From reference genes to global mean normalization
|
|
- Charity Hampton
- 5 years ago
- Views:
Transcription
1 From reference genes to global mean normalization Jo Vandesompele professor, Ghent University co-founder and CEO, Biogazelle qpcr Symposium USA November 9, 2009 Millbrae, CA
2 outline what is normalization gold standard for mrna normalization global mean normalization and selection of stable small RNAs for microrna normalization
3 introduction to normalization 2 sources of variation in gene expression results biological variation (true fold changes) experimentally induced variation (noise and bias) purpose of normalization is reduction of the experimental variation input quantity: RNA quantity, cdna synthesis efficiency, input quality: RNA integrity, RNA purity, gold standard is the use of multiple stably expressed reference genes which genes? how many? how to do the calculations?
4 normalization: genorm solution framework for qpcr gene expression normalisation using the reference gene concept: quantified errors related to the use of a single reference gene (> 3 fold in 25% of the cases; > 6 fold in 10% of the cases) developed a robust algorithm for assessment of expression stability of candidate reference genes proposed the geometric mean of at least 3 reference genes for accurate and reliable normalisation Vandesompele et al., Genome Biology, 2002
5 genorm software automated analysis ranking of candidate reference genes according to their stability determination of how many genes are required for reliable normalization
6 genorm validation (I) cancer patients survival curve statistically more significant results log rank statistics NF NF Hoebeeck et al., Int J Cancer, 2006
7 genorm validation (II) mrna haploinsufficiency measurements accurate assessment of small expression differences patient / control 3 independent experiments 95% confidence intervals Hellemans et al., Nature Genetics, 2004
8 normalization using multiple stable reference genes genorm is the de facto standard for reference gene validation and normalization > 2,000 citations of our genorm technology > 10,000 genorm software downloads in 100 countries
9
10 global mean normalization when a large set of genes are measured, the average expression level reflects the input amount and could be used for normalization e.g. microarray based normalization o lowess, mean ratio, SAGE / NGS sequencing counts the set of genes must be unbiased and sufficiently large we make use of this principle to normalize microrna data from experiments in which we quantify a substantial number of mirnas (450 or 650) in a given sample
11 global mean normalization small-rna controls classic normalization strategy small nuclear RNAs, small nucleolar RNAs 18 available from Applied Biosystems global mean normalization method applied for microarray data universal: applicable for every mirna dataset many datapoints needed (megaplex vs. multiplex) mirnas/controls that resemble the mean minimal standard deviation when comparing mirna expression with mean ( genorm V value, standard deviation of log transformed ratios) compatible with multiplex assays need to determine mean
12 small RNA controls How stable is the global mean compared to controls? genorm analysis using controls and mean as input variables exclusion of potentially co-regulated controls HY3 7q36 RNU19 5q31.2 RNU24 9q34 RNU38B 1p34.1-p32 RNU43 22q13 RNU44 1q25.1 RNU48 6p21.32 RNU49 17p11.2 RNU58A 18q21 RNU58B 18q21 RNU66 1p22.1 RNU6B 10p13 U18 15q22 U47 1q25.1 U54 8q12 U75 1q25.1 Z30 17q12 RPL21 13q12.2
13 mirna expression datasets neuroblastoma tumour samples T-ALL samples EVI1 deregulated leukemias retinoblastoma tumour samples normal tissues normal bone marrow
14 expression stability T-ALL genorm ranking 1,8 1,6 1,4 1,2 1 0,8 0,6 0,4 0,2 0
15 genorm ranking neuroblastoma leukemia EVI1 overexpression bone marrow pool normal tissues
16 neuroblastoma removal of variation not normalised stable controls mean mirnas
17 removal of variation T-ALL leukemia EVI1 overexpression bone marrow pool normal tissues
18 Fold enrichment CATGTG CATGTG CATGTG CACGTG CACGTG CATGTG CATGTG biological validation MYCN binds to the mir promoter -5 kb CpG island mir cluster +5 kb A B C IMR5 WAC2 A B C Amplicon
19 biological validation choice of normalization strategy influences differential mirna expression 3,5 Mir expression in neuroblastoma tumours 3 2,5 2 1,5 1 0,5 stable controls mean mirnas 0
20 biological validation choice of normalization strategy influences differential mirna expression 3,5 Mir expression in neuroblastoma tumours 3 2,5 2 1,5 1 0,5 stable controls mean mirnas 0
21 biological validation choice of normalization strategy influences differential mirna expression 3,5 Mir expression in neuroblastoma tumours 3 2,5 2 1,5 1 0,5 stable controls mean mirnas 0
