Combined Analysis of Genome-Wide Expression and Copy Number
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Comprehensive Identification and Characterization of Somatic Copy Number Alterations in Triple‑Negative Breast Cancer
INTERNATIONAL JOURNAL OF ONCOLOGY 56: 522-530, 2020 Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer ZAIBING LI1,2*, XIAO ZHANG3*, CHENXIN HOU4, YUQING ZHOU4, JUNLI CHEN1, HAOYANG CAI5, YIFENG YE3, JINPING LIU3 and NING HUANG1 1Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041; 2Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000; 3Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731; 4West China Medical School, Sichuan University, Chengdu, Sichuan 610041; 5Center of Growth, Metabolism and Aging, Key Laboratory of Bio‑Resources and Eco‑Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China Received January 30, 2019; Accepted August 30, 2019 DOI: 10.3892/ijo.2019.4950 Abstract. Triple-negative breast cancer (TNBC) accounts hierarchical clustering of tumors resulted in three main for ~15% of all breast cancer diagnoses each year. Patients subgroups that exhibited distinct CNA profiles, which with TNBC tend to have a higher risk for early relapse and may reveal the heterogeneity of molecular mechanisms in a worse prognosis. TNBC is characterized by extensive TNBC subgroups. These results will extend the molecular somatic copy number alterations (CNAs). However, the DNA understanding of TNBC and will facilitate the discovery of CNA profile of TNBC remains to be extensively investigated. therapeutic and diagnostic target candidates. The present study assessed the genomic profile of CNAs in 201 TNBC samples, aiming to identify recurrent CNAs that Introduction may drive the pathogenesis of TNBC. -
Bppart and Bpmax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model
BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, and Hamidreza Chitsaz ∗ Department of Computer Science, Colorado State University Abstract A few elite classes of RNA-RNA interaction (RRI), with complex roles in cellular functions such as miRNA-target and lncRNAs in human health, have already been studied. Accordingly, RRI bioinfor- matics tools tailored for those elite classes have been proposed in the last decade. Interestingly, there are somewhat unnoticed mRNA-mRNA interactions in the literature with potentially drastic biological roles. Hence, there is a need for high-throughput generic RRI bioinformatics tools. We revisit our RRI partition function algorithm, piRNA, which happens to be the most comprehensive and computationally-intensive thermodynamic model for RRI. We propose simpler models that are shown to retain the vast majority of the thermodynamic information that piRNA captures. We simplify the energy model and instead consider only weighted base pair counting to obtain BPPart for Base-pair Partition function and BPMax for Base-pair Maximization which are 225 and 1350 faster ◦ × × than piRNA, with a correlation of 0.855 and 0.836 with piRNA at 37 C on 50,500 experimentally charac- terized RRIs. This correlation increases to 0.920 and 0.904, respectively, at 180◦C. − Finally, we apply our algorithm BPPart to discover two disease-related RNAs, SNORD3D and TRAF3, and hypothesize their potential roles in Parkinson's disease and Cerebral Autosomal Dominant Arteri- opathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL). 1 Introduction Since mid 1990s with the advent of RNA interference discovery, RNA-RNA interaction (RRI) has moved to the spotlight in modern, post-genome biology. -
Dynamic Clonal Progression in Xenografts of Acute Lymphoblastic Leukemia with Intrachromosomal Amplification of Chromosome 21
