CA2393482A1 - Amplification based polymorphism detection - Google Patents
Amplification based polymorphism detection Download PDFInfo
- Publication number
- CA2393482A1 CA2393482A1 CA002393482A CA2393482A CA2393482A1 CA 2393482 A1 CA2393482 A1 CA 2393482A1 CA 002393482 A CA002393482 A CA 002393482A CA 2393482 A CA2393482 A CA 2393482A CA 2393482 A1 CA2393482 A1 CA 2393482A1
- Authority
- CA
- Canada
- Prior art keywords
- nucleic acid
- acid sequence
- amplification
- target nucleic
- test sample
- Prior art date
- Legal status (The legal status 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 status listed.)
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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
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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
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6858—Allele-specific amplification
-
- 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
- C12Q2600/156—Polymorphic or mutational markers
Abstract
Methods for detecting various types of polymorphic nucleic acid sequences are provided herein. The detection methods are based upon nucleic acid amplification procedures and the ability to detect "large" deletions or insertions in an automated fashion. For example, a deletion or an insertion in a target nucleic acid sequence in a test sample, wherein the deletion or insertion is at least 8 or more consecutive nucleotides, can be detected according to the following steps: a) contacting the test sample with amplification reagents and a set of amplification primers to form a reaction mixture wherein the set of amplification primers hybridize with the target nucleic acid sequence and a standard nucleic acid sequence in the test sample;
b) subjecting the reaction mixture to amplification conditions to form a target nucleic acid sequence amplification product and a standard nucleic acid amplification product; c) hybridizing a first labeled probe to the target sequence amplification product and a second labeled probe to the standard nucleic acid sequence amplification product; d) detecting signals from the first probe and the second probe; and e) comparing the signals from the first and second labeled probes to determine the presence of the deletion or insertion in the target nucleic acid sequence in the test sample.
b) subjecting the reaction mixture to amplification conditions to form a target nucleic acid sequence amplification product and a standard nucleic acid amplification product; c) hybridizing a first labeled probe to the target sequence amplification product and a second labeled probe to the standard nucleic acid sequence amplification product; d) detecting signals from the first probe and the second probe; and e) comparing the signals from the first and second labeled probes to determine the presence of the deletion or insertion in the target nucleic acid sequence in the test sample.
Claims (37)
1. A method for distinguishing between the presence of a target nucleic acid sequence and a variant of the target nucleic acid sequence in a test sample, wherein the variant nucleic acid contains a variation from the target nucleic acid sequence comprising a deletion of eight or more consecutive nucleotides, the method comprises the steps of:
a) contacting the test sample with amplification reagents and a first and second amplification primer to form a reaction mixture, wherein the first primer hybridizes with the target nucleic acid sequence at the site containing the variation in the variant sequence;
b) subjecting the reaction mixture to amplification conditions; and c) detecting the presence of an amplification product from the first and second primers as an indication of the presence of the target nucleic acid sequence in the test sample.
a) contacting the test sample with amplification reagents and a first and second amplification primer to form a reaction mixture, wherein the first primer hybridizes with the target nucleic acid sequence at the site containing the variation in the variant sequence;
b) subjecting the reaction mixture to amplification conditions; and c) detecting the presence of an amplification product from the first and second primers as an indication of the presence of the target nucleic acid sequence in the test sample.
2. The method of claim 1 wherein detecting the presence of the amplification product comprises hybridizing a labeled probe to the amplification product.
3. The method of claim 1 wherein a failure to detect an amplification product is an indication of the presence of the variant nucleic acid sequence in the test sample.
4. The method of claim 1 wherein a) the reaction mixture further comprises a control nucleic acid sequence and primers for amplifying the control nucleic acid sequence, and b) the method further comprises the step of detecting the amplified control nucleic acid sequence as an indication that the amplification reagents and conditions were efficacious for producing an amplification product.
5. The method of claim 4 wherein a failure to detect an amplification product is an indication of the presence of the variant nucleic acid sequence in the test sample.
6. The method of claim 4 wherein detecting the presence of the amplification product and detecting the amplified control nucleic acid sequence comprises hybridizing a first labeled probe to the amplification product and second labeled probe to the amplified control nucleic acid sequence.
7. The method of claim 4 wherein the control nucleic acid sequence is a sequence contained within a gene or pseudogene homologous to a gene containing the target nucleic acid sequence.
8. The method of claim 7 wherein one of the primers for amplifying the control nucleic acid sequence is selected from the first and the second primer.