22 fold change (MYCN amplified vs. MYCN single copy) balanced differential expression 3 2 controls mean average FC controls = average Fc mean = average FC mirnas =
23 correlation MYCN downregulated genes 2 normalization strategies stable mirna control normalisation mean normalisation
24 strategy also works for microarray data each sample is measured by RT-qPCR and microarray global mean normalization standardization per method hierarchical clustering samples cluster by sample (and NOT by method)
25 conclusions global mean normalization novel and powerful mirna normalization strategy maximal reduction of technical noise improved identification of differentially expressed genes balancing of differential expression universally applicable o global mean o multiple stable endogenous controls Mestdagh et al., Genome Biology, 2009
26 qbase PLUS normalization most powerful, flexible and user-friendly real-time PCR data-analysis software based on Ghent University s genorm and qbase technology state of the art normalization procedures o one or more classic reference genes o global mean normalization o expressed repeat normalization detection and correction of inter-run variation dedicated error propagation fully automated analysis; no manual interaction required booth 19
27 conclusions proper normalization has a major impact on your results provides statistically more significant results enables accurate assessment of small expression differences gold standard for mrna gene expression analysis genorm evaluation of candidate reference genes geometric mean of multiple stably expressed reference genes global mean normalization and subsequent genorm based selection of reference genes that resemble the mean is a valid option when measuring a large and unbiased set of genes (e.g. all mirnas)
28 acknowledgments mirna Pieter Mestdagh (UGent) Frank Speleman (UGent) Applied Biosystems qbase PLUS Jan Hellemans (Biogazelle UGent) Stefaan Derveaux (Biogazelle UGent)
29 January 28-29, 2010 Ghent, Belgium
A novel and universal method for microrna RT-qPCR data normalization
A novel and universal method for microrna RT-qPCR data normalization Jo Vandesompele professor, Ghent University co-founder and CEO, Biogazelle 4 th International qpcr Symposium Weihenstephan, March 1,
More informationChapter 18. mirna Expression Profiling: From Reference Genes to Global Mean Normalization
Chapter 18 mirna Expression Profiling: From Reference Genes to Global Mean Normalization Barbara D haene, Pieter Mestdagh, Jan Hellemans, and Jo Vandesompele Abstract MicroRNAs (mirnas) are an important
More informationPieter Mestdagh *, Pieter Van Vlierberghe *, An De Weer *, Daniel Muth, Frank Westermann, Frank Speleman * and Jo Vandesompele *
2009 Mestdagh Volume al. 10, Issue 6, Article R64 Open Access Method A novel and universal method for microrna RT-qPCR data normalization Pieter Mestdagh *, Pieter Van Vlierberghe *, An De Weer *, Daniel
More informationProfiles of gene expression & diagnosis/prognosis of cancer. MCs in Advanced Genetics Ainoa Planas Riverola
Profiles of gene expression & diagnosis/prognosis of cancer MCs in Advanced Genetics Ainoa Planas Riverola Gene expression profiles Gene expression profiling Used in molecular biology, it measures the
More informationDeploying the full transcriptome using RNA sequencing. Jo Vandesompele, CSO and co-founder The Non-Coding Genome May 12, 2016, Leuven
Deploying the full transcriptome using RNA sequencing Jo Vandesompele, CSO and co-founder The Non-Coding Genome May 12, 2016, Leuven Roadmap Biogazelle the power of RNA reasons to study non-coding RNA
More informationReference mirnas for mirnaome Analysis of Urothelial Carcinomas
Reference mirnas for mirnaome Analysis of Urothelial Carcinomas Nadine Ratert 1,2, Hellmuth-Alexander Meyer 1,3, Monika Jung 1, Hans-Joachim Mollenkopf 4, Ina Wagner 4, Kurt Miller 1, Ergin Kilic 5, Andreas
More informationGene-microRNA network module analysis for ovarian cancer
Gene-microRNA network module analysis for ovarian cancer Shuqin Zhang School of Mathematical Sciences Fudan University Oct. 4, 2016 Outline Introduction Materials and Methods Results Conclusions Introduction
More informationSupplementary Figure 1: Experimental design. DISCOVERY PHASE VALIDATION PHASE (N = 88) (N = 20) Healthy = 20. Healthy = 6. Endometriosis = 33
DISCOVERY PHASE (N = 20) Healthy = 6 Endometriosis = 7 EAOC = 7 Quantitative PCR (mirnas = 1113) a Quantitative PCR Verification of Candidate mirnas (N = 24) VALIDATION PHASE (N = 88) Healthy = 20 Endometriosis
More informationmicrorna PCR System (Exiqon), following the manufacturer s instructions. In brief, 10ng of
SUPPLEMENTAL MATERIALS AND METHODS Quantitative RT-PCR Quantitative RT-PCR analysis was performed using the Universal mircury LNA TM microrna PCR System (Exiqon), following the manufacturer s instructions.
