myeloid leukemia (CN-AML) varies greatly among patients. Achievement of complete remission (CR) after chemotherapy is indispensable for a better prognosis. To develop a gene signature predicting overall survival (OS) in CN-AML, we performed data mining procedure based on whole genome expression data of both blood cancer cell lines and AML patients from open access database. A gene expression signature including 42 probes was derived. These probes were significantly associated with both cytarabine half maximal inhibitory concentration values in blood cancer cell lines and OS in CN-AML patients...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27903463/her2-transmembrane-mutations-v659-g660-that-stabilize-homo-and-hetero-dimerization-are-rare-oncogenic-drivers-in-lung-adenocarcinoma-that-respond-to-afatinib
#3
Sai-Hong Ignatius Ou, Alexa B Schrock, Eduard V Bocharov, Samuel J Klempner, Carolina Kawamura Haddad, Gary Steinecker, Melissa Johnson, Barbara J Gitlitz, Jon Chung, Paulo V Campregher, Jeffrey S Ross, Philip J Stephens, Vincent A Miller, James H Suh, Siraj M Ali, Vamsidhar Velcheti
INTRODUCTION: HER2 transmembrane domain (TMD) mutations (HER2(V659E), HER2(G660D)) have previously been identified in lung adenocarcinomas, but their frequency and clinical significance is unknown. METHODS: We prospectively analyzed 8,551 consecutive lung adenocarcinomas using hybrid-capture based comprehensive genomic profiling (CGP) at the request of the individual treating physicians for the purpose of making therapy decisions. RESULTS: We identified 15 cases (0...
November 26, 2016: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/27903314/pudong-white-pig-a-unique-genetic-resource-disclosed-by-sequencing-data
#4
Q Xiao, Z Zhang, H Sun, Q Wang, Y Pan
Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data...
December 1, 2016: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/27902432/self-replicating-shuttle-vectors-based-on-pans-a-small-endogenous-plasmid-of-the-unicellular-cyanobacterium-synechococcus-elongatus-pcc-7942
#5
You Chen, Arnaud Taton, Michaela Go, Ross E London, Lindsey M Pieper, Susan S Golden, James W Golden
To facilitate development of synthetic biology tools for genetic engineering of cyanobacterial strains, we constructed pANS-derived self-replicating shuttle vectors that are based on the minimal replication element of the Synechococcus elongatus strain PCC 7942 plasmid pANS. To remove the possibility of homologous recombination events between the shuttle plasmids and the native pANS plasmid, the endogenous pANS was cured through plasmid incompatibility-mediated spontaneous loss. A heterologous toxin-antitoxin cassette was incorporated into the shuttle vectors for stable plasmid maintenance in the absence of antibiotic selection...
October 14, 2016: Microbiology
https://www.readbyqxmd.com/read/27899679/atpid-a-genome-scale-resource-for-genotype-phenotype-associations-in-arabidopsis
#6
Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype-phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899624/microscope-in-2017-an-expanding-and-evolving-integrated-resource-for-community-expertise-of-microbial-genomes
#7
David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoe Rouy, David Roche, Claude Scarpelli, Claudine Médigue
The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899622/uniprot-the-universal-protein-knowledgebase
#8
(no author information available yet)
The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each protein. The remainder are automatically annotated based on rule systems that rely on the expert curated knowledge. Since our last update in 2014, we have more than doubled the number of reference proteomes to 5631, giving a greater coverage of taxonomic diversity...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899621/cooperative-genomic-alteration-network-reveals-molecular-classification-across-12-major-cancer-types
#9
Hongyi Zhang, Yulan Deng, Yong Zhang, Yanyan Ping, Hongying Zhao, Lin Pang, Xinxin Zhang, Li Wang, Chaohan Xu, Yun Xiao, Xia Li
The accumulation of somatic genomic alterations that enables cells to gradually acquire growth advantage contributes to tumor development. This has the important implication of the widespread existence of cooperative genomic alterations in the accumulation process. Here, we proposed a computational method HCOC that simultaneously consider genetic context and downstream functional effects on cancer hallmarks to uncover somatic cooperative events in human cancers. Applying our method to 12 TCGA cancer types, we totally identified 1199 cooperative events with high heterogeneity across human cancers, and then constructed a pan-cancer cooperative alteration network...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899617/epigenetic-and-genetic-deregulation-in-cancer-target-distinct-signaling-pathway-domains
