WO2014042497A1 - Probes and primers for detecting the bcr-abl gene in a duplex reaction - Google Patents

Probes and primers for detecting the bcr-abl gene in a duplex reaction Download PDF

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WO2014042497A1
WO2014042497A1 PCT/MA2013/000005 MA2013000005W WO2014042497A1 WO 2014042497 A1 WO2014042497 A1 WO 2014042497A1 MA 2013000005 W MA2013000005 W MA 2013000005W WO 2014042497 A1 WO2014042497 A1 WO 2014042497A1
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bcr
abl
seq
gene
primers
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El Hassan SEFRIOUI
Manale EL AMRANI
Denise KOTTWITZ
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Mascir (Moroccan Foundation For Advanced Science, Research And Innovation)
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    • C—CHEMISTRY; METALLURGY
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    • 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
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Definitions

  • the present invention concerned !! the use of new probes, primers, primer sets, probe sets and qf CR primers for the detection and quantification of BCR-ABL translocation and a simplex or multiplexed control gene.
  • the qPCR of the present invention will allow the detection of chronic myeloid leukemia (CML), treatment monitoring as well as residual disease.
  • CML chronic myeloid leukemia
  • Chronic myelogenous leukemia is a disease characterized by the presence of the Philadelphia chromosome which is chromosome 22 shortened on its long arm by a translocation t (9, 22) (q34). This exchange between the long arms of chromosomes 9 and 22 is constantly present in the cells of patients with CML and results in a fusion gene termed functional BCR BL which will be transcribed into chimeric mRNA (Shtivelman, 1985. Nature 1985; 315: 550-4) which is translated into fusion proteins bcr-abl, responsible for CML.
  • CML chronic myelogenous leukemia
  • BCR-ABL translocation (t (9, 22) (q34; qll)) is present in 90-95% of patients with CML and 20-25% in patients with acute lymphoid leukemia (ALL) (Prist, 1980; Blood 56). : 15-22).
  • ALL acute lymphoid leukemia
  • M-bcr 'major breakpoint cluster region'
  • the fundamental criterion for the diagnosis of CML or LLA is the presence of BCR-ABL fusion gene, which can be demonstrated by current cytogenetic methods such as karyotype, FISH (Flilorescent in situ hybridization) or hematological examinations. .
  • FISH Fluorescent in situ hybridization
  • hematological examinations are mostly lacking in quantitative and qualitative tests, they are less specific, use complex hybridizations or isotopes, take a lot of time (more days), may be invasive (bone marrow use), or more expensive.
  • these cytogenetic methods can detect only one LMC u 500 cell. cells and therefore can not be used in the case of the treatment follow-up of the MC or in the case of the residual disease which requires a high sensitivity (detection of a CML cell on 100000 cells).
  • qPCR real-time quantitative PCR
  • the qPCR uses in parallel a housekeeping gene gene expressed ubiquitously in all the cells of the body and which will facilitate the normalization and quantification of the targeted gene.
  • a housekeeping gene gene expressed ubiquitously in all the cells of the body and which will facilitate the normalization and quantification of the targeted gene.
  • several control genes have been tested, such as GAPDH, beta-actin, microglobilin, G6PDH
  • the primers for detecting the BCR-ABL transcript in a sample test have oligonucleotide sequences selected from a group of: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO : 3, and SEQ ID NO: 4, b) the primers for detecting the ABL1 control gene in a sample test have oligonucleotide sequences selected from a group of: SEQ ID NO: 5, SEQ ID NO:
  • the probe for detecting BCR-ABL in a sample test has a sequence: SEQ ID: 9.
  • the probe for detecting ABL1 in a sample test has a sequence SEQ ID: 10.
  • a forward primer having a sequence from the group:
  • SEQ ID NO: 5 SEQ ID NO: 6
  • a reverse primer having a sequence selected from
  • the amplification reaction may be at least one PCR, qPCR or PCR.
  • At least one probe contains a fluorescent unit (reporter) attached to the 5 'region of DNA.
  • at least one probe may contain a quenched portion ⁇ r
  • the amplification of BCR-ABL and ABL1 by the qPCR of the present invention can be carried out in a simplex or multiplexed reaction.
  • Figure la Delta Rn-versus-cycle threshold (Ct) graph for BCR-ABL in simplex format.
  • Figure 1b Standard curve Cycle threshold (Ct) -versus-log cDNA quantity for BCR-ABL in simplex format.
  • Ct Standard curve Cycle threshold
  • Figure 2 Standard curve Cylle threshold (Ct) -versus-log cDNA amount for BCR-ABL in simplex format.
  • Figure 3b Standard Curve C cle threshold (Ct) -versus-log cDNA amount for BCR-ABL in multiplexed format.
  • Figure 4a Standard Curve 'Éycle threshold (Ct) -versus-log quantity cDNA for ABL in simplex and multiplexed format!
  • the present invention relates to probes, primers, primer set, set of probes and primers that can be util ⁇ easy to amplify, detect and quantify the BCR-ABL gene or gene control ABL1 in ur3 ⁇ 4échantillon test.
  • the amplification of BCR-ABL and the ABL1 control gene is at least in qPCR format! simplex or multiplex thus allowing a better quantification of BCR-ABL and uj gain in time and cost
  • the more sensitive and more specific quantification of BCR-ABL will permeate better monitoring of the treatment of CML as well as the residual disease.
  • the word 'BCR-ABL' or t (9,22) already in the present invention is a translocation between the ABL1 gene of chromosome 9 and the breakpoint cluster region (BCR) on chromosome 22.
  • Detection and quantification of BCR-ABL can support clinical diagnosis of CML, monitoring of its treatment and monitoring of residual disease.
  • the word 'gene' refers to a nucleic acid sequence in the DNA molecule that occupies a specific region in a chromosome and allows coding of the instructions for RNA synthesis.
