WO2014134728A1 - Procédés et gènes pour la normalisation de l'expression génétique - Google Patents

Procédés et gènes pour la normalisation de l'expression génétique Download PDF

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Publication number
WO2014134728A1
WO2014134728A1 PCT/CA2014/050174 CA2014050174W WO2014134728A1 WO 2014134728 A1 WO2014134728 A1 WO 2014134728A1 CA 2014050174 W CA2014050174 W CA 2014050174W WO 2014134728 A1 WO2014134728 A1 WO 2014134728A1
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WO
WIPO (PCT)
Prior art keywords
samples
expression
gene
genes
rna
Prior art date
Application number
PCT/CA2014/050174
Other languages
English (en)
Inventor
Guy Sauvageau
Tara MACRAE
Tobias SARGEANT
Original Assignee
Université de Montréal
The Walter And Eliza Hall Institute Of Medical Research
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Université de Montréal, The Walter And Eliza Hall Institute Of Medical Research filed Critical Université de Montréal
Publication of WO2014134728A1 publication Critical patent/WO2014134728A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • Hybridization or “nucleic acid hybridization” or “hybridization” refers generally to the hybridization of two single stranded nucleic acid molecules having complementary base sequences, which under appropriate conditions will form a thermodynamically favored double stranded structure.
  • hybridizes as used herein may relate to hybridizations under stringent or non-stringent conditions. The setting of conditions is well within the skill of the artisan and can be determined according to protocols described in the art.
  • the expression of the one or more control genes and/or test gene is measured at the protein levels.
  • methods to measure the amount/level of a protein in a sample include, but are not limited to: Western blot, immunoblot, enzyme-linked immunosorbent assay (ELISA), "sandwich” immunoassays, radioimmunoassay (RIA), immunoprecipitation, surface plasmon resonance (SPR), chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemical (IHC) analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, microcytometry, microarray, antibody array, microscopy (e.g., electron microscopy), flow cytometry, and proteomic-based assays.
  • the above method further comprises the following step b1 ): performing an amplification reaction on said control gene cDNA and test gene cDNA prior to said contacting.
  • Example 1 Materials and methods
  • Isoform 3 does not possess phosphatase activity adenosine deaminase, RNA-specific; Converts multiple adenosines to inosines and creates l/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. Has been found to modify more frequently adenosines in AU-rich regions, probably due to the relative ease
  • anaphase promoting complex subunit 5 Component of the anaphase promoting complex cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1
  • This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senesce Colour
  • OCIAD1 OCIA domain containing 1
  • HBV hepatitis B virus
  • VPS4A III components to the cytoplasm for further rounds of MVB sorting.
  • MVBs contain intraluminal vesicles
  • YME1-like 1 (S. cerevisiae); Putative ATP-dependent protease which plays a role in mitochondrial
  • Table 8 functional classification of the entire list of 119 genes identified from the Leucegene data set, as assessed using the DAVID algorithm

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • Analytical Chemistry (AREA)
  • Pathology (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Oncology (AREA)
  • Microbiology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne de nouveaux gènes présentant une variation minimale de leur niveau d'expression dans plusieurs échantillons et pouvant être utilisés comme gènes domestiques pour la normalisation de l'expression génétique dans les mesures quantitatives de l'expression génétique. L'invention concerne un nouveau procédé permettant l'identification de gènes domestiques à l'aide de la méthode de séquençage RNA-seq (whole Transcriptome Shotgun Sequencing).
PCT/CA2014/050174 2013-03-07 2014-03-06 Procédés et gènes pour la normalisation de l'expression génétique WO2014134728A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361774271P 2013-03-07 2013-03-07
US61/774,271 2013-03-07

Publications (1)

Publication Number Publication Date
WO2014134728A1 true WO2014134728A1 (fr) 2014-09-12

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/CA2014/050174 WO2014134728A1 (fr) 2013-03-07 2014-03-06 Procédés et gènes pour la normalisation de l'expression génétique

Country Status (1)

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WO (1) WO2014134728A1 (fr)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020033585A1 (fr) * 2018-08-07 2020-02-13 The Broad Institute, Inc. Procédés de criblage combinatoire et utilisation de cibles thérapeutiques associées
CN112041933A (zh) * 2018-03-14 2020-12-04 皇家飞利浦有限公司 使用局部独特特征来解释rna测序数据的转录本表达水平的系统和方法
CN114574582A (zh) * 2022-03-21 2022-06-03 暨南大学 一种转录组学标准品及其制备方法

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010065940A1 (fr) * 2008-12-04 2010-06-10 The Regents Of The University Of California Matériels et méthodes de diagnostic et de pronostic d'un cancer de la prostate
EP2405022A2 (fr) * 2008-07-08 2012-01-11 Genomic Health, Inc. Profilage de l'expression génétique pour prédire la capacité de survie de sujets atteints de cancer de la prostate

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2405022A2 (fr) * 2008-07-08 2012-01-11 Genomic Health, Inc. Profilage de l'expression génétique pour prédire la capacité de survie de sujets atteints de cancer de la prostate
WO2010065940A1 (fr) * 2008-12-04 2010-06-10 The Regents Of The University Of California Matériels et méthodes de diagnostic et de pronostic d'un cancer de la prostate

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
ENQUOBAHRIE, D. ET AL.: "Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study.", BMC PREGNANCY AND CHILDBIRTH., vol. 9, no. 56, 10 December 2009 (2009-12-10) *
HELLEMANS, J. ET AL.: "qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data.", GENOME BIOLOGY., vol. 8, no. R19, 9 February 2007 (2007-02-09) *
MACRAE, T. ET AL.: "RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells.", PLOS ONE., vol. 8, no. 9, 17 September 2013 (2013-09-17), pages E72884 *
WANG, Z. ET AL.: "RNA-Seq: a revolutionary tool for transcriptomics.", NATURE REVIEWS, GENETICS., vol. 10, no. 1, 1 January 2009 (2009-01-01), pages 57 - 63, XP055152757, DOI: doi:10.1038/nrg2484 *

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN112041933A (zh) * 2018-03-14 2020-12-04 皇家飞利浦有限公司 使用局部独特特征来解释rna测序数据的转录本表达水平的系统和方法
WO2020033585A1 (fr) * 2018-08-07 2020-02-13 The Broad Institute, Inc. Procédés de criblage combinatoire et utilisation de cibles thérapeutiques associées
CN114574582A (zh) * 2022-03-21 2022-06-03 暨南大学 一种转录组学标准品及其制备方法

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