9. The method of claim 1 wherein the test sample is from a patient and the method further comprises the step of altering the patient's medical care regimen based upon the presence or absence of the target sequence in the test sample.
10. The method of claim I further comprising the steps of:
a) contacting the test sample with additional amplification primers and amplification reagents, wherein the amplification primers amplify a second target nucleic acid sequence and a variant of the second target nucleic acid sequence wherein the variant of the second target nucleic acid sequence contains a one to seven nucleotide variation from the second target nucleic acid sequence;
b) subjecting the test sample and additional amplification primers and amplification reagents to amplification conditions to form a second amplification product;
and c) detecting the presence of a second amplification product as an indication of the second target nucleic acid sequence or variant of the second target nucleic acid sequence in the test sample.
a) contacting the test sample with additional amplification primers and amplification reagents, wherein the amplification primers amplify a second target nucleic acid sequence and a variant of the second target nucleic acid sequence wherein the variant of the second target nucleic acid sequence contains a one to seven nucleotide variation from the second target nucleic acid sequence;
b) subjecting the test sample and additional amplification primers and amplification reagents to amplification conditions to form a second amplification product;
and c) detecting the presence of a second amplification product as an indication of the second target nucleic acid sequence or variant of the second target nucleic acid sequence in the test sample.
11. The method of claim 10 wherein the reaction mixture comprising amplification reagents and the first and second amplification primers, also includes the additional amplification primers and amplification reagents.
12. The method of claim 10 wherein detecting the presence of the amplification product and second amplification product comprises hybridizing a first labeled probe to the amplification product and a second labeled probe to the second amplification product.
13. The method of claim 10 wherein the first and second labeled probes are detected on the same apparatus.
14. The method of claim 10 wherein the variant of the second target nucleic acid sequence contains a single nucleotide variation.
15. The method of claim 10 wherein the target nucleic acid is a nucleic acid sequence within the cytochrome P-450 2D (CYP2D) family.
16. The method of claim 13 wherein the deletion is CYP2D6*5 and the variant of the second target nucleic acid sequence is selected from CYP2D6*3, CYPZD6*4, CYP2D6*6, and any combination of CYP2D6*3, CYP2D6*4, and CYP2D6*6.
17. A method for detecting a target nucleic acid sequence in a test sample comprising the steps of:
a) contacting the test sample with amplification reagents comprising a polymerase, a PCR primer pair, and a probe to form a reaction mixture;
b) performing the following cycle (i) raising the temperature of the reaction mixture to a temperature sufficient to dissociate double stranded nucleic acid sequences, (ii) lowering the temperature of the reaction mixture to allow the PCR
primers and probe to hybridize to the nucleic acid and thereby form primer hybrids and probe hybrids, (iii) raising the temperature of the reaction mixture to a temperature sufficient to dissociate the probe hybrids, if the probe is not completely complementary to the nucleic acid, but not sufficient to dissociate the primer hybrids, (iv) raising the temperature of the reaction mixture to a temperature sufficient to activate the polymerase;
c) repeatedly performing the cycle of step b) to form an amplification product;
and d) detecting the amplification product as an indication of the presence of the nucleic acid sequence in the test sample.
a) contacting the test sample with amplification reagents comprising a polymerase, a PCR primer pair, and a probe to form a reaction mixture;
b) performing the following cycle (i) raising the temperature of the reaction mixture to a temperature sufficient to dissociate double stranded nucleic acid sequences, (ii) lowering the temperature of the reaction mixture to allow the PCR
primers and probe to hybridize to the nucleic acid and thereby form primer hybrids and probe hybrids, (iii) raising the temperature of the reaction mixture to a temperature sufficient to dissociate the probe hybrids, if the probe is not completely complementary to the nucleic acid, but not sufficient to dissociate the primer hybrids, (iv) raising the temperature of the reaction mixture to a temperature sufficient to activate the polymerase;
c) repeatedly performing the cycle of step b) to form an amplification product;
and d) detecting the amplification product as an indication of the presence of the nucleic acid sequence in the test sample.
