WO2000022171A3 - Systems and methods for sequencing by hybridization - Google Patents

Systems and methods for sequencing by hybridization Download PDF

Info

Publication number
WO2000022171A3
WO2000022171A3 PCT/US1999/023944 US9923944W WO0022171A3 WO 2000022171 A3 WO2000022171 A3 WO 2000022171A3 US 9923944 W US9923944 W US 9923944W WO 0022171 A3 WO0022171 A3 WO 0022171A3
Authority
WO
WIPO (PCT)
Prior art keywords
probes
sequencing
gapped
systems
hybridization
Prior art date
Application number
PCT/US1999/023944
Other languages
French (fr)
Other versions
WO2000022171A2 (en
Inventor
Franco P Preparata
Eli Upfal
Original Assignee
Univ Brown Res Found
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 Univ Brown Res Found filed Critical Univ Brown Res Found
Priority to AU12046/00A priority Critical patent/AU1204600A/en
Priority to EP99970428A priority patent/EP1121472B1/en
Priority to DE69929365T priority patent/DE69929365T2/en
Publication of WO2000022171A2 publication Critical patent/WO2000022171A2/en
Publication of WO2000022171A3 publication Critical patent/WO2000022171A3/en

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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (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)
  • Saccharide Compounds (AREA)

Abstract

The systems and methods described herein relate to nucleic acid probes comprising a pattern of universal and designate nucleotides, or 'gapped' probes, and the use of sets of gapped probes in sequencing by hybridization to determine the sequence of nucleic acid sequences. The inclusion of universal nucleotides in the probes allows for efficient and rapid sequencing of longer nucleotide sequences than can be sequenced using traditional probes. The systems and methods described herein also relate to apparatus for sequencing nucleic acids which include gapped probes, as well as computer systems capable of analyzing data generated using gapped probes in such apparatus.
PCT/US1999/023944 1998-10-13 1999-10-13 Systems and methods for sequencing by hybridization WO2000022171A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU12046/00A AU1204600A (en) 1998-10-13 1999-10-13 Systems and methods for sequencing by hybridization
EP99970428A EP1121472B1 (en) 1998-10-13 1999-10-13 Systems and methods for sequencing by hybridization
DE69929365T DE69929365T2 (en) 1998-10-13 1999-10-13 SYSTEMS AND METHODS FOR SEQUENCING THROUGH HYBRIDATION

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US10399898P 1998-10-13 1998-10-13
US60/103,998 1998-10-13
US12570499P 1999-03-23 1999-03-23
US60/125,704 1999-03-23

Publications (2)

Publication Number Publication Date
WO2000022171A2 WO2000022171A2 (en) 2000-04-20
WO2000022171A3 true WO2000022171A3 (en) 2000-08-31

Family

ID=26801084

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/023944 WO2000022171A2 (en) 1998-10-13 1999-10-13 Systems and methods for sequencing by hybridization

Country Status (5)

Country Link
EP (1) EP1121472B1 (en)
AT (1) ATE315106T1 (en)
AU (1) AU1204600A (en)
DE (1) DE69929365T2 (en)
WO (1) WO2000022171A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8882980B2 (en) 2008-09-03 2014-11-11 Nabsys, Inc. Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7071324B2 (en) 1998-10-13 2006-07-04 Brown University Research Foundation Systems and methods for sequencing by hybridization
US6949340B2 (en) 2001-03-28 2005-09-27 Creative Mines Llc Optical phase modulator
US7138506B2 (en) 2001-05-09 2006-11-21 Genetic Id, Na, Inc. Universal microarray system
EP1442137A4 (en) * 2001-11-07 2005-08-31 Applera Corp Universal nucleotides for nucleic acid analysis
US8278047B2 (en) 2007-10-01 2012-10-02 Nabsys, Inc. Biopolymer sequencing by hybridization of probes to form ternary complexes and variable range alignment
US9650668B2 (en) 2008-09-03 2017-05-16 Nabsys 2.0 Llc Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels
US8262879B2 (en) 2008-09-03 2012-09-11 Nabsys, Inc. Devices and methods for determining the length of biopolymers and distances between probes bound thereto
US8715933B2 (en) 2010-09-27 2014-05-06 Nabsys, Inc. Assay methods using nicking endonucleases
EP2640849B1 (en) 2010-11-16 2016-04-06 Nabsys 2.0 LLC Methods for sequencing a biomolecule by detecting relative positions of hybridized probes
WO2012109574A2 (en) 2011-02-11 2012-08-16 Nabsys, Inc. Assay methods using dna binding proteins
US9914966B1 (en) 2012-12-20 2018-03-13 Nabsys 2.0 Llc Apparatus and methods for analysis of biomolecules using high frequency alternating current excitation
EP2956550B1 (en) 2013-01-18 2020-04-08 Nabsys 2.0 LLC Enhanced probe binding
EP4055159A4 (en) * 2019-11-06 2024-04-17 Adaptive Biotechnologies Corp Synthetic strands for nucleic acid sequencing and related methods and systems
WO2021216627A1 (en) * 2020-04-21 2021-10-28 Roche Sequencing Solutions, Inc. High-throughput nucleic acid sequencing with single-molecule sensor arrays

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1996017957A1 (en) * 1994-12-09 1996-06-13 Hyseq, Inc. Methods and apparatus for dna sequencing and dna identification

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1996017957A1 (en) * 1994-12-09 1996-06-13 Hyseq, Inc. Methods and apparatus for dna sequencing and dna identification

Non-Patent Citations (9)

* Cited by examiner, † Cited by third party
Title
A.M. FRIEZE ET AL: "Optimal Reconstruction of a Sequence from its Probes", JOURNAL OF COMPUTATIONAL BIOLOGY, 11 August 1999 (1999-08-11), XP002138287 *
B. HUDSON: "An Experimental Study of SBH with Gapped Probes", TECHNICAL REPORT CS-99-07, DEPT. OF COMPUTER SCIENCE, BROWN UNIVERSITY, April 1999 (1999-04-01), Rhode Island, USA, XP002138288 *
CHETVERIN AND KRAMER: "OLIGONUCLEOTIDE ARRAYS:NEW CONCEPTS AND POSSIBILITIES", BIO/TECHNOLOGY,US,NATURE PUBLISHING CO. NEW YORK, vol. 12, 1 November 1994 (1994-11-01), pages 1093 - 1099, XP002080897, ISSN: 0733-222X *
F.P. PREPARATA ET AL: "On the Power of Universal Bases in Sequencing by Hybridization", THIRD ANNUAL INTERNATIONAL CONFERENCE ON COMPUTATIONAL MOLECULAR BIOLOGY, 11 April 1999 (1999-04-11) - 14 April 1999 (1999-04-14), Lyon, France, pages 295 - 301, XP002138286 *
LOAKES D ET AL: "3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR", NUCLEIC ACIDS RESEARCH,GB,OXFORD UNIVERSITY PRESS, SURREY, vol. 23, no. 13, 1995, pages 2361 - 2366-2366, XP002109690, ISSN: 0305-1048 *
NICHOLS R ET AL: "A UNