WO2002029006A3 - Methods for parallel measurement of genetic variations - Google Patents
Methods for parallel measurement of genetic variations Download PDFInfo
- Publication number
- WO2002029006A3 WO2002029006A3 PCT/US2001/042432 US0142432W WO0229006A3 WO 2002029006 A3 WO2002029006 A3 WO 2002029006A3 US 0142432 W US0142432 W US 0142432W WO 0229006 A3 WO0229006 A3 WO 0229006A3
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- nucleotide
- interest
- primer
- sequence
- extension product
- Prior art date
Links
Classifications
-
- 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
-
- 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
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
Landscapes
- Chemical & Material Sciences (AREA)
- Organic Chemistry (AREA)
- Life Sciences & Earth Sciences (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- Physics & Mathematics (AREA)
- Molecular Biology (AREA)
- Biotechnology (AREA)
- Biophysics (AREA)
- Analytical Chemistry (AREA)
- Immunology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Genetics & Genomics (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
Abstract
The identity of a nucleotide of interest in a target nucleic acid molecule is determined by combining the target with two primers. The first primer is immobilized to a substrate and hybridizes to and extends from a location 3' of the nucleotide of interest in the target, so as to incorporate the complement of the nucleotide of interest in a first extension product. The second primer then hybridizes to and extends based on the first extension product, which is immobilized to the substrate via the first primer, at a location 3' of the complement of the nucleotide of interest, so as to incorporate the nucleotide of interest in a second extension product. The second extension product then dissociates from the first extension product and thus from the substrate and re-hybridizes to another first primer molecule that has not extended. The non-extended first primer then extends from a location 3' of the nucleotide of interest in the second extension product, so as to form, in combination with the second extension product, a double-stranded nucleic acid fragment. The first and second primers are designed to incorporate a portion of the recognition sequence of a restriction endonuclease (RE) that recognizes a partially variable interrupted nucleotide sequence, i.e., a sequence of the form D-N-S where D and S refer to specific nucleotide sequences essential for RE recognition, and N is a sequence consisting of n viable nucleotides also required for RE recognition. The first primer incorporates the sequence D, the second primer incorporates the sequence S, and they are designed, in view of the target, to product a nucleic acid fragment where constant sequences D and S are separated by variable sequence N, where the nucleotide of interest is within region N. Action of the RE on the nucleic acid fragment provides a small nucleic acid fragment that is amendable to characterization, to thereby reveal the identity of the nucleotide of interest.
Priority Applications (2)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| AU1183902A AU1183902A (en) | 2000-10-02 | 2001-09-28 | Methods for parallel measurement of genetic variations |
| US10/398,006 US20040019005A1 (en) | 2001-10-01 | 2001-10-01 | Methods for parallel measurement of genetic variations |
Applications Claiming Priority (22)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US23740900P | 2000-10-02 | 2000-10-02 | |
| US60/237,409 | 2000-10-02 | ||
| US24727500P | 2000-11-10 | 2000-11-10 | |
| US24716600P | 2000-11-10 | 2000-11-10 | |