  • the word gene amplification as used in this invention refers to one or more methods capable of copying a nucleic acid thereby allowing an increase in the number of copies of a target nucleic acid sequence.
  • the amplified sequence may be a deoxyribonucleotide acid (DNA) or a ribonucleotide acid (RNA).
  • the word 'primer' oligonucleotide sequence that can be synthesized chemically or the primer is the point of initiation of DNA synthesis under optimal temperature conditions and in the presence of specific complementary buffers, enzyme, nucleotides and nucleotide sequences.
  • the word 'probe' represents a nucleotide sequence which forms a hybrid structure with a target sequence in a riflecule of a test sample.
  • invention refers to a method from an RNA molecule.
  • 'RT-PCR' reverse trypscriptase-PCR
  • Ct Chip Threshold
  • the TaqMan and molecular beacons which use the fluorogenic jexonuclease activity of the Taq polymerase enzyme to measure the amount of the DNA sequence in a test sample.
  • the probe reporter can be FAM, JOE, YAKYE (YY) and BBQ quencher, BHQ1, or TAMRA.
  • control gene as used in "housekeeping gene” represents a gene generally expressed in such a hair-like manner by all the cells of an organism.
  • control genes are glycera dehyd-3-phosphate dehydrogenase (GAPDH), albumin, beta-actin, and ABL1.
  • qPCR in simplex reflects the detection of copy number of a single gene in a reaction tube.
  • the multiplex word of the present invention refers to an assay that occurs simultaneously with at least one other test.
  • the multiplexed qPCR reflects the detection of the copy number of at least 2 genes in the same reaction tube.
  • the 2 BCR-ABL jet ABL1 genes are simultaneously detected by qPCR.
  • the qPCR of the present invention makes it possible to determine the number of copies of the BCR gene.
  • ABL in human cellsI quantifying the number of copies of
  • BCR-ABL relating to a control gene
  • the control gene here is ABL1.
  • Example 1 describes a protocol used in the qPCR assay of the present invention.
  • the protocol describes the step of extra RNA, cDNA synthesis and qPCR.
  • Example 2 shows the performance of the qPCR of the present invention for detecting the BCR-ABL gene in the human K562 leukemic line (LMC), in the blood of a LMC patient as well as in the blood of an individual. control.
  • LMC human K562 leukemic line
  • the performance of the qPCR of the present invention is according to international IVD standards (R2> 0.95, slope between -3.0 and 3.9 and efficiency close to 100) with standard curves (amount of K562 cDNA). vs-values Ct) at 100.02 and 100.44 efficiency and a R2 of 0.993 and 0.99 i, 8! respectively for Figure lb and Figure 2.
  • the cycle amplification cycle-vs-Deltaj ⁇ in ( Figure la) also shows a perfect pace.
  • Example 3 shows that the qPCR of the present invention in simplex or multiplexed format allows the simultaneous or simultaneous detection of BCR-ABL and ABL1 with high accuracy.
  • Example 1 qPCR Protocol of the present invention for the detection of
  • the mastermix of the qPCR reaction contains the primers and the BCR-ABL probe and the primers and the ABL1 probe, 5u ADDc and the whole is added to the Mastermix (TaqMan Fast Universal Master PCR mix: App:
  • step 1 at 95 ° C. for 20 seconds
  • step 2 cycle 5, cj
  • step 3 at 60 ° C for 30 seconds.
  • Reverse primer 5 'accctgaggctcaaa gg tcag 3' (SEQ ID IM ° 4)
  • SEQ ID NO: 4 R-BCR-ABL
  • SEQ ID NO: 7 R-ABL1
  • SEQ ID NO: 8 R-ABL1

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Abstract

The present invention concerns the use of new probes, primers, primer sets, and probe and primer sets in qPCR for detecting and quantifying the BCR-ABL translocation and a control gene in a single or multiplex reaction. By quantifying the BCR-ABL gene and the control gene, the qPCR of the present invention makes it possible to detect chronic myelogenous leukemia (CML), and to monitor the treatment and the residual disease.

Description

DOMAINE TECHNIQUE  TECHNICAL AREA
La présente invention concerné!! l'utilisation de nouvelles sondes, amorces, sets d'amorces, sets de sondes et amorces en qf CR pour la détection et la quantification de la translocation BCR-ABL et un gène contrôle enfréaction simplexe ou multiplexe.  The present invention concerned !! the use of new probes, primers, primer sets, probe sets and qf CR primers for the detection and quantification of BCR-ABL translocation and a simplex or multiplexed control gene.
En quantifiant le gène BCR-A$L et le gène contrôle, la qPCR de la présente invention permettra la détection de la leujçémie chronique myéloïde (LMC), le suivi du traitement ainsi que de la maladie résiduelle.  By quantifying the BCR-A $ L gene and the control gene, the qPCR of the present invention will allow the detection of chronic myeloid leukemia (CML), treatment monitoring as well as residual disease.
ETAT DE LA TECHNIQUE ANTERIEURE STATE OF THE PRIOR ART
La leucémie myéloïde chronique (LMC) est une maladie caractérisée par la présence du chromosome de Philadelphie qui est le chromosome 22 raccourci sur son bras long par une translocation t(9 ,22)(q34 ;qll¾ Cet échange entre les bras longs des chromosomes 9 et 22 est constamment présent dans] les cellules des patients atteint de LMC et il en résulte un gène de fusion appelé BCR BL fonctionnel qui sera transcrit en ARNm chimérique (Shtivelman, 1985. Nature 1985; 315:550-4) qui est traduit en protéines de fusion bcr-abl, responsable de la LMC.  Chronic myelogenous leukemia (CML) is a disease characterized by the presence of the Philadelphia chromosome which is chromosome 22 shortened on its long arm by a translocation t (9, 22) (q34). This exchange between the long arms of chromosomes 9 and 22 is constantly present in the cells of patients with CML and results in a fusion gene termed functional BCR BL which will be transcribed into chimeric mRNA (Shtivelman, 1985. Nature 1985; 315: 550-4) which is translated into fusion proteins bcr-abl, responsible for CML.