Sinclair PB, Blair HH, Ryan SL, Buechler L, Cheng J, Clayton J, Hanna R, Hollern S, Hawking Z, Bashton M, Schwab CJ, Jones L, Russell LJ, Marr H, Carey P, Halsey C, Heidenreich O, Moorman AV, Harrison CJ. Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21. Haematologica 2018, https://doi.org/10.3324/haematol.2017.172304 Copyright: © 2018, Ferrata Storti Foundation. Authors will grant copyright of their article to the Ferrata Storti Foundation. No formal permission will be required to reproduce parts (tables or illustrations) of published papers, provided the source is quoted appropriately and reproduction has no commercial intent. Reproductions with commercial intent will require written permission and payment of royalties. Please contact the office for requests: [email protected] DOI link to article: https://doi.org/10.3324/haematol.2017.172304 Date deposited: 20/03/2018 This work is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License Newcastle University ePrints - eprint.ncl.ac.uk Published Ahead of Print on February 15, 2018, as doi:10.3324/haematol.2017.172304. Copyright 2018 Ferrata Storti Foundation. Dynamic clonal progression in xenografts of acute lymphoblastic leukemia with intrachromosomal amplification of chromosome 21 by Paul B. Sinclair, Helen H. Blair, Sarra L. Ryan, Lars Buechler, Joanna Cheng, Jake Clayton, Rebecca Hanna, Shaun Hollern, Zoe Hawking, Matthew Bashton, Claire J. Schwab, Lisa Jones, Lisa J. Russell, Helen Marr, Peter Carey, Christina Halsey, Olaf Heidenreich, Anthony V. Moorman, and Christine J. Harrison Haematologica 2018 [Epub ahead of print] Citation: Paul B. Sinclair, Helen H. -
Differentially Expressed on Collagen Networks 1, 2, 10 © 2000-2009 Ingenuity Systems, Inc. All Rights Reserved. Symbol Entrez
Differentially expressed on collagen Networks 1, 2, 10 © 2000-2009 Ingenuity Systems, Inc. All rights reserved. Symbol Entrez Gene Name Affymetrix Fold Change Location Family ALDH1A3 aldehyde dehydrogenase 1 family, member A3 203180_at -5.43125168 Cytoplasm enzyme 209772_s_ Plasma CD24 CD24 molecule at -4.32890229 Membrane other HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 204130_at -4.1099197 Cytoplasm enzyme Plasma AMOTL2 angiomotin like 2 203002_at -2.82872773 Membrane other transcription DLX2 distal-less homeobox 2 207147_at -2.74996362 Nucleus regulator 221215_s_ RIPK4 receptor-interacting serine-threonine kinase 4 at -2.56556472 Nucleus kinase PLK2 polo-like kinase 2 (Drosophila) 201939_at -2.47054478 Nucleus kinase ALDH3A1 aldehyde dehydrogenase 3 family, memberA1 205623_at -2.30532989 Cytoplasm enzyme TXNRD1 thioredoxin reductase 1 201266_at -2.27936909 Cytoplasm enzyme Extracellular CYR61 cysteine-rich, angiogenic inducer, 61 201289_at -2.09052668 Space other 214212_x_ FERMT2 fermitin family homolog 2 (Drosophila) at -1.87478183 Cytoplasm other Plasma RIT1 Ras-like without CAAX 1 209882_at -1.77586775 Membrane enzyme 210297_s_ Extracellular MSMB microseminoprotein, beta- at -1.72177723 Space other Extracellular PI3 peptidase inhibitor 3, skin-derived 203691_at -1.68135697 Space other ALDH3B1 aldehyde dehydrogenase 3 family, member B1 205640_at -1.67376791 Cytoplasm enzyme 202124_s_ Plasma TRAK2 trafficking protein, kinesin binding 2 at -1.6367793 Membrane transporter BMP and activin membrane-bound inhibitor Plasma BAMBI -
MOLECULAR G EN ETICS of the January, HUMAN X
MOLECULAR GENETICS OF THE HUMAN X CHROMOSOME BY DAVID ANDREW HARTLEY a thesis submitted for the degree of Doctor of Philosophy in the University of London January, 1984 Department of Biochemistry St. Mary's Hospital Medical School London W2 IPG 1 Abstract The comparison of frequency of recombination with chromosomal position has been possible only in Drosophila melanogaster but it is known that chiasma distribution in the human male (and many other species) is not random. A number of cloned DNA sequences have been isolated from a library enriched for X chromosome DNA by flow cytometry. The chromosomal loci complementary to these cloned sequences have been investigated by hybridization to somatic cell hybrid DNAs and by direct hybridization 1 in situ' to human metaphase spreads. In this way a cytological map of the X chromosome defined by DNA sequence markers has been constructed. Genetic distances complementary to the physical separations determined have been estimated by determining the segregation of DNA sequence variants at each locus in three generation p e d i g r e e s . The sequence variation is manifested as altered restriction fragment migration in agarose gels. It is intimated from these analyses that the pattern of recombination frequency along the human X chromosome mirrors the non-random chiasma distribution seen along male autosomes. This supports the chiasmatype theory and has implications on the availability of genetic components of the X chromosome to recombination. 