#10
Yang Gao, Andrew E Teschendorff
Cancer is characterized by both genetic and epigenetic alterations. While cancer driver mutations and copy-number alterations have been studied at a systems-level, relatively little is known about the systems-level patterns exhibited by their epigenetic counterparts. Here we perform a pan-cancer wide systems-level analysis, mapping candidate cancer-driver DNA methylation (DNAm) alterations onto a human interactome. We demonstrate that functional DNAm alterations in cancer tend to map to nodes of lower connectivity and inter-connectivity, compared to the corresponding alterations at the genomic level...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898829/gapit-version-2-an-enhanced-integrated-tool-for-genomic-association-and-prediction
#11
You Tang, Xiaolei Liu, Jiabo Wang, Meng Li, Qishan Wang, Feng Tian, Zhongbin Su, Yuchun Pan, Di Liu, Alexander E Lipka, Edward S Buckler, Zhiwu Zhang
Most human diseases and agriculturally important traits are complex. Dissecting their genetic architecture requires continued development of innovative and powerful statistical methods. Corresponding advances in computing tools are critical to efficiently use these statistical innovations and to enhance and accelerate biomedical and agricultural research and applications. The genome association and prediction integrated tool (GAPIT) was first released in 2012 and became widely used for genome-wide association studies (GWAS) and genomic prediction...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27895417/glycoproteins-and-glycoproteomics-in-pancreatic-cancer
#12
REVIEW
Sheng Pan, Teresa A Brentnall, Ru Chen
Aberrations in protein glycosylation and polysaccharides play a pivotal role in pancreatic tumorigenesis, influencing cancer progression, metastasis, immuno-response and chemoresistance. Abnormal expression in sugar moieties can impact the function of various glycoproteins, including mucins, surface receptors, adhesive proteins, proteoglycans, as well as their effectors and binding ligands, resulting in an increase in pancreatic cancer invasiveness and a cancer-favored microenvironment. Recent advance in glycoproteomics, glycomics and other chemical biology techniques have been employed to better understand the complex mechanism of glycosylation events and how they orchestrate molecular activities in genomics, proteomics and metabolomics implicated in pancreatic adenocarcinoma...
November 14, 2016: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/27890709/role-of-major-and-brain-specific-sgce-isoforms-in-the-pathogenesis-of-myoclonus-dystonia-syndrome
#13
Jianfeng Xiao, Satya R Vemula, Yi Xue, Mohammad M Khan, Francesca A Carlisle, Adrian J Waite, Derek J Blake, Ioannis Dragatsis, Yu Zhao, Mark S LeDoux
Loss-of-function mutations in SGCE, which encodes ε-sarcoglycan (ε-SG), cause myoclonus-dystonia syndrome (OMIM159900, DYT11). A "major" ε-SG protein derived from CCDS5637.1 (NM_003919.2) and a "brain-specific" protein, that includes sequence derived from alternative exon 11b (CCDS47642.1, NM_001099400.1), are reportedly localized in post- and pre-synaptic membrane fractions, respectively. Moreover, deficiency of the "brain-specific" isoform and other isoforms derived from exon 11b may be central to the pathogenesis of DYT11...
November 24, 2016: Neurobiology of Disease
https://www.readbyqxmd.com/read/27889782/molecular-pathology-a-requirement-for-precision-medicine-in-cancer
#14
Manfred Dietel
The increasing importance of targeting drugs and check-point inhibitors in the treatment of several tumor entities (breast, colon, lung, malignant melanoma, lymphoma, etc.) and the necessity of a companion diagnostic (HER2, (pan)RAS, EGFR, ALK, BRAF, ROS1, MET, PD-L1, etc.) is leading to new challenges for surgical pathology. Since almost all the biomarkers to be specifically detected are tissue based, a precise and reliable diagnostic is absolutely crucial. To meet this challenge surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization, PCR and its multiple variants, (pyro/Sanger) sequencing, next generation sequencing (amplicon, whole exome, whole genome), DNA arrays, methylation analyses, etc...