La translocation BCR-ABL (t (9 ,22) (q34;qll)) est présente chez 90-95% des patients LMC et 20-25% chez les patients de lalliucémie lymphoïde aiguë (LLA) (Prist, 1980; Blood 56: 15-22). La majorité des translocation! de la LMC frappe la région du 'major breakpoint cluster région' (M-bcr) au niveau du gène BCR et résulte en 2 transcrits qui sont b2a2 et b3a2 codant pour une protéine de fusion P210. La détection et la quantification des 2 derniers transcrits permettront de statuer sur l'évolution de la LMC. En effet, l'ARNm du gène BCR- ABL peut être détecté et quariltifié spécifiquement et efficacement par la méthode RT-PCR parce que ce gène de fusion eist spécifique à la LMC et peut être utilisé comme marqueur permettant d'identifier cette rrfaladie.  BCR-ABL translocation (t (9, 22) (q34; qll)) is present in 90-95% of patients with CML and 20-25% in patients with acute lymphoid leukemia (ALL) (Prist, 1980; Blood 56). : 15-22). The majority of translocations! CML strikes the region of the 'major breakpoint cluster region' (M-bcr) at the level of the BCR gene and results in 2 transcripts that are b2a2 and b3a2 encoding a P210 fusion protein. The detection and quantification of the last 2 transcripts will make it possible to decide on the evolution of CML. Indeed, the mRNA of the BCR-ABL gene can be detected and specifically and efficiently quarilified by the RT-PCR method because this eist fusion gene is specific for LMC and can be used as a marker to identify this disease.
Le critère fondamental du diagnostic de la LMC ou LLA est la présence de gène de fusion BCR-ABL, qui peut être mis en évidence par des méthodes cytogénétiques actuelles comme celles du caryotype, la FISH (Flilorescent in situe hybridation) ou d'examens hématologiques. Cependant, ces méthodes manquent surtout d'essais quantitatifs et qualitatifs, elles sont moins spécifiques, utilisent des hybridations complexes ou des isotopes, prennent énormément de temps (plus; eurs jours), peuvent être invasives (utilisation de la moelle osseuse), ou plus coûteuses De plus, ces méthodes cytogénétiques peuvent détecter seulement une cellule LMC u 500 cellules et donc ne peuvent pas être utilisées dans le cas du suivie de traitement de la |MC ni dans le cas de la maladie résiduelle qui nécessite une grande sensibilité (détection une cellule LMC sur 100000 cellules). The fundamental criterion for the diagnosis of CML or LLA is the presence of BCR-ABL fusion gene, which can be demonstrated by current cytogenetic methods such as karyotype, FISH (Flilorescent in situ hybridization) or hematological examinations. . However, these methods are mostly lacking in quantitative and qualitative tests, they are less specific, use complex hybridizations or isotopes, take a lot of time (more days), may be invasive (bone marrow use), or more expensive. Moreover, these cytogenetic methods can detect only one LMC u 500 cell. cells and therefore can not be used in the case of the treatment follow-up of the MC or in the case of the residual disease which requires a high sensitivity (detection of a CML cell on 100000 cells).
C'est pour les raisons citées !i-dessus qu'il est préférable de chercher des méthodes de quantification de BCR-ABL aajvel plus de sensibilité et de fiabilité, de meilleures répetabilité quantitatives et qualitatives, jjhoins coûteuses et pouvant facilement détecter la maladie résiduelle. It is for the reasons mentioned above that it is preferable to look for methods of quantification of BCR-ABL with more sensitivity and reliability, better quantitative and qualitative reputability, more costly and easily detectable residual disease. .
Une méthode alternative à jijt antérieur décrit ci-dessus est la PCR quantitative en temps réel (qPCR) qui a été bien jécrite auparavant pour l'amplification et la détection de différents gènes dont BCR-ABi il (Fossey S et al ; Mol Diagn. 2005;9(4):187-93; Gibson et al, 1996 Genomic Res 6 :995-10,0  An alternative method described above is the real-time quantitative PCR (qPCR) that has been well described before for the amplification and detection of various genes including BCR-ABi II (Fossey S et al Mol Diagn. 2005; 9 (4): 187-93; Gibson et al., 1996 Genomic Res 6: 995-10.0;
Pour la quantification d'u| |ène cible, la qPCR utilise en parallèle un gène contrôle 'housekeeping gene' exprimé è manière ubiquitaire dans toutes les cellules du corps et qui facilitera la normalisation jstj la quantification du gène ciblé. Dans le cas de BCR-ABL, plusieurs gènes contrôles orjt été testés comme GAPDH, beta-actine, microglobiline, G6PDHFor the quantification of u | At the same time, the qPCR uses in parallel a housekeeping gene gene expressed ubiquitously in all the cells of the body and which will facilitate the normalization and quantification of the targeted gene. In the case of BCR-ABL, several control genes have been tested, such as GAPDH, beta-actin, microglobilin, G6PDH
(Glucose-6-Phosphate-Déshydnpgénase) (Ullmannov. V, 2003 ; Folia Biologica (Praha) 49,(Glucose-6-Phosphate-Dehydrogenase) (Ullmannov V, 2003, Folia Biologica (Praha) 49,
211-216 (2003). Plus tard, ur e étude incluant 38 laboratoires Nord Américains a étudié certains gènes contrôles en pî allèle pour quantifier BCR-ABL (Tong et al ; 2007 ; Journal of molecular Diagnostics, vol N4 : p 421-429). Dans cette étude, l'amplification et la détection de BCR-ABL et les gênes contrôles a été faite avec des séquences nucléotidiques spécifiques tout en utilisant la qPCR en format simplex. Avec cette méthode, la sensibilité et le cout reste raisonnables et; railleurs que l'art antérieur 211-216 (2003). Later, a study involving 38 North American laboratories studied some control genes in allele to quantify BCR-ABL (Tong et al, 2007, Journal of molecular diagnostics, flight N4: p 421-429). In this study, amplification and detection of BCR-ABL and control genes was done with specific nucleotide sequences while using qPCR in simplex format. With this method, the sensitivity and cost remains reasonable and; scoffers that the prior art
Il est souhaitable d'identifier ne méthode de qPCR pour quantifier BCR-ABL qui peut être encore plus sensible et plus ble mais surtout moins coûteuse que l'art antérieur décrit ci- dessus. EXPOSE DE L'INVENTION It is desirable to identify a qPCR method for quantifying BCR-ABL which may be even more sensitive and less expensive but above all less expensive than the prior art described above. SUMMARY OF THE INVENTION
Figure imgf000004_0001
Figure imgf000004_0001
m t o es ant rieurs, vue e ai e sensi iit e tection. Before, you have seen the sensitivity.