More informationExtracellular Vesicle RNA isolation Kits
Extracellular Vesicle RNA isolation Kits Summary Section 4 Introduction 42 Exo-TotalRNA and TumorExo-TotalRNA isolation kits 43 Extracellular Vesicle RNA extraction kits Ordering information Products can
More informationdeveloping new tools for diagnostics Join forces with IMGM Laboratories to make your mirna project a success
micrornas developing new tools for diagnostics Join forces with IMGM Laboratories to make your mirna project a success Dr. Carola Wagner IMGM Laboratories GmbH Martinsried, Germany qpcr 2009 Symposium
More informationGenome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
RESEARCH Open Access Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers Anneleen Decock 1, Maté Ongenaert 1, Jasmien Hoebeeck 1,2, Katleen De Preter
More informationncounter TM Analysis System
ncounter TM Analysis System Molecules That Count TM www.nanostring.com Agenda NanoString Technologies History Introduction to the ncounter Analysis System CodeSet Design and Assay Principals System Performance
More informationIdentification of suitable reference genes for the relative quantification of micrornas in pleural effusion
ONCOLOGY LETTERS 8: 1889-1895, 2014 Identification of suitable reference genes for the relative quantification of micrornas in pleural effusion HYE SUK HAN 1, YEONG NANG JO 2, JIN YONG LEE 3, SONG YI CHOI
More informationSupplementary webappendix
Supplementary webappendix This webappendix formed part of the original submission and has been peer reviewed. We post it as supplied by the authors. Supplement to: Kratz JR, He J, Van Den Eeden SK, et
More informationMicroRNA expression profiling and functional analysis in prostate cancer. Marco Folini s.c. Ricerca Traslazionale DOSL
MicroRNA expression profiling and functional analysis in prostate cancer Marco Folini s.c. Ricerca Traslazionale DOSL What are micrornas? For almost three decades, the alteration of protein-coding genes
More informationTitle: Dysregulated mir-183 Inhibits Migration in Breast Cancer
Author's response to reviews Title: Dysregulated mir-183 Inhibits Migration in Breast Cancer Authors: Aoife J Lowery (aoife.lowery@gmail.com) Nicola Miller (nicola.miller@nuigalway.ie) Roisin M Dwyer (roisin.dwyer@nuigalway.ie)
More informationGenomic explorations have offered us a great deal. Buried Treasure
18 Buried Treasure Noncoding DNA makes up the majority of our genomes, much of it being conserved and transcribed. Though the functions of small regulatory RNA molecules are well known, what about so-called
More informationHALLA KABAT * Outreach Program, mircore, 2929 Plymouth Rd. Ann Arbor, MI 48105, USA LEO TUNKLE *
CERNA SEARCH METHOD IDENTIFIED A MET-ACTIVATED SUBGROUP AMONG EGFR DNA AMPLIFIED LUNG ADENOCARCINOMA PATIENTS HALLA KABAT * Outreach Program, mircore, 2929 Plymouth Rd. Ann Arbor, MI 48105, USA Email:
More informationSimple, rapid, and reliable RNA sequencing
Simple, rapid, and reliable RNA sequencing RNA sequencing applications RNA sequencing provides fundamental insights into how genomes are organized and regulated, giving us valuable information about the
More informationIso-Seq Method Updates and Target Enrichment Without Amplification for SMRT Sequencing
Iso-Seq Method Updates and Target Enrichment Without Amplification for SMRT Sequencing PacBio Americas User Group Meeting Sample Prep Workshop June.27.2017 Tyson Clark, Ph.D. For Research Use Only. Not
More informationARTICLE IN PRESS. Critical Reviews in Oncology/Hematology xxx (2010) xxx xxx
Critical Reviews in Oncology/Hematology xxx (2010) xxx xxx Circulating micrornas: Association with disease and potential use as biomarkers Glen Reid, Michaela B. Kirschner, Nico van Zandwijk Asbestos Diseases
More informationQIAsymphony DSP Circulating DNA Kit
QIAsymphony DSP Circulating DNA Kit February 2017 Performance Characteristics 937556 Sample to Insight Contents Performance Characteristics... 4 Basic performance... 4 Run precision... 6 Equivalent performance
More informationSTAT1 regulates microrna transcription in interferon γ stimulated HeLa cells
CAMDA 2009 October 5, 2009 STAT1 regulates microrna transcription in interferon γ stimulated HeLa cells Guohua Wang 1, Yadong Wang 1, Denan Zhang 1, Mingxiang Teng 1,2, Lang Li 2, and Yunlong Liu 2 Harbin
More informationIdentification of mirna expression profiles for diagnosis and prognosis of prostate cancer
Identification of mirna expression profiles for diagnosis and prognosis of prostate cancer To my grandfather Curt "Cula" Carlsson "Research is to see what everybody else has seen, and to think what nobody
More informationAssaying micrornas in biofluids for detection of drug induced cardiac injury. HESI Annual Meeting State of the Science Session June 8, 2011