2 To ray father in the hope of convincing him of life outside o f E.coli 3 ...scientists getting their kicks when deadly disease can do as it pleases results ain't hard to predict Gil Scott-Heron 4 Ack n ov; ledgements To my supervisor Bob Williamson for support. -
Reproduction
REPRODUCTIONRESEARCH Focus on Mammalian Embryogenomics Molecular and subcellular characterisation of oocytes screened for their developmental competence based on glucose-6-phosphate dehydrogenase activity Helmut Torner2, Nasser Ghanem, Christina Ambros2, Michael Ho¨lker, Wolfgang Tomek2, Chirawath Phatsara, Hannelore Alm2, Marc-Andre´ Sirard1, Wilhelm Kanitz2, Karl Schellander and Dawit Tesfaye Animal Breeding and Husbandry Group, Department of Animal Breeding and Husbandry, Institute of Animal Science, University of Bonn, Endenicher allee 15, 53115 Bonn, Germany, 1De´partement des Sciences Animales, Centre de Recherche en Biologie de la Reproduction, Universite´ Laval, Pav. Comtois, Laval, Sainte-Foy, Que´bec, G1K 7P4, Canada and 2Research Institute for the Biology of Farm Animals, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany Correspondence should be addressed to D Tesfaye; Email: [email protected] Abstract Oocyte selection based on glucose-6-phosphate dehydrogenase (G6PDH) activity has been successfully used to differentiate between competent and incompetent bovine oocytes. However, the intrinsic molecular and subcellular characteristics of these oocytes have not yet been investigated. Here, we aim to identify molecular and functional markers associated with oocyte developmental potential when selected based on G6PDH activity. Immature compact cumulus–oocyte complexes were stained with brilliant cresyl blue (BCB) for 90 min. Based on K C their colouration, oocytes were divided into BCB (colourless cytoplasm, high G6PDH activity) and BCB (coloured cytoplasm, low G6PDH activity). The chromatin configuration of the nucleus and the mitochondrial activityof oocytes were determined by fluorescence labelling and photometric measurement. The abundance and phosphorylation pattern of protein kinases Akt and MAP were estimated by Western blot C K analysis. -
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex
UCSF UC San Francisco Previously Published Works Title Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex. Permalink https://escholarship.org/uc/item/8j92s7z1 Journal Cell reports, 31(1) ISSN 2211-1247 Authors Werling, Donna M Pochareddy, Sirisha Choi, Jinmyung et al. Publication Date 2020-04-01 DOI 10.1016/j.celrep.2020.03.053 Peer reviewed eScholarship.org Powered by the California Digital Library University of California HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Cell Rep Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 June 15. Published in final edited form as: Cell Rep. 2020 April 07; 31(1): 107489. doi:10.1016/j.celrep.2020.03.053. Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex Donna M. Werling1,2,32, Sirisha Pochareddy3,32, Jinmyung Choi3,32, Joon-Yong An1,4,5,32, Brooke Sheppard1, Minshi Peng6, Zhen Li3,7, Claudia Dastmalchi1, Gabriel Santpere3,8, André M.M. Sousa3, Andrew T.N Tebbenkamp3, Navjot Kaur3, Forrest O. Gulden3, Michael S. Breen9,10,11,12, Lindsay Liang1, Michael C. Gilson1, Xuefang Zhao13,14,15, Shan Dong1, Lambertus Klei16, A. Ercument Cicek17,18, Joseph D. Buxbaum9,10,11,19, Homa Adle- Biassette20, Jean-Leon Thomas21,22, Kimberly A. Aldinger23,24, Diana R. O’Day25, Ian A. Glass25, Noah A. Zaitlen26, Michael E. Talkowski13,14,15, Kathryn Roeder6,18, Matthew W. State1,27, Bernie Devlin16, Stephan J. Sanders1,27,33,*, -
Primepcr™Assay Validation Report