2016: Oncology Research and Treatment
https://www.readbyqxmd.com/read/27888796/altered-dna-methylation-in-neonates-born-large-for-gestational-age-is-associated-with-cardiometabolic-risk-in-children
#15
Xian-Hua Lin, Dan-Dan Wu, Ling Gao, Jun-Yu Zhang, Hai-Tao Pan, Hui Wang, Cheng Li, Ping Zhang, Meng-Xi Guo, Yan-Ting Wu, Ya-Jing Tan, Li Jin, Yu-Qian Xiang, Ju-Xue Li, Jian-Zhong Sheng, He-Feng Huang
BACKGROUND: Infants being born Large-for-gestational-age (LGA) are prone to developing cardiometabolic disease. However, the underlying mechanisms remain unclear. RESULTS: Clinical investigation showed that children born LGA had significantly higher serum level of total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-c), and insulin, ratio of TC/high-density lipoprotein-cholesterol (HDL-c) compared to children born appropriate for gestational age (AGA)...
November 18, 2016: Oncotarget
https://www.readbyqxmd.com/read/27887642/rapid-scoring-of-genes-in-microbial-pan-genome-wide-association-studies-with-scoary
#16
Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS...
November 25, 2016: Genome Biology
https://www.readbyqxmd.com/read/27883053/measuring-intratumor-heterogeneity-by-network-entropy-using-rna-seq-data
#17
Youngjune Park, Sangsoo Lim, Jin-Wu Nam, Sun Kim
Intratumor heterogeneity (ITH) is observed at different stages of tumor progression, metastasis and reouccurence, which can be important for clinical applications. We used RNA-sequencing data from tumor samples, and measured the level of ITH in terms of biological network states. To model complex relationships among genes, we used a protein interaction network to consider gene-gene dependency. ITH was measured by using an entropy-based distance metric between two networks, nJSD, with Jensen-Shannon Divergence (JSD)...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881993/transcriptome-analysis-and-identification-of-genes-associated-with-floral-transition-and-flower-development-in-sugar-apple-annona-squamosa-l
#18
Kaidong Liu, Shaoxian Feng, Yaoling Pan, Jundi Zhong, Yan Chen, Changchun Yuan, Haili Li
Sugar apple (Annona squamosa L.) is a semi-deciduous subtropical tree that progressively sheds its leaves in the spring. However, little information is available on the mechanism involved in flower developmental pattern. To gain a global perspective on the floral transition and flower development of sugar apple, cDNA libraries were prepared independently from inflorescent meristem and three flowering stages. Illumina sequencing generated 107,197,488 high quality reads that were assembled into 71,948 unigenes, with an average sequence length of 825...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27881098/genomic-determination-of-minimum-multi-locus-sequence-typing-schemas-to-represent-the-genomic-phylogeny-of-mycoplasma-hominis
#19
Aleksey Jironkin, Rebecca J Brown, Anthony Underwood, Victoria J Chalker, Owen B Spiller
BACKGROUND: Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms...
November 23, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27879658/the-emergence-of-pan-cancer-cimp-and-its-elusive-interpretation
#20
REVIEW
Brendan F Miller, Francisco Sánchez-Vega, Laura Elnitski
Epigenetic dysregulation is recognized as a hallmark of cancer. In the last 16 years, a CpG island methylator phenotype (CIMP) has been documented in tumors originating from different tissues. However, a looming question in the field is whether or not CIMP is a pan-cancer phenomenon or a tissue-specific event. Here, we give a synopsis of the history of CIMP and describe the pattern of DNA methylation that defines the CIMP phenotype in different cancer types. We highlight new conceptual approaches of classifying tumors based on CIMP in a cancer type-agnostic way that reveal the presence of distinct CIMP tumors in a multitude of The Cancer Genome Atlas (TCGA) datasets, suggesting that this phenotype may transcend tissue-type specificity...
November 22, 2016: Biomolecules
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