| US24717200P | 2000-11-10 | 2000-11-10 | |
| US24716700P | 2000-11-10 | 2000-11-10 | |
| US24717300P | 2000-11-10 | 2000-11-10 | |
| US60/247,172 | 2000-11-10 | ||
| US60/247,173 | 2000-11-10 | ||
| US60/247,166 | 2000-11-10 | ||
| US60/247,167 | 2000-11-10 | ||
| US60/247,275 | 2000-11-10 | ||
| US26397101P | 2001-01-24 | 2001-01-24 | |
| US60/263,971 | 2001-01-24 | ||
| US26924401P | 2001-02-15 | 2001-02-15 | |
| US60/269,244 | 2001-02-15 | ||
| US30035001P | 2001-06-21 | 2001-06-21 | |
| US30031901P | 2001-06-21 | 2001-06-21 | |
| US60/300,319 | 2001-06-21 | ||
| US60/300,350 | 2001-06-21 | ||
| US30139401P | 2001-06-27 | 2001-06-27 | |
| US60/301,394 | 2001-06-27 |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| WO2002029006A2 WO2002029006A2 (en) | 2002-04-11 |
| WO2002029006A3 true WO2002029006A3 (en) | 2002-08-29 |
Family
ID=27582742
Family Applications (4)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2001/042432 WO2002029006A2 (en) | 2000-10-02 | 2001-10-01 | Methods for parallel measurement of genetic variations |
| PCT/US2001/030828 WO2002028501A1 (en) | 2000-10-02 | 2001-10-01 | Genotyping by liquid chromatographic analysis of short nucleic acid fragments |
| PCT/US2001/030743 WO2002040126A2 (en) | 2000-10-02 | 2001-10-01 | Methods for identifying nucleotides at defined positions in target nucleic acids using fluorescence polarization |
| PCT/US2001/030742 WO2002046447A2 (en) | 2000-10-02 | 2001-10-01 | Methods for identifying nucleotides at defined positions in target nucleic acids |
Family Applications After (3)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| PCT/US2001/030828 WO2002028501A1 (en) | 2000-10-02 | 2001-10-01 | Genotyping by liquid chromatographic analysis of short nucleic acid fragments |
| PCT/US2001/030743 WO2002040126A2 (en) | 2000-10-02 | 2001-10-01 | Methods for identifying nucleotides at defined positions in target nucleic acids using fluorescence polarization |
| PCT/US2001/030742 WO2002046447A2 (en) | 2000-10-02 | 2001-10-01 | Methods for identifying nucleotides at defined positions in target nucleic acids |
Country Status (2)
| Country | Link |
|---|---|
| AU (4) | AU3922802A (en) |
| WO (4) | WO2002029006A2 (en) |
Families Citing this family (14)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| MXPA04000432A (en) * | 2001-07-15 | 2004-10-27 | Keck Graduate Inst | Amplification of nucleic acid fragments using nicking agents. |
| US7223541B2 (en) | 2001-08-29 | 2007-05-29 | Ge Healthcare Bio-Sciences Corp. | Terminal-phosphate-labeled nucleotides and methods of use |
| US7033762B2 (en) | 2001-08-29 | 2006-04-25 | Amersham Biosciences Corp | Single nucleotide amplification and detection by polymerase |
| ATE458067T1 (en) | 2001-08-29 | 2010-03-15 | Ge Healthcare Bio Sciences | LABELED NUCLEOSIDE POLYPHOSPHATES |
| US7052839B2 (en) | 2001-08-29 | 2006-05-30 | Amersham Biosciences Corp | Terminal-phosphate-labeled nucleotides and methods of use |
| US7256019B2 (en) | 2001-08-29 | 2007-08-14 | Ge Healthcare Bio-Sciences Corp. | Terminal phosphate blocked nucleoside polyphosphates |
| US7560254B2 (en) | 2001-08-29 | 2009-07-14 | Ge Healthcare Bio-Sciences Corp. | Allele specific primer extension |
| GB0228614D0 (en) * | 2002-12-07 | 2003-01-15 | Fu Guoliang | Oligonucleotide guided analysis of gene expression |
| CA2524255C (en) | 2003-03-21 | 2014-02-11 | Academisch Ziekenhuis Leiden | Modulation of exon recognition in pre-mrna by interfering with the secondary rna structure |
| USRE48468E1 (en) | 2007-10-26 | 2021-03-16 | Biomarin Technologies B.V. | Means and methods for counteracting muscle disorders |