Selon une autre caractéristiqi| é de l'invention, a) les amorces permettant la détection du transcrit BCR-ABL dans uf test échantillon ont des séquences d'oligonucleotides sélectionnées parmi un groJ pe de : SEQ ID NO :1, SEQ ID NO :2, SEQ ID NO :3, et SEQ ID NO :4, b) les amorces pour détfècter le gène contrôle ABLl dans un test échantillon ont des séquences d'oligonucleotides sélectionnées parmi un groupe de : SEQ ID NO :5, SEQ IDAccording to another characteristic | Of the invention, a) the primers for detecting the BCR-ABL transcript in a sample test have oligonucleotide sequences selected from a group of: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO : 3, and SEQ ID NO: 4, b) the primers for detecting the ABL1 control gene in a sample test have oligonucleotide sequences selected from a group of: SEQ ID NO: 5, SEQ ID
NO :6, SEQ ID NO :7, et SEQ IDi; O :8. NO: 6, SEQ ID NO: 7, and SEQ IDi; O: 8.
En accord avec cette invention | In accordance with this invention |
a) la sonde pour détectejr BCR-ABL dans un test échantillon a une séquence : SEQ ID : 9.  a) the probe for detecting BCR-ABL in a sample test has a sequence: SEQ ID: 9.
b) la sonde pour détecter ABLl dans un test échantillon a une séquence SEQ ID : 10.  b) the probe for detecting ABL1 in a sample test has a sequence SEQ ID: 10.
En accord aussi avec cette intention, les sets d'amorces pour amplifier BCR-ABL ou ABLl dans un test échantillon inclus Also in agreement with this intention, the sets of primers to amplify BCR-ABL or ABL1 in an included sample test
a) au moins pour BCRjjjABL une amorce forward ayant une séquence sélectionnée parmi le groupe : SEQ ID NO : L, SEQ ID NO : 2, et une amorce reverse ayant une séquence sélectionnée parmi SEQ ID NO 3, QEQ ID NO : 4  a) at least for BCRjjjABL a forward primer having a sequence selected from the group: SEQ ID NO: L, SEQ ID NO: 2, and a reverse primer having a sequence selected from SEQ ID NO 3, QEQ ID NO: 4
b) au moins pour ABLl J, une amorce forward ayant une séquence parmi le group : b) at least for ABL1 J, a forward primer having a sequence from the group:
SEQ ID NO : 5, SEQ ID NO : 6 , et une amorce reverse ayant une séquence sélectionnée parmiSEQ ID NO: 5, SEQ ID NO: 6, and a reverse primer having a sequence selected from
SEQ ID NO :7, SEQ ID NO : 8. SEQ ID NO: 7, SEQ ID NO: 8.
Figure imgf000005_0001
Figure imgf000006_0001
Figure imgf000005_0001
Figure imgf000006_0001
réactifs d'amplification. La réaç tion d'amplification peut être au moins une PCR, qPCR ou PCR. amplification reagents. The amplification reaction may be at least one PCR, qPCR or PCR.
Selon cette invention et en j ïccordance avec, au moins une sonde contient une unité fluorescente (reporter) attachée à la région 5' d'ADN. En plus au moins une sonde peut contenir une partie quenche ■r | ';I|l la région 3' D'ADN. La quantification de l'unité fluorescence permet la quantification du gèrije cible (BCR-ABL ou ABL1). According to this invention and in correspondence with, at least one probe contains a fluorescent unit (reporter) attached to the 5 'region of DNA. In addition at least one probe may contain a quenched portion ■ r | The DNA region 3 '. Quantification of the fluorescence unit allows quantification of the target gene (BCR-ABL or ABL1).
Selon une autre caractéristiql Lie de l'invention, l'amplification de BCR-ABL et ABL1 par la qPCR de la présente invention beuvent se faire en réaction simplexe ou multiplexe. According to another characteristic of the invention, the amplification of BCR-ABL and ABL1 by the qPCR of the present invention can be carried out in a simplex or multiplexed reaction.
BREVE DESCRIPTION DES FIG BRIEF DESCRIPTION OF FIGS
Figure la : Graphique Delta Rn-versus- cycle threshold (Ct) pour BCR-ABL en format simplexe. La lignée cellulaire leucémique K562 subissant une qPCR de la présente invention. 7 concentrations d'ADNc (4pg†25ng) ont été utilisées. Figure la: Delta Rn-versus-cycle threshold (Ct) graph for BCR-ABL in simplex format. The leukemic cell line K562 undergoing qPCR of the present invention. 7 cDNA concentrations (4pg † 25ng) were used.