Assaying micrornas in biofluids for detection of drug induced cardiac injury HESI Annual Meeting State of the Science Session June 8, 2011 Karol Thompson, PhD Center for Drug Evaluation & Research US Food
More informationNature Methods: doi: /nmeth.3115
Supplementary Figure 1 Analysis of DNA methylation in a cancer cohort based on Infinium 450K data. RnBeads was used to rediscover a clinically distinct subgroup of glioblastoma patients characterized by
More informationCellecta Overview. Started Operations in 2007 Headquarters: Mountain View, CA
Cellecta Overview Started Operations in 2007 Headquarters: Mountain View, CA Focus: Development of flexible, scalable, and broadly parallel genetic screening assays to expedite the discovery and characterization
More informationRNA-Seq profiling of circular RNAs in human colorectal Cancer liver metastasis and the potential biomarkers
Xu et al. Molecular Cancer (2019) 18:8 https://doi.org/10.1186/s12943-018-0932-8 LETTER TO THE EDITOR RNA-Seq profiling of circular RNAs in human colorectal Cancer liver metastasis and the potential biomarkers
More informationMicro-RNA web tools. Introduction. UBio Training Courses. mirnas, target prediction, biology. Gonzalo
Micro-RNA web tools UBio Training Courses Gonzalo Gómez//ggomez@cnio.es Introduction mirnas, target prediction, biology Experimental data Network Filtering Pathway interpretation mirs-pathways network
More informationCirculating Cell-Free DNA Pre-analytics: Importance of ccfdna Stabilization and Extraction for Liquid Biopsy Applications
Circulating Cell-Free DNA Pre-analytics: Importance of ccfdna Stabilization and Extraction for Liquid Biopsy Applications Martin Schlumpberger, Ass.Director R&D, QIAGEN GmbH IQNpath 2017 - Circulating
More informationSupplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63.
Supplementary Figure Legends Supplementary Figure S1. Gene expression analysis of epidermal marker genes and TP63. A. Screenshot of the UCSC genome browser from normalized RNAPII and RNA-seq ChIP-seq data
More informationMature microrna identification via the use of a Naive Bayes classifier
Mature microrna identification via the use of a Naive Bayes classifier Master Thesis Gkirtzou Katerina Computer Science Department University of Crete 13/03/2009 Gkirtzou K. (CSD UOC) Mature microrna identification
More informationDetection of copy number variations in PCR-enriched targeted sequencing data
Detection of copy number variations in PCR-enriched targeted sequencing data German Demidov Parseq Lab, Saint-Petersburg University of Russian Academy of Sciences, current: Center for Genomic Regulation
More informationExpert-guided Visual Exploration (EVE) for patient stratification. Hamid Bolouri, Lue-Ping Zhao, Eric C. Holland
Expert-guided Visual Exploration (EVE) for patient stratification Hamid Bolouri, Lue-Ping Zhao, Eric C. Holland Oncoscape.sttrcancer.org Paul Lisa Ken Jenny Desert Eric The challenge Given - patient clinical
More informationSUPPLEMENTARY FIGURES AND TABLES
SUPPLEMENTARY FIGURES AND TABLES Supplementary Figure S1: CaSR expression in neuroblastoma models. A. Proteins were isolated from three neuroblastoma cell lines and from the liver metastasis of a MYCN-non
More informationDroplet Digital PCR, the new tool in HIV reservoir quantification? Ward De Spiegelaere
Droplet Digital PCR, the new tool in HIV reservoir quantification? Ward De Spiegelaere Droplet Digital PCR, the new tool in HIV reservoir quantification? Content: - Digital PCR - Applications - Total HIV
More informationSALSA MLPA probemix P315-B1 EGFR
SALSA MLPA probemix P315-B1 EGFR Lot B1-0215 and B1-0112. As compared to the previous A1 version (lot 0208), two mutation-specific probes for the EGFR mutations L858R and T709M as well as one additional
More informationSet the stage: Genomics technology. Jos Kleinjans Dept of Toxicogenomics Maastricht University, the Netherlands
Set the stage: Genomics technology Jos Kleinjans Dept of Toxicogenomics Maastricht University, the Netherlands Amendment to the latest consolidated version of the REACH legislation REACH Regulation 1907/2006:
More informationThe Role of micrornas in Pain. Phd Work of: Rehman Qureshi Advisor: Ahmet Sacan
The Role of micrornas in Pain Phd Work of: Rehman Qureshi Advisor: Ahmet Sacan 1 Motivation for molecular analysis of Pain Chronic pain one of the most common causes for seeking medical treatment Approximate
More informationmirna Whole Transcriptome Assay
mirna Whole Transcriptome Assay HTG EdgeSeq mirna Whole Transciptome Assay The HTG EdgeSeq mirna Whole Transcriptome Assay (WTA) is a next generation sequencing (NGS) application that measures the expression
More informationSoft Agar Assay. For each cell pool, 100,000 cells were resuspended in 0.35% (w/v)
SUPPLEMENTARY MATERIAL AND METHODS Soft Agar Assay. For each cell pool, 100,000 cells were resuspended in 0.35% (w/v) top agar (LONZA, SeaKem LE Agarose cat.5004) and plated onto 0.5% (w/v) basal agar.