PrimePCR™Assay Validation Report Gene Information Gene Name oligodendrocytic myelin paranodal and inner loop protein Gene Symbol OPALIN Organism Human Gene Summary Description Not Available Gene Aliases HTMP10, TMEM10, TMP10 RefSeq Accession No. NC_000010.10, NT_030059.13 UniGene ID Hs.12449 Ensembl Gene ID ENSG00000197430 Entrez Gene ID 93377 Assay Information Unique Assay ID qHsaCID0015438 Assay Type SYBR® Green Detected Coding Transcript(s) ENST00000371172, ENST00000393871, ENST00000393870, ENST00000419479, ENST00000536387 Amplicon Context Sequence GGGCCTCTTGTGCTCCCATCGTATTCTTCTCATGTGTGGGTGATCTCCTAGGATT CTCAGATATCTTGGGATTGTCATCAATTTCTGAAAT Amplicon Length (bp) 61 Chromosome Location 10:98105820-98108081 Assay Design Intron-spanning Purification Desalted Validation Results Efficiency (%) 99 R2 0.9996 cDNA Cq Target not expressed in universal RNA cDNA Tm (Celsius) Target not expressed in universal RNA gDNA Cq Target not expressed in universal RNA Specificity (%) No cross reactivity detected Information to assist with data interpretation is provided at the end of this report. Page 1/4 PrimePCR™Assay Validation Report OPALIN, Human Amplification Plot Amplification of cDNA generated from 25 ng of universal reference RNA Melt Peak Melt curve analysis of above amplification Standard Curve Standard curve generated using 20 million copies of template diluted 10-fold to 20 copies Page 2/4 PrimePCR™Assay Validation Report Products used to generate validation data Real-Time PCR Instrument CFX384 Real-Time PCR Detection System Reverse Transcription Reagent iScript™ Advanced cDNA Synthesis Kit for RT-qPCR Real-Time PCR Supermix SsoAdvanced™ SYBR® Green Supermix Experimental Sample qPCR Human Reference Total RNA Data Interpretation Unique Assay ID This is a unique identifier that can be used to identify the assay in the literature and online. Detected Coding Transcript(s) This is a list of the Ensembl transcript ID(s) that this assay will detect. -
1471-2164-10-261.Pdf
BMC Genomics BioMed Central Research article Open Access Molecular signature of cell cycle exit induced in human T lymphoblasts by IL-2 withdrawal Magdalena Chechlinska*1, Jan Konrad Siwicki1, Monika Gos2, Malgorzata Oczko-Wojciechowska3, Michal Jarzab4, Aleksandra Pfeifer3, Barbara Jarzab3 and Jan Steffen1 Address: 1Department of Immunology, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland, 2Department of Cell Biology, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Warsaw, Poland, 3Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland and 4Department of Tumor Biology and Clinical Oncology, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland Email: Magdalena Chechlinska* - [email protected]; Jan Konrad Siwicki - [email protected]; Monika Gos - [email protected]; Malgorzata Oczko-Wojciechowska - [email protected]; Michal Jarzab - [email protected]; Aleksandra Pfeifer - [email protected]; Barbara Jarzab - [email protected]; Jan Steffen - [email protected] * Corresponding author Published: 8 June 2009 Received: 20 February 2009 Accepted: 8 June 2009 BMC Genomics 2009, 10:261 doi:10.1186/1471-2164-10-261 This article is available from: http://www.biomedcentral.com/1471-2164/10/261 © 2009 Chechlinska et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The molecular mechanisms of cell cycle exit are poorly understood. -
Download Special Issue
International Journal of Genomics Noncoding RNAs in Health and Disease Lead Guest Editor: Michele Purrello Guest Editors: Massimo Romani and Davide Barbagallo Noncoding RNAs in Health and Disease International Journal of Genomics Noncoding RNAs in Health and Disease Lead Guest Editor: Michele Purrello Guest Editors: Massimo Romani and Davide Barbagallo Copyright © 2018 Hindawi. All rights reserved. This is a special issue published in “International Journal of Genomics.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Andrea C. Belin, Sweden M. Hadzopoulou-Cladaras, Greece Ferenc Olasz, Hungary Jacques Camonis, France Sylvia Hagemann, Austria Elena Pasyukova, Russia Prabhakara V. Choudary, USA Henry Heng, USA Graziano Pesole, Italy Martine A. Collart, Switzerland Eivind Hovig, Norway Giulia Piaggio, Italy Monika Dmitrzak-Weglarz, Poland Hieronim Jakubowski, USA Mohamed Salem, USA Marco Gerdol, Italy B.