Figure lb : Courbe standard Cycle threshold (Ct)-versus-log quantité ADNc pour BCR-ABL en format simplexe. La lignée çël ulaire leucémique K562 subissant une qPCR de la présente invention. 7 concentrations d' DNc (4pg-25ng) ont été utilisées. Figure 1b: Standard curve Cycle threshold (Ct) -versus-log cDNA quantity for BCR-ABL in simplex format. The k562 leukemia ulcer cell undergoing qPCR of the present invention. 7 concentrations of DNc (4 μg-25 ng) were used.
Figure 2 : Courbe standard Cylle threshold (Ct)-versus-log quantité ADNc pour BCR-ABL en format simplexe. La lignée çe | ulaire leucémique K562, un échantillon de sang d'un patient LMC et un autre d'un indivi u control subissant une qPCR de la présente invention. 9 concentrations d'ADNc (0,16pg-25ng) ont été utilisées Figure 2: Standard curve Cylle threshold (Ct) -versus-log cDNA amount for BCR-ABL in simplex format. The lineage çe | K562 leukemic ulaire, a blood sample of a LMC patient and another of an individual control undergoing qPCR of the present invention. 9 cDNA concentrations (0.16pg-25ng) were used
Figure imgf000006_0002
des échantillons d'ADNc dansjlijdhaque puits du triplicata ainsi que la courbe moyenne sont montrées.
Figure imgf000006_0002
cDNA samples from the well of the triplicate as well as the average curve are shown.
Figure 3b : Courbe standard C cle threshold (Ct)-versus-log quantité ADNc pour BCR-ABL en format multiplexe. La lignée jà jlulaire leucémique K562 subissant une qPCR de la présente invention. 7 concentrations d'ADNc (4pg-25ng) on été utilisées. Figure 3b: Standard Curve C cle threshold (Ct) -versus-log cDNA amount for BCR-ABL in multiplexed format. The k562 leukemia cell line undergoing qPCR of the present invention. 7 cDNA concentrations (4 μg-25 ng) were used.
Les courbes des valeurs Ct des échantillons d'ADNc dans chaque puits du triplicata ainsi que la courbe moyenne sont montrées  Ct curves of the cDNA samples in each well of the triplicate as well as the average curve are shown.
Figure 4a : Courbe standard 'Éycle threshold (Ct)-versus-log quantité ADNc pour ABL en format simplexe et multiplexe! La lignée cellulaire leucémique K562 subissant une qPCR de la présente invention. 6 conçèjntrations d'ADNc (20pg-25ng) on été utilisées. Les courbes moyennes des valeurs Ct des échantillons d'ADNc du triplicata sont montrées. Figure 4a: Standard Curve 'Éycle threshold (Ct) -versus-log quantity cDNA for ABL in simplex and multiplexed format! The leukemic cell line K562 undergoing qPCR of the present invention. Six cDNA constructs (20 μg-25 ng) were used. The average curves of the Ct values of the triplicate cDNA samples are shown.
Figure imgf000007_0001
Figure imgf000007_0001
EXPOSE DETAILLE DETAILED DESCRIPTION
La présente invention concerne des sondes, amorces, set d'amorces, set de sondes et amorces qui peuvent être util ■aisés pour amplifier, détecter et quantifier le gène BCR-ABL ou le gène contrôle ABL1 dans ur¾échantillon test.
Figure imgf000007_0002
The present invention relates to probes, primers, primer set, set of probes and primers that can be util ■ easy to amplify, detect and quantify the BCR-ABL gene or gene control ABL1 in ur¾échantillon test.
Figure imgf000007_0002
et sondes de la présente invention permettent une meilleur sensibilité et spécificité pour détecter BCR-ABL et ABL1. Selon la présente invention, llâinplification de BCR-ABL et du gène contrôle ABLl se fait au moins en qPCR en format! simplexe ou multiplexe permettant ainsi une meilleure quantification de BCR-ABL et u j gain en temps et en cout and probes of the present invention provide improved sensitivity and specificity for detecting BCR-ABL and ABL1. According to the present invention, the amplification of BCR-ABL and the ABL1 control gene is at least in qPCR format! simplex or multiplex thus allowing a better quantification of BCR-ABL and uj gain in time and cost
Selon une autre caractéristique de l'invention, la quantification plus sensible et plus spécifique de BCR-ABL perméftra un meilleur suivi du traitement de la LMC ainsi que la maladie résiduelle. According to another characteristic of the invention, the more sensitive and more specific quantification of BCR-ABL will permeate better monitoring of the treatment of CML as well as the residual disease.
Le mot 'BCR-ABL' ou t(9,22) djej it dans la présente invention est une translocation entre le gène ABLl du chromosome 9 e le breakpoint cluster région (BCR) sur le chromosome 22. The word 'BCR-ABL' or t (9,22) already in the present invention is a translocation between the ABL1 gene of chromosome 9 and the breakpoint cluster region (BCR) on chromosome 22.
La détection et la quantificatjo'n de BCR-ABL peut supporter le diagnostic clinique LMC, le suivi de son traitement et le suivi de la maladie résiduelle. Detection and quantification of BCR-ABL can support clinical diagnosis of CML, monitoring of its treatment and monitoring of residual disease.
Le mot 'gène' réfère à une séquence d'acide nucléique dans la molécule d'ADN qui occupe une région précise dans un ji'chromosome et permet de coder les instructions pour la synthèse de l'ARN. The word 'gene' refers to a nucleic acid sequence in the DNA molecule that occupies a specific region in a chromosome and allows coding of the instructions for RNA synthesis.