More informationPaternal exposure and effects on microrna and mrna expression in developing embryo. Department of Chemical and Radiation Nur Duale
Paternal exposure and effects on microrna and mrna expression in developing embryo Department of Chemical and Radiation Nur Duale Our research question Can paternal preconceptional exposure to environmental
More informationHigh AU content: a signature of upregulated mirna in cardiac diseases
https://helda.helsinki.fi High AU content: a signature of upregulated mirna in cardiac diseases Gupta, Richa 2010-09-20 Gupta, R, Soni, N, Patnaik, P, Sood, I, Singh, R, Rawal, K & Rani, V 2010, ' High
More informationIPA Advanced Training Course
IPA Advanced Training Course October 2013 Academia sinica Gene (Kuan Wen Chen) IPA Certified Analyst Agenda I. Data Upload and How to Run a Core Analysis II. Functional Interpretation in IPA Hands-on Exercises
More informationCircular RNAs (circrnas) act a stable mirna sponges
Circular RNAs (circrnas) act a stable mirna sponges cernas compete for mirnas Ancestal mrna (+3 UTR) Pseudogene RNA (+3 UTR homolgy region) The model holds true for all RNAs that share a mirna binding
More informationBCL2 inhibition by ABT-199 in T-cell acute lymphoblastic leukemia (T-ALL)
BCL2 inhibition by ABT-199 in T-cell acute lymphoblastic leukemia (T-ALL) Pieter Van Vlierberghe Bioluminescent Cell-based Assay Seminar Day Monday 31 march 2014 UCL De Duve institute Brussels, Belgium
More informationResearch Article Malignancy Associated MicroRNA Expression Changes in Canine Mammary Cancer of Different Malignancies
ISRN Veterinary Science, Article ID 148597, 5 pages http://dx.doi.org/10.1155/2014/148597 Research Article Malignancy Associated MicroRNA Expression Changes in Canine Mammary Cancer of Different Malignancies
More informationEXOSOMES & MICROVESICLES
The Sample Preparation Experts EXOSOMES & MICROVESICLES The New Standard in Exosome Purification and RNA Isolation Best-in-Class, Pure & Simple Exosome Purification, Fractionation of Exosomal Free & Circulating
More informationSupplementary Figure 1 IMQ-Induced Mouse Model of Psoriasis. IMQ cream was
Supplementary Figure 1 IMQ-Induced Mouse Model of Psoriasis. IMQ cream was painted on the shaved back skin of CBL/J and BALB/c mice for consecutive days. (a, b) Phenotypic presentation of mouse back skin
More informationA complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis
APPLICATION NOTE Cell-Free DNA Isolation Kit A complete next-generation sequencing workfl ow for circulating cell-free DNA isolation and analysis Abstract Circulating cell-free DNA (cfdna) has been shown
More informationA two-microrna signature in urinary exosomes for diagnosis of prostate cancer
Poster # B4 A two-microrna signature in urinary exosomes for diagnosis of prostate cancer Anne Karin Ildor Rasmussen 1, Peter Mouritzen 1, Karina Dalsgaard Sørensen 3, Thorarinn Blondal 1, Jörg Krummheuer
More informationRECENT ADVANCES IN THE MOLECULAR DIAGNOSIS OF BREAST CANCER
Technology Transfer in Diagnostic Pathology. 6th Central European Regional Meeting. Cytopathology. Balatonfüred, Hungary, April 7-9, 2011. RECENT ADVANCES IN THE MOLECULAR DIAGNOSIS OF BREAST CANCER Philippe
More informationChapter 1. Introduction
Chapter 1 Introduction 1.1 Motivation and Goals The increasing availability and decreasing cost of high-throughput (HT) technologies coupled with the availability of computational tools and data form a
More informationmicrorna-200b and microrna-200c promote colorectal cancer cell proliferation via
Supplementary Materials microrna-200b and microrna-200c promote colorectal cancer cell proliferation via targeting the reversion-inducing cysteine-rich protein with Kazal motifs Supplementary Table 1.