-H. Jeong, Republic of Korea Wilfred van IJcken, Netherlands João Paulo Gomes, Portugal Atsushi Kurabayashi, Japan Brian Wigdahl, USA Soraya E. Gutierrez, Chile Giuliana Napolitano, Italy Jinfa Zhang, USA Contents Noncoding RNAs in Health and Disease Davide Barbagallo, Gaetano Vittone, Massimo Romani , and Michele Purrello Volume 2018, Article ID 9135073, 2 pages Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers Luka Bolha, -
Candidate Genes for Alcohol Preference Identified by Expression
Liang et al. Genome Biology 2010, 11:R11 http://genomebiology.com/2010/11/2/R11 RESEARCH Open Access Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats Tiebing Liang1*, Mark W Kimpel2, Jeanette N McClintick3, Ashley R Skillman1, Kevin McCall4, Howard J Edenberg3, Lucinda G Carr1 Abstract Background: Selectively bred alcohol-preferring (P) and alcohol-nonpreferring (NP) rats differ greatly in alcohol preference, in part due to a highly significant quantitative trait locus (QTL) on chromosome 4. Alcohol consumption scores of reciprocal chromosome 4 congenic strains NP.P and P.NP correlated with the introgressed interval. The goal of this study was to identify candidate genes that may influence alcohol consumption by comparing gene expression in five brain regions of alcohol-naïve inbred alcohol-preferring and P.NP congenic rats: amygdala, nucleus accumbens, hippocampus, caudate putamen, and frontal cortex. Results: Within the QTL region, 104 cis-regulated probe sets were differentially expressed in more than one region, and an additional 53 were differentially expressed in a single region. Fewer trans-regulated probe sets were detected, and most differed in only one region. Analysis of the average expression values across the 5 brain regions yielded 141 differentially expressed cis-regulated probe sets and 206 trans-regulated probe sets. Comparing the present results from inbred alcohol-preferring vs. congenic P.NP rats to earlier results from the reciprocal congenic NP.P vs. inbred alcohol-nonpreferring rats demonstrated that 74 cis-regulated probe sets were differentially expressed in the same direction and with a consistent magnitude of difference in at least one brain region. -
ECOP Shrna (H) Lentiviral Particles: Sc-89730-V
SANTA CRUZ BIOTECHNOLOGY, INC. ECOP shRNA (h) Lentiviral Particles: sc-89730-V BACKGROUND APPLICATIONS ECOP (EGFR-coamplified and overexpressed protein), also known as VOPP1 ECOP shRNA (h) Lentiviral Particles is recommended for the inhibition of (vesicular, overexpressed in cancer, prosurvival protein 1) or GASP (glioblas- ECOP expression in human cells. toma-amplified secreted protein), is a 172 amino acid protein that is coam- plified with EGFR and overexpressed in multiple glioblastomas. Highly ex- SUPPORT REAGENTS pressed in ovary and thymus, ECOP is found at moderate levels in testis, Control shRNA Lentiviral Particles: sc-108080. Available as 200 µl frozen colon, small intestine, and spleen, and at low levels in liver, placenta and viral stock containing 1.0 x 106 infectious units of virus (IFU); contains an κ prostate. ECOP regulates NF B signaling and may have a role in resistance shRNA construct encoding a scrambled sequence that will not lead to the to apoptosis. The gene encoding ECOP maps to human chromosome 7, which specific degradation of any known cellular mRNA. houses over 1,000 genes, comprises nearly 5% of the human genome and has been linked to Osteogenesis imperfecta, Pendred syndrome, Lissencephaly, RT-PCR REAGENTS Citrullinemia and Shwachman-Diamond syndrome. Semi-quantitative RT-PCR may be performed to monitor ECOP gene expres- REFERENCES sion knockdown using RT-PCR Primer: ECOP (h)-PR: sc-89730-PR (20 µl). Annealing temperature for the primers should be 55-60° C and the extension 1. Tsipouras, P., Myers, J.C., Ramirez, F. and Prockop, D.J. 1983. Restriction temperature should be 68-72° C.