18. The method of claim 17 wherein the target nucleic acid sequence is a polymorphic nucleic acid sequence.
19. A method for detecting the presence a deletion or an insertion in a target nucleic acid sequence in a test sample, wherein the deletion or insertion is at least 8 or more consecutive nucleotides, the method comprises the steps of:
a) contacting the test sample with amplification reagents and a set of amplification primers to form a reaction mixture wherein the set of amplification primers hybridize with the target nucleic acid sequence and a standard nucleic acid sequence in the test sample;
b) subjecting the reaction mixture to amplification conditions to form a target nucleic acid sequence amplification product and a standard nucleic acid amplification product;
c) hybridizing a first probe to the target sequence amplification product and a second probe to the standard nucleic acid sequence amplification product to form first probe/target sequence amplification product hybrids and second probe/standard nucleic acid amplification product hybrids;
d) detecting the hybrids; and e) comparing the signals from the first and second labeled probes to determine the presence of the deletion or insertion in the target nucleic acid sequence in the test sample.
a) contacting the test sample with amplification reagents and a set of amplification primers to form a reaction mixture wherein the set of amplification primers hybridize with the target nucleic acid sequence and a standard nucleic acid sequence in the test sample;
b) subjecting the reaction mixture to amplification conditions to form a target nucleic acid sequence amplification product and a standard nucleic acid amplification product;
c) hybridizing a first probe to the target sequence amplification product and a second probe to the standard nucleic acid sequence amplification product to form first probe/target sequence amplification product hybrids and second probe/standard nucleic acid amplification product hybrids;
d) detecting the hybrids; and e) comparing the signals from the first and second labeled probes to determine the presence of the deletion or insertion in the target nucleic acid sequence in the test sample.
20. The method of claim 19 wherein the standard nucleic acid sequence is a nucleic acid sequence added to the reaction mixture.
21. The method of claim 19 wherein the standard nucleic acid sequence is a nucleic acid sequence within a gene or pseudogene homologous to a gene containing the target nucleic acid sequence.
22. The method of claim 19 wherein the first and second probes differ by a single nucleotide.
23. The method of claim 19 wherein the test sample is from a patient and the method further comprises the step of altering the patient's medical care regimen based upon the presence or absence of the target sequence in the test sample.
24. The method of claim 19 wherein the set of amplification primers comprises four amplification primers.
25. The method of claim 19 wherein the set of amplification primers comprises less than four primers and at least one primer of the set of amplification primers hybridizes to the target nucleic acid sequence and standard nucleic acid sequence.
26. The method of claim 19 further comprising the steps of:
a) contacting the test sample with additional amplification primers and amplification reagents, wherein the amplification primers amplify a second target nucleic acid sequence and a variant of the second target nucleic acid sequence wherein the variant of the second target nucleic acid sequence contains a one to seven nucleotide variation from the second target nucleic acid sequence;
b) subjecting the test sample and additional amplification primers and amplification reagents to amplification conditions to form a second amplification product;
and c) detecting the presence of a second amplification product as an indication of the second target nucleic acid sequence or variant of the second target nucleic acid sequence in the test sample.
a) contacting the test sample with additional amplification primers and amplification reagents, wherein the amplification primers amplify a second target nucleic acid sequence and a variant of the second target nucleic acid sequence wherein the variant of the second target nucleic acid sequence contains a one to seven nucleotide variation from the second target nucleic acid sequence;
b) subjecting the test sample and additional amplification primers and amplification reagents to amplification conditions to form a second amplification product;
and c) detecting the presence of a second amplification product as an indication of the second target nucleic acid sequence or variant of the second target nucleic acid sequence in the test sample.
27. The method of claim 26 wherein the reaction mixture comprising the test sample, amplification reagents and a set of amplification primers, further comprises the additional amplification primers and amplification reagents.
28. The method of claim 26 wherein detecting the presence of the second amplification product amplification product comprises hybridizing a labeled probe to the second amplification product.
29. The method of claim 19 wherein the primers are labeled and detecting the hybrids comprises detecting the labeled primers that have been incorporated into the hybrids.
30. The method of claim 19 wherein the first and second probes are labeled and detecting the hybrids comprises detecting the labeled probes that have been incorporated into the hybrids.
31. The method of claim 28 wherein the first and second probes are labeled and detecting the hybrids comprises detecting the labeled probes that have been incorporated into the hybrids with the same apparatus employed to detect the second amplification product.
32. The method of claim 26 wherein at least one member of the primer set and the additional amplification primers are labeled and detecting the presence of the hybrids and second amplification product comprises contacting the amplification product, second amplification product, and standard nucleic acid sequence amplification product with probes immobilized to a solid support in an array.
33. The method of claim 26 wherein the first and second target nucleic acid sequences are nucleic acid sequences within CYP2D family.