More informationGENE EXPRESSION AND microrna PROFILING IN LYMPHOMAS. AN INTEGRATIVE GENOMICS ANALYSIS
GENE EXPRESSION AND microrna PROFILING IN LYMPHOMAS. AN INTEGRATIVE GENOMICS ANALYSIS Dra. Margarita Sánchez-Beato Lymphoma Group Molecular Pathology Programme CNIO Agilent Microarray and Sequencing Roadshow,
More informationMicroRNA and Male Infertility: A Potential for Diagnosis
Review Article MicroRNA and Male Infertility: A Potential for Diagnosis * Abstract MicroRNAs (mirnas) are small non-coding single stranded RNA molecules that are physiologically produced in eukaryotic
More informationEXPression ANalyzer and DisplayER
EXPression ANalyzer and DisplayER Tom Hait Aviv Steiner Igor Ulitsky Chaim Linhart Amos Tanay Seagull Shavit Rani Elkon Adi Maron-Katz Dorit Sagir Eyal David Roded Sharan Israel Steinfeld Yossi Shiloh
More informationInferring Biological Meaning from Cap Analysis Gene Expression Data
Inferring Biological Meaning from Cap Analysis Gene Expression Data HRYSOULA PAPADAKIS 1. Introduction This project is inspired by the recent development of the Cap analysis gene expression (CAGE) method,
More informationPackage TargetScoreData
Title TargetScoreData Version 1.14.0 Author Yue Li Package TargetScoreData Maintainer Yue Li April 12, 2018 Precompiled and processed mirna-overexpression fold-changes from 84 Gene
More informationAnalysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers Gordon Blackshields Senior Bioinformatician Source BioScience 1 To Cancer Genetics Studies
More informationMRC-Holland MLPA. Description version 13;
SALSA MLPA probemix P027-C1 Uveal Melanoma Lot C1-0211: A large number of probes have been replaced by other probes in the same chromosomal regions as compared to previous lots, and several reference probes
More informationScreening for novel oncology biomarker panels using both DNA and protein microarrays. John Anson, PhD VP Biomarker Discovery
Screening for novel oncology biomarker panels using both DNA and protein microarrays John Anson, PhD VP Biomarker Discovery Outline of presentation Introduction to OGT and our approach to biomarker studies
More informationInferring condition-specific mirna activity from matched mirna and mrna expression data
Inferring condition-specific mirna activity from matched mirna and mrna expression data Junpeng Zhang 1, Thuc Duy Le 2, Lin Liu 2, Bing Liu 3, Jianfeng He 4, Gregory J Goodall 5 and Jiuyong Li 2,* 1 Faculty
More informationAirway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer
Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer Avrum Spira, Jennifer E Beane, Vishal Shah, Katrina Steiling, Gang Liu, Frank Schembri, Sean Gilman, Yves-Martine
More informationMPS for translocations
MPS for translocations Filip Van Nieuwerburgh, Ph.D. Lab of Pharmaceutical Biotechnology NXTGNT massively parallel sequencing facility, Ghent University In collaboration with: Center for Medical Genetics,
More informationBenchmark study: Exiqon mircury LNA microrna arrays vs. Supplier A s DNA based capture probes. Includes comparison of:
Benchmark study: Exiqon mircury LNA microrna arrays vs. Supplier A s DNA based capture probes Includes comparison of: I. II. III. Signal levels Relative quantification False differences For complete experimental
More informationT H E J O U R N A L O F C E L L B I O L O G Y
Supplemental material Díaz et al., http://www.jcb.org/cgi/content/full/jcb.201209151/dc1 T H E J O U R N A L O F C E L L B I O L O G Y Figure S1. Hypoxia induces invadopodia formation in different epithelial
More informationMRC-Holland MLPA. Description version 29; 31 July 2015
SALSA MLPA probemix P081-C1/P082-C1 NF1 P081 Lot C1-0114. As compared to the previous B2 version (lot 0813 and 0912), 11 target probes are replaced or added, and 10 new reference probes are included. P082
More informationThe 16th KJC Bioinformatics Symposium Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis
The 16th KJC Bioinformatics Symposium Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis Tieliu Shi tlshi@bio.ecnu.edu.cn The Center for bioinformatics
More information7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans.