Le mot amplification de gène comme utilisé dans cette invention réfère à une ou plusieurs méthodes capables de copie iun acide nucléique permettant ainsi une augmentation du nombre de copie d'une séquence d'acide nucléique cible. La séquence amplifiée peut être un acide desoxyribonucléotid j !(ADN) ou un acide ribonucléotide (ARN). The word gene amplification as used in this invention refers to one or more methods capable of copying a nucleic acid thereby allowing an increase in the number of copies of a target nucleic acid sequence. The amplified sequence may be a deoxyribonucleotide acid (DNA) or a ribonucleotide acid (RNA).
Figure imgf000008_0001
Figure imgf000008_0001
Le mot 'amorce' séquence d'oligonucléotides qui peut être synthétisée chimiquement ou L'amorce est le point d'initiation de la synthèse d'ADN
Figure imgf000008_0002
dans des conditions optimalesf|de température et en présence de tampons, d'enzyme, de nucléotides et de séquences nùjçléotidiques complémentaires spécifiques. The word 'primer' oligonucleotide sequence that can be synthesized chemically or the primer is the point of initiation of DNA synthesis
Figure imgf000008_0002
under optimal temperature conditions and in the presence of specific complementary buffers, enzyme, nucleotides and nucleotide sequences.
Le mot 'sonde' représente une séquence nucléotidique qui forme une structure hybride avec une séquence cible dans une rifLécule d'un échantillon test. invention réfère à une méthode partir de molécule d'ARN. L'ADNc
Figure imgf000009_0001
The word 'probe' represents a nucleotide sequence which forms a hybrid structure with a target sequence in a riflecule of a test sample. invention refers to a method from an RNA molecule. The cDNA
Figure imgf000009_0001
peut être utilisée dans la méthjid e PCR. can be used in the PCR method.
Figure imgf000009_0002
Figure imgf000009_0002
polymérase de catalyser l'attachement des dNTPs aux amorces. polymerase to catalyze the attachment of dNTPs to primers.
Le mot 'RT-PCR' (reverse trjàhscriptase-PCR) de la présente invention représente une méthode de PCR dont le produit de départ n'est pas directement un ADN mais un ARN traduit en ADNc après transcription inverse. The word 'RT-PCR' (reverse trypscriptase-PCR) of the present invention represents a PCR method whose starting material is not directly DNA but an RNA translated into cDNA after reverse transcription.
Figure imgf000009_0003
Figure imgf000009_0003
logarithme. Pour déterminer la positivité d'une PCR et/ou quantifier un échantillon par qPCR, on détermine le nombre de cycles à partir duquel le produit PCR est détectable. Le moment d'apparition de ce signal seuil dénommé cycle seuil ou Ct (Cycle Threshold) est dépendant de la quantité de m ''Ialtrice initialement présente dans l'échantillon amplifié. Le Ct calculé est inversement proportionnel au logarithme décimal du nombre de copies initiales. logarithm. To determine the positivity of a PCR and / or quantify a sample by qPCR, the number of cycles from which the PCR product is detectable is determined. The time of appearance of this threshold signal called threshold cycle or Ct (Cycle Threshold) is dependent on the amount of m ' Ialtrice initially present in the amplified sample. The calculated Ct is inversely proportional to the decimal logarithm of the number of initial copies.
Parmi les sondes les plus utilisées en qPCR on trouve les sondes TaqMan et molecular beacons qui utilisent l'activité jexonucléase 5 fluorogénique de l'enzyme Taq polymerase pour mesurer la quantité de la séquence d'ADN dans un échantillon test. Among the most used probes in qPCR are the TaqMan and molecular beacons which use the fluorogenic jexonuclease activity of the Taq polymerase enzyme to measure the amount of the DNA sequence in a test sample.
Figure imgf000010_0001
Figure imgf000010_0001
présente invention, le reporteur de la sonde peut être FAM, JOE, YAKYE (YY) et le quencher BBQ, BHQ1, ou TAMRA. In the present invention, the probe reporter can be FAM, JOE, YAKYE (YY) and BBQ quencher, BHQ1, or TAMRA.
Le mot 'gène contrôle' comr ijè utilisé dans ou 'housekeeping gene' représente un gène exprimé en général da façon si pilaire par toutes les cellules d'un organisme. Parmi les gènes contrôle, on trouve le glycera |dehyd-3-phosphate dehydrogenase (GAPDH), l'albumine, la beta-actine, et ABL1. The term "control gene" as used in "housekeeping gene" represents a gene generally expressed in such a hair-like manner by all the cells of an organism. Among the control genes are glycera dehyd-3-phosphate dehydrogenase (GAPDH), albumin, beta-actin, and ABL1.
Le mot simplexe de la présente] [invention réfère à un essai qui ne se The word simplex of the present] [invention refers to an essay which does not
déroule pas simultanément avec d'autres essais. Dans notre invention, la qPCR en simplexe reflète la détection de nombre de copies d'un seul gène dans un tube de réaction. not proceed simultaneously with other tests. In our invention, qPCR in simplex reflects the detection of copy number of a single gene in a reaction tube.
Le mot multiplexe de la présente invention réfère à un essai qui se déroule simultanément avec au moins un autre essài La qPCR en multiplexe reflète la détection du nombre de copies d'au moins 2 gènes dans un même tube de réaction. Par exemple, dans la présente invention, les 2 gènes BCR-ABL jet ABL1 sont détectés simultanément par qPCR.
Figure imgf000011_0001
The multiplex word of the present invention refers to an assay that occurs simultaneously with at least one other test. The multiplexed qPCR reflects the detection of the copy number of at least 2 genes in the same reaction tube. For example, in the present invention, the 2 BCR-ABL jet ABL1 genes are simultaneously detected by qPCR.
Figure imgf000011_0001
sondes de la présente invention; probes of the present invention;
La qPCR de la présente invention permet de déterminer le nombre de copies du gène BCR-The qPCR of the present invention makes it possible to determine the number of copies of the BCR gene.