34. The method of claim 33 wherein the deletion is *5 and the variant of the second target nucleic acid sequence is selected from *3, *4, *6, and any combination of *3, *4, and *6.
35 The method of claim 26 wherein the test sample is from a patient and the method further comprises the step of altering the patient's medical care regimen based upon the presence or absence of the first or variant of the second target sequence in the test sample.
36. The method of claim 1 wherein the first or second amplification primer is labeled.
37. The method of claim 1 wherein the first or second amplification primer is labeled and a additional amplification primer is labeled.
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US17369999P | 1999-12-30 | 1999-12-30 | |
US60/173,699 | 1999-12-30 | ||
PCT/US2000/035186 WO2001049883A2 (en) | 1999-12-30 | 2000-12-22 | Amplification based polymorphism detection |
Publications (2)
Publication Number | Publication Date |
---|---|
CA2393482A1 true CA2393482A1 (en) | 2001-07-12 |
CA2393482C CA2393482C (en) | 2012-10-02 |
Family
ID=22633130
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
CA2393482A Expired - Fee Related CA2393482C (en) | 1999-12-30 | 2000-12-22 | Amplification based polymorphism detection |
Country Status (8)
Country | Link |
---|---|
US (1) | US7250252B2 (en) |
EP (1) | EP1244813B1 (en) |
JP (1) | JP4828069B2 (en) |
AT (1) | ATE545709T1 (en) |
CA (1) | CA2393482C (en) |
ES (1) | ES2380073T3 (en) |
PT (1) | PT1244813E (en) |
WO (1) | WO2001049883A2 (en) |
Families Citing this family (33)
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JP2005176601A (en) * | 2001-12-06 | 2005-07-07 | Tsumura & Co | Cyp2d6 mutant gene |
US20040241714A1 (en) * | 2003-02-04 | 2004-12-02 | Branch Robert A. | Methods of assessment of drug metabolizing enzymes |
WO2006039663A2 (en) | 2004-09-30 | 2006-04-13 | Vanda Pharmaceuticals, Inc | Methods for the administration of iloperidone |
WO2008076856A2 (en) * | 2006-12-14 | 2008-06-26 | Siemens Healthcare Diagnostics Inc. | Reagents and methods for detecting cyp2d6 polymorphisms |
US20100299773A1 (en) * | 2009-05-20 | 2010-11-25 | Monsanto Technology Llc | Methods and compositions for selecting an improved plant |
US10172305B2 (en) | 2011-04-29 | 2019-01-08 | Monsanto Technology Llc | Diagnostic molecular markers for seed lot purity traits in soybeans |
WO2012151254A1 (en) | 2011-05-02 | 2012-11-08 | Board Of Regents Of The University Of Nebraska | Plants with useful traits and related methods |
HUE059863T2 (en) | 2011-08-31 | 2023-01-28 | Seminis Vegetable Seeds Inc | Methods and compositions for watermelon firmness |
CN110187122A (en) * | 2012-09-05 | 2019-08-30 | 亚利桑那州评议委员会,亚利桑那州法人团体,代理和代表亚利桑那州立大学 | It was found that therapeutic target calibration method |
US10314253B2 (en) | 2012-12-04 | 2019-06-11 | Seminis Vegetable Seeds, Inc. | Methods and compositions for watermelon sex expression |
US10294489B2 (en) | 2013-03-15 | 2019-05-21 | Board Of Trustees Of Southern Illinois University | Soybean resistant to cyst nematodes |
US10059999B2 (en) | 2013-06-10 | 2018-08-28 | Monsanto Technology Llc | Molecular markers associated with soybean tolerance to low iron growth conditions |
US10767188B2 (en) | 2013-09-25 | 2020-09-08 | Nutech Ventures | Methods and compositions for obtaining useful plant traits |
NZ728726A (en) | 2013-11-27 | 2018-09-28 | Seminis Vegetable Seeds Inc | Disease resistance loci in onion |
CN110607321A (en) | 2014-02-21 | 2019-12-24 | 先正达参股股份有限公司 | Genetic loci associated with increased fertility in maize |
NZ630710A (en) | 2014-02-27 | 2016-03-31 | Seminis Vegetable Seeds Inc | Compositions and methods for peronospora resistance in spinach |