Supplementary Figure 1 7SK ChIRP-seq is specifically RNA dependent and conserved between mice and humans. Regions targeted by the Even and Odd ChIRP probes mapped to a secondary structure model 56 of the
More informationMicroRNAs Modulate the Noncanonical NF- B Pathway by Regulating IKK Expression During Macrophage Differentiation
MicroRNAs Modulate the Noncanonical NF- B Pathway by Regulating IKK Expression During Macrophage Differentiation Tao Li 1 *, Michael J. Morgan 1 *, Swati Choksi 1, Yan Zhang 1, You-Sun Kim 2#, Zheng-gang
More informationFAQs for UK Pathology Departments
FAQs for UK Pathology Departments This is an educational piece written for Healthcare Professionals FAQs for UK Pathology Departments If you would like to discuss any of the listed FAQs further, or have
More informationIdentification of Suitable Reference Genes for qpcr Analysis of Serum microrna in Gastric Cancer Patients
DOI 10.1007/s10620-011-1981-7 ORIGINAL ARTICLE Identification of Suitable Reference Genes for qpcr Analysis of Serum microrna in Gastric Cancer Patients Jianning Song Zhigang Bai Wei Han Jun Zhang Hua
More informationSupplementary. properties of. network types. randomly sampled. subsets (75%
Supplementary Information Gene co-expression network analysis reveals common system-level prognostic genes across cancer types properties of Supplementary Figure 1 The robustness and overlap of prognostic
More informationMRC-Holland MLPA. Description version 08; 18 November 2016
SALSA MLPA probemix P122-D1 NF1 AREA Lot D1-1016. As compared to lot C2-0312, four probes in the NF1 area and one reference probe have been removed, four reference probes have been replaced and several
More informationCOMPARISON OF HIV DRUG-RESISTANT MUTANT DETECTION BY NGS WITH AND WITHOUT UNIQUE MOLECULAR IDENTIFIERS (UMI)
COMPARISON OF HIV DRUG-RESISTANT MUTANT DETECTION BY NGS WITH AND WITHOUT UNIQUE MOLECULAR IDENTIFIERS (UMI) Kevin D McCormick; Kerri J Penrose; Rahil Sethi; Jacob Waldman; William Schwarzmann; Uma Chandran;
More informationSALSA MLPA Probemix P014-B1 Chromosome 8 Lot B and B
SALSA MLPA Probemix P014-B1 Chromosome 8 Lot B1-0916 and B1-0713. Copy number changes of the human chromosome 8 are common in many types of tumours. In most cases, losses of 8p sequences and gains of 8q
More informationSALSA MLPA probemix P241-D2 MODY mix 1 Lot D As compared to version D1 (lot D1-0911), one reference probe has been replaced.
mix P241-D2 MODY mix 1 Lot D2-0413. As compared to version D1 (lot D1-0911), one reference has been replaced. Maturity-Onset Diabetes of the Young (MODY) is a distinct form of non insulin-dependent diabetes
More informationMRC-Holland MLPA. Description version 08; 30 March 2015
SALSA MLPA probemix P351-C1 / P352-D1 PKD1-PKD2 P351-C1 lot C1-0914: as compared to the previous version B2 lot B2-0511 one target probe has been removed and three reference probes have been replaced.
More informationMRC-Holland MLPA. Description version 06; 07 August 2015
SALSA MLPA probemix P323-B1 CDK4-HMGA2-MDM2 Lot B1-0711. As compared to version A1 (test version sent to test labs), this product has been completely redesigned. Probes for HMGA2 and several other genes
More informationSupplementary Figure S1. Venn diagram analysis of mrna microarray data and mirna target analysis. (a) Western blot analysis of T lymphoblasts (CLS)
Supplementary Figure S1. Venn diagram analysis of mrna microarray data and mirna target analysis. (a) Western blot analysis of T lymphoblasts (CLS) and their exosomes (EXO) in resting (REST) and activated
More informationSupplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells.
SUPPLEMENTAL FIGURE AND TABLE LEGENDS Supplemental Figure S1. Expression of Cirbp mrna in mouse tissues and NIH3T3 cells. A) Cirbp mrna expression levels in various mouse tissues collected around the clock
More informationSALSA MLPA probemix P175-A3 Tumour Gain Lot A3-0714: As compared to the previous version A2 (lot A2-0411), nine probes have a small change in length.
SALSA MLPA probemix P175-A3 Tumour Gain Lot A3-0714: As compared to the previous version A2 (lot A2-0411), nine probes have a small change in length. This SALSA probemix is for basic research only! This
More informationAbout OMICS Group Conferences
About OMICS Group OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the year 2007 with the sole aim of
More informationiplex genotyping IDH1 and IDH2 assays utilized the following primer sets (forward and reverse primers along with extension primers).