ABL dans des cellules humainsieIh quantifiant le nombre de copies de ABL in human cellsI quantifying the number of copies of
BCR-ABL relative à un gène con IItrôle Le gène contrôle ici est ABL1.  BCR-ABL relating to a control gene The control gene here is ABL1.
L'exemple 1 décrit un protocole i!j utilisé dans le test de qPCR de la présente invention. Le protocole décrit l'étape d'extra Iction d'ARN, de synthèse d'ADNc et de qPCR. Example 1 describes a protocol used in the qPCR assay of the present invention. The protocol describes the step of extra RNA, cDNA synthesis and qPCR.
L'exemple 2 montre la perforrij) nce de la qPCR de la présente invention pour détecter le gène BCR-ABL dans la lignée leucémique (LMC) humaine K562, dans le sang d'un patient LMC ainsi que dans le sang d'uni individu control. Example 2 shows the performance of the qPCR of the present invention for detecting the BCR-ABL gene in the human K562 leukemic line (LMC), in the blood of a LMC patient as well as in the blood of an individual. control.
La performance de la qPCR de la présente invention est suivant les normes IVD internationales (R2>0,95, slope entre -3,0 et 3,9 et efficacité proche de 100) avec des courbes standards (quantité d'ADNc de K562-vs-valeurs Ct) à efficacité de 100,02 et 100,44 et un R2 de 0,993 et 0,99 i,8! respectivement pour Figure lb et Figure 2. La courbe d'amplification cycle-vs-Deltaj ■in (Figure la) montre aussi une parfaite allure. Le patient LMC positif pour BCR-ABL païf lia méthode FISH est bien confirmé pour sa positivité dans la présente invention avec un Ct=32,5 (cercle, Figure 2) alors que l'individu control est négatif pour BCR-ABL avec un Ct=40 (tjjangle, Figure 2). The performance of the qPCR of the present invention is according to international IVD standards (R2> 0.95, slope between -3.0 and 3.9 and efficiency close to 100) with standard curves (amount of K562 cDNA). vs-values Ct) at 100.02 and 100.44 efficiency and a R2 of 0.993 and 0.99 i, 8! respectively for Figure lb and Figure 2. The cycle amplification cycle-vs-Deltaj ■ in (Figure la) also shows a perfect pace. The BCR-ABL-positive LMC patient with the FISH method is well confirmed for its positivity in the present invention with a Ct = 32.5 (circle, Figure 2) while the individual control is negative for BCR-ABL with a Ct = 40 (tjjangle, Figure 2).
L'exemple 3 montre la qPCR dl la présente invention en format simplexe ou multiplexe permet la détection séparée o i simultanée de BCR-ABL et ABL1 avec une grande précision.Example 3 shows that the qPCR of the present invention in simplex or multiplexed format allows the simultaneous or simultaneous detection of BCR-ABL and ABL1 with high accuracy.
La lignée LMC K562 positive pour BCR-ABL a été utilisée.
Figure imgf000012_0001
LMC K562 positive for BCR-ABL was used.
Figure imgf000012_0001
réaction simplexe et multiplexe^ été aussi observée (Figures 4a & 4b). Simplex and multiplex reaction was also observed (Figures 4a & 4b).
EXPERIENCES EXPERIENCES
Exemple 1 : Protocole de qPCR tie la présente invention pour la détection de Example 1: qPCR Protocol of the present invention for the detection of
BCR-ABL et ABLl  BCR-ABL and ABLl
Figure imgf000012_0002
Figure imgf000012_0002
Reverse Transcription suivant jj s recommandations du fournisseur Applied Biosystems. Reverse Transcription according to the supplier's recommendations Applied Biosystems.
Le mastermix de la réaction qPCR contient les amorces et la sonde de BCR-ABL et les amorces et la sonde d'ABLl, 5u ADDc et le tout est ajouté au Mastermix (TaqMan Fast Universal PCR Master mix : App:|ied Biosystems) pour un volume final de 25μΙ. The mastermix of the qPCR reaction contains the primers and the BCR-ABL probe and the primers and the ABL1 probe, 5u ADDc and the whole is added to the Mastermix (TaqMan Fast Universal Master PCR mix: App: | ied Biosystems) for a final volume of 25μΙ.
Figure imgf000012_0003
Figure imgf000012_0003
Le cycle thermal de la qPCR esjtjjfait dans les conditions suivantes : étape 1 à 95C° pendant 20 secondes; étape 2 (cycle de 5;cj) à 95C° pendant 1 seconde ; et une étape 3 à 60°C pendant 30 secondes.
Figure imgf000013_0001
The thermal cycle of the qPCR is carried out under the following conditions: step 1 at 95 ° C. for 20 seconds; step 2 (cycle 5, cj) at 95 ° C for 1 second; and step 3 at 60 ° C for 30 seconds.
Figure imgf000013_0001
Les séquences des amorces et de la sonde BCR-ABL utilisées en Figure
Figure imgf000013_0002
The sequences of the primers and the BCR-ABL probe used in FIG.