US10316369B2 (en) | 2014-06-27 | 2019-06-11 | Seminis Vegetable Seeds, Inc. | Methods and assays for male sterile watermelon |
EP3005862A1 (en) | 2014-10-10 | 2016-04-13 | Seminis Vegetable Seeds, Inc. | Melon plants with improved disease tolerance |
EP3889274A3 (en) | 2015-04-28 | 2022-01-19 | Monsanto Technology LLC | Methods and compositions for producing brachytic corn plants |
UA126326C2 (en) | 2015-04-30 | 2022-09-21 | Монсанто Текнолоджі Елелсі | Methods for producing canola plants with clubroot resistance and compositions thereof |
US10767189B2 (en) | 2015-08-18 | 2020-09-08 | Monsanto Technology Llc | Methods for producing cotton plants with enhanced drought tolerance and compositions thereof |
US10448595B2 (en) | 2015-09-03 | 2019-10-22 | Seminis Vegetable Seeds, Inc. | Downy mildew resistant lettuce plants |
WO2017044744A2 (en) | 2015-09-10 | 2017-03-16 | Monsanto Technology Llc | Methods for producing corn plants with downy mildew resistance and compositions thereof |
CA3006080A1 (en) | 2015-12-18 | 2017-06-22 | Monsanto Technology Llc | Methods for producing corn plants with northern leaf blight resistance and compositions thereof |
WO2018031874A1 (en) | 2016-08-11 | 2018-02-15 | Monsanto Technology Llc | Methods and compositions for producing corn plants with resistance to late wilt |
AU2017232187B2 (en) | 2016-09-30 | 2023-11-09 | Seminis Vegetable Seeds, Inc. | Xanthomonas resistant brassica oleracea plants |
US11268102B2 (en) | 2018-05-16 | 2022-03-08 | University Of Florida Research Foundation, Incorporated | Compositions and methods for identifying and selecting brachytic locus in solanaceae |
MX2021008494A (en) | 2019-01-15 | 2021-08-19 | Seminis Vegetable Seeds Inc | Green bean plants with improved disease resistance. |
US11542513B2 (en) | 2019-09-26 | 2023-01-03 | Seminis Vegetable Seeds, Inc. | Lettuce plants having resistance to Nasonovia ribisnigri biotype Nr:1 |
AU2021204717A1 (en) | 2020-07-15 | 2022-02-03 | Seminis Vegetable Seeds, Inc. | Green Bean Plants with Improved Disease Resistance |
CN112501265A (en) * | 2020-09-24 | 2021-03-16 | 杭州百迈生物股份有限公司 | Reagent, detection method and kit for detecting CYP2D6 gene |
US20230193310A1 (en) | 2021-12-10 | 2023-06-22 | Seminis Vegetabe Seeds, Inc. | Lettuce plants having resistance to downy mildew |
WO2023250288A2 (en) | 2022-06-21 | 2023-12-28 | Seminis Vegetable Seeds, Inc. | Novel qtls conferring resistance to cucumber mosaic virus |
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-
2000
- 2000-12-21 US US09/747,538 patent/US7250252B2/en not_active Expired - Fee Related
- 2000-12-22 PT PT00989462T patent/PT1244813E/en unknown
- 2000-12-22 EP EP00989462A patent/EP1244813B1/en not_active Expired - Lifetime
- 2000-12-22 WO PCT/US2000/035186 patent/WO2001049883A2/en active Application Filing
- 2000-12-22 CA CA2393482A patent/CA2393482C/en not_active Expired - Fee Related
- 2000-12-22 ES ES00989462T patent/ES2380073T3/en not_active Expired - Lifetime
- 2000-12-22 JP JP2001550410A patent/JP4828069B2/en not_active Expired - Fee Related
- 2000-12-22 AT AT00989462T patent/ATE545709T1/en active
Also Published As
Publication number | Publication date |
---|---|
PT1244813E (en) | 2012-05-09 |
EP1244813A2 (en) | 2002-10-02 |
US20020102549A1 (en) | 2002-08-01 |
WO2001049883A2 (en) | 2001-07-12 |
US7250252B2 (en) | 2007-07-31 |
JP4828069B2 (en) | 2011-11-30 |
CA2393482C (en) | 2012-10-02 |
JP2004500073A (en) | 2004-01-08 |
EP1244813B1 (en) | 2012-02-15 |
WO2001049883A3 (en) | 2002-01-31 |
ES2380073T3 (en) | 2012-05-08 |
ATE545709T1 (en) | 2012-03-15 |
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EEER | Examination request | ||
MKLA | Lapsed |
Effective date: 20141222 |