Supplementary Materials Supplementary Methods iplex genotyping IDH1 and IDH2 assays utilized the following primer sets (forward and reverse primers along with extension primers). IDH1 R132H and R132L Forward:
More informationCirculating MicroRNAs as Biomarkers of Colorectal Cancer: Results From a Genome-Wide Profiling and Validation Study
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY 2013;11:681 688 Circulating MicroRNAs as Biomarkers of Colorectal Cancer: Results From a Genome-Wide Profiling and Validation Study MARÍA DOLORES GIRÁLDEZ,* JUAN
More informationSALSA MLPA probemix P185-C2 Intersex Lot C2-1015: As compared to the previous version C1 (lot C1-0611), the lengths of four probes have been adjusted.
mix P185-C2 Intersex Lot C2-1015: As compared to the previous version C1 (lot C1-0611), the lengths of four s have been adjusted. The sex-determining region on chromosome Y (SRY) is the most important
More informationNature Neuroscience: doi: /nn Supplementary Figure 1
Supplementary Figure 1 Illustration of the working of network-based SVM to confidently predict a new (and now confirmed) ASD gene. Gene CTNND2 s brain network neighborhood that enabled its prediction by
More informationSupplemental figures
Supplemental figures Supplemental Figure 1. Impact of immunogenic-llc tumors (LLC-OVA) on peripheral OVA-specific CD8 T cells. Tetramer analysis showing percent OVA-specific CD8 T cells in peripheral blood
More informationPhosphate buffered saline (PBS) for washing the cells TE buffer (nuclease-free) ph 7.5 for use with the PrimePCR Reverse Transcription Control Assay
Catalog # Description 172-5080 SingleShot Cell Lysis Kit, 100 x 50 µl reactions 172-5081 SingleShot Cell Lysis Kit, 500 x 50 µl reactions For research purposes only. Introduction The SingleShot Cell Lysis
More informationA Strategy for Identifying Putative Causes of Gene Expression Variation in Human Cancer
A Strategy for Identifying Putative Causes of Gene Expression Variation in Human Cancer Hautaniemi, Sampsa; Ringnér, Markus; Kauraniemi, Päivikki; Kallioniemi, Anne; Edgren, Henrik; Yli-Harja, Olli; Astola,
More informationSUPPLEMENTAY FIGURES AND TABLES
SUPPLEMENTAY FIGURES AND TABLES Supplementary Figure S1: Validation of mir expression by quantitative real-time PCR and time course studies on mir- 29a-3p and mir-210-3p. A. The graphs illustrate the expression
More informationComparison of open chromatin regions between dentate granule cells and other tissues and neural cell types.
Supplementary Figure 1 Comparison of open chromatin regions between dentate granule cells and other tissues and neural cell types. (a) Pearson correlation heatmap among open chromatin profiles of different
More informationSupplementary Material
Supplementary Material Identification of mir-187 and mir-182 as biomarkers for early diagnosis and prognosis in prostate cancer patients treated with radical prostatectomy Irene Casanova-Salas 1, José
More informationPatnaik SK, et al. MicroRNAs to accurately histotype NSCLC biopsies
Patnaik SK, et al. MicroRNAs to accurately histotype NSCLC biopsies. 2014. Supplemental Digital Content 1. Appendix 1. External data-sets used for associating microrna expression with lung squamous cell
More informationProducts for cfdna and mirna isolation. Subhead Circulating Cover nucleic acids from plasma
MACHEREY-NAGEL Products for cfdna and mirna isolation Bioanalysis Subhead Circulating Cover nucleic acids from plasma n Flexible solutions for small and large blood plasma volumes n Highly efficient recovery
More informationBioimaging and Functional Genomics
Bioimaging and Functional Genomics Elisa Ficarra, EPF Lausanne Giovanni De Micheli, EPF Lausanne Sungroh Yoon, Stanford University Luca Benini, University of Bologna Enrico Macii,, Politecnico di Torino
More informationMRC-Holland MLPA. Description version 29;
SALSA MLPA KIT P003-B1 MLH1/MSH2 Lot 1209, 0109. As compared to the previous lots 0307 and 1006, one MLH1 probe (exon 19) and four MSH2 probes have been replaced. In addition, one extra MSH2 exon 1 probe,
More informationP323-B1 CDK4-HMGA2-MDM2
SALSA MLPA probemix P323-B1 CDK4-HMGA2-MDM2 Lot B1-0714, B1-0711. As compared to previous test version (lot A1-0508), this probemix has been completely redesigned. Probes for HMGA2 and several other genes
More information