Figure imgf000013_0002
Figure imgf000013_0003
Les séquences des amorces et q| la sonde BCR-ABL utilisées en Figures 3b & 4b
Figure imgf000013_0003
The sequences of the primers and q | the BCR-ABL probe used in Figures 3b & 4b
Amorce Forward : 5'Ticçlgctgaccatcaataagg 3' (SEQ ID N° 1) Forward Forward: 5'Ticçlgctgaccatcaataagg 3 '(SEQ ID NO: 1)
Amorce reverse : 5' accctgaggctcaaa gg tcag 3' (SEQ ID IM° 4)  Reverse primer: 5 'accctgaggctcaaa gg tcag 3' (SEQ ID IM ° 4)
Sonde : 5' R-ccc ttcagcggccagtagca- Q 3' (SEQ ID N° 9)  Probe: 5 'R-ccc ttcagcggccagtagca- Q 3' (SEQ ID NO: 9)
Pour la sonde : R= F A M et Q=BHQ1 For the probe: R = F A M and Q = BHQ1
LISTE DES SEQUENCES NUCLE {O ITI:IDIQUES  LIST OF NUCLEIC SEQUENCES {O ITI: IDIC
SEQ ID N° 1 : F-BCR-ABL SEQ ID NO: 1: F-BCR-ABL
Longueur : 20 Length: 20
Tccgctgaccatcaataagg (F3) Tccgctgaccatcaataagg (F3)
SEQ ID N° 2 : F- BCR-ABL SEQ ID NO: 2 - F-BCR-ABL
Longueur : 20 Length: 20
Actccagactgtccacagca (F4) Actccagactgtccacagca (F4)
SEQ ID ° 3: R- BCR-ABL SEQ ID NO: 3-R-BCR-ABL
Longueur : 20 Length: 20
Ccctgaggctcaaagtcaga (RI) Ccctgaggctcaaagtcaga (RI)
SEQ ID N° 4 : R- BCR-ABL SEQ ID NO: 4: R-BCR-ABL
Longueur : 20 Length: 20
Accctgaggctcaaagtcag (R2) Accctgaggctcaaagtcag (R2)
SEQ ID NO° 5: F-ABL1 SEQ ID NO: 5: F-ABL1
Gtggccagtggagataacac (Fl) Gtggccagtggagataacac (Fl)
SEQ ID N° 6 : F-ABL1 SEQ ID NO: 6: F-ABL1
Longueur : 31 Length: 31
Tggagataacactctaagcataactaaaigt (F2)  Tggagataacactctaagcataactaaaigt (F2)
SEQ ID N° 7: R-ABL1 SEQ ID NO: 7: R-ABL1
Longueur : 20 Length: 20
Tgttgactggcgtgatgtag (RI) Tgttgactggcgtgatgtag (RI)
SEQ ID N° 8: R-ABL1 SEQ ID NO: 8: R-ABL1
Longueur: 21 Length: 21
Gatgtagttgcttgggaccca (R2)  Gatgtagttgcttgggaccca (R2)
SEQ ID N°9 : S- BCR-ABL SEQ ID No. 9: S-BCR-ABL
Longueur : 20 Length: 20
Cccttcagcggccagtagca (PI) SEQ ID N° 10 : S-ABL1 Longueur : 20 Cccttcagcggccagtagca (PI) SEQ ID NO: 10: S-ABL1 Length: 20
Aaatggccaaggctgggtcc (PI) Aaatggccaaggctgggtcc (PI)
F = amorce forward R = amorce reverse S = sonde F = forward primer R = reverse primer S = probe

Claims

REVENDICATIONS
1. Une méthode pour la détection des gènes BCR-ABL (responsable de la LMC) et 1. A method for the detection of BCR-ABL genes (responsible for CML) and
Figure imgf000016_0001
Figure imgf000016_0001
2. Méthode selon la reyer j ication 1, où deux amorces pour amplifier le gène BCR-ABL 2. Method according to the reagent j ication 1, where two primers to amplify the BCR-ABL gene
3.
Figure imgf000016_0002
3.
Figure imgf000016_0002
4. Méthode selon la reverdi ication 1, où deux amorces pour amplifier le gène ABLl dans un échantillon test : c! t constituées d'une amorce forward ayant une séquence sélectionnée parmi le! bupe de séquences : SEQ ID N° 5, SEQ ID N° 6, et une amorce reverse sélectionnée mi le groupe de séquences : SEQ ID N° 7, SEQ ID N°8. la détection du gène ABLl
Figure imgf000016_0003
4. Method according to Reverdiication 1, where two primers for amplifying the ABL1 gene in a test sample: c! t consisting of a forward primer having a sequence selected from the! sequence skirt: SEQ ID NO: 5, SEQ ID NO: 6, and a reverse primer selected in the sequence group: SEQ ID NO: 7, SEQ ID NO: 8. the detection of the ABLl gene
Figure imgf000016_0003
6. Méthode selon les reve ndications 1 à 5, où Les sondes pour détecter 6. Method according to the claims 1 to 5, where the probes to detect
Figure imgf000016_0004
Figure imgf000016_0004
7. Méthode selon les reve Ijndications 1 à 6, où la détection des gènes BCR-ABL et ABL1 dans un échantillon test est effectuée de façon séparée (Simplexe) ou simultanée7. A method according to r eve Ijndications 1 to 6, wherein the detection of BCR-ABL genes and ABL1 in a test sample is carried out separately (simplex) or simultaneously
(Multiplexe) dans un m ! ê Hme puits de qPCR. (Multiplexed) in a m! ê Well qPCR wells.
8. Méthode selon les revendications 1 à 7, où les sondes et amorces du gène permet la détection simultanée f de v; 2 transcrits de BCR-ABL, à savoir b2a3 et b3a2. The method of claims 1 to 7, wherein the probes and primers of the gene allow the simultaneous detection of v; 2 transcripts of BCR-ABL, namely b2a3 and b3a2.
9. Méthode selon les reveji indications 1 à 8, où l'utilisation de ladite méthode comprend au moins une des techn bues PCR, PCR en temps réel (qPCR) ou transcriptase reverse PCR (RT-PCR). 9. Method according to reveji indications 1 to 8, wherein the use of said method comprises at least one of PCR, real-time PCR (qPCR) or reverse transcriptase PCR (RT-PCR) techniques.
10. Nouvelle application dé la méthode des revendications précédentes caractérisée en ce qu'elle permet le d ia'gnostique et le suivi de traitement de la LMC et de la maladie résiduelle. 10. New application of the method of the preceding claims characterized in that it allows diagnosis and follow-up treatment of CML and residual disease.
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