| EP2203173B1 (en) | 2007-10-26 | 2015-12-23 | Academisch Ziekenhuis Leiden | Means and methods for counteracting muscle disorders |
| EP2119783A1 (en) | 2008-05-14 | 2009-11-18 | Prosensa Technologies B.V. | Method for efficient exon (44) skipping in Duchenne Muscular Dystrophy and associated means |
| US20120046342A1 (en) | 2009-04-24 | 2012-02-23 | Prosensa Technologies B.V. | Oligonucleotide comprising an inosine for treating dmd |
| CN104203289B (en) | 2012-01-27 | 2020-11-03 | 比奥马林技术公司 | RNA-regulatory oligonucleotides with improved properties for the treatment of duchenne muscular dystrophy and becker muscular dystrophy |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6040166A (en) * | 1985-03-28 | 2000-03-21 | Roche Molecular Systems, Inc. | Kits for amplifying and detecting nucleic acid sequences, including a probe |
| US6103463A (en) * | 1992-02-19 | 2000-08-15 | The Public Health Research Institute Of The City Of New York, Inc. | Method of sorting a mixture of nucleic acid strands on a binary array |
| US6110709A (en) * | 1994-03-18 | 2000-08-29 | The General Hospital Corporation | Cleaved amplified modified polymorphic sequence detection methods |
Family Cites Families (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP0646171A4 (en) * | 1992-05-22 | 1998-01-07 | Us Health | Improved expression of human multidrug resistance genes and improved selection of cells transduced with such genes. |
| US5284758A (en) * | 1992-08-14 | 1994-02-08 | Merck & Co., Inc. | Process for forming cholesterol lowering compound using pseudodiplodia sp. |
| JPH078289A (en) * | 1993-06-29 | 1995-01-13 | Osaka Gas Co Ltd | Method for synthesizing peptide and protein using ribosome |
| US6027898A (en) * | 1997-08-18 | 2000-02-22 | Transgenomic, Inc. | Chromatographic method for mutation detection using mutation site specifically acting enzymes and chemicals |
| US6180408B1 (en) * | 1998-08-21 | 2001-01-30 | Washington University | Fluorescence polarization in nucleic acid analysis |
-
2001
- 2001-08-31 AU AU3922802A patent/AU3922802A/en active Pending
- 2001-09-28 AU AU1183902A patent/AU1183902A/en active Pending
- 2001-10-01 WO PCT/US2001/042432 patent/WO2002029006A2/en active Application Filing
- 2001-10-01 WO PCT/US2001/030828 patent/WO2002028501A1/en active Application Filing
- 2001-10-01 WO PCT/US2001/030743 patent/WO2002040126A2/en active Search and Examination
- 2001-10-01 AU AU2001296491A patent/AU2001296491A1/en not_active Abandoned
- 2001-10-01 WO PCT/US2001/030742 patent/WO2002046447A2/en active Search and Examination
- 2001-12-05 AU AU4146002A patent/AU4146002A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6040166A (en) * | 1985-03-28 | 2000-03-21 | Roche Molecular Systems, Inc. | Kits for amplifying and detecting nucleic acid sequences, including a probe |
| US6103463A (en) * | 1992-02-19 | 2000-08-15 | The Public Health Research Institute Of The City Of New York, Inc. | Method of sorting a mixture of nucleic acid strands on a binary array |
| US6110709A (en) * | 1994-03-18 | 2000-08-29 | The General Hospital Corporation | Cleaved amplified modified polymorphic sequence detection methods |
Also Published As
| Publication number | Publication date |
|---|---|
| WO2002046447A3 (en) | 2003-12-24 |
| AU3922802A (en) | 2002-05-27 |
| AU2002239228A8 (en) | 2006-11-02 |
| WO2002046447A2 (en) | 2002-06-13 |
| AU2001296491A1 (en) | 2002-04-15 |
| WO2002040126A2 (en) | 2002-05-23 |
| WO2002040126A3 (en) | 2006-04-06 |
| WO2002028501A1 (en) | 2002-04-11 |
| AU1183902A (en) | 2002-04-15 |
| AU4146002A (en) | 2002-06-18 |
| WO2002029006A2 (en) | 2002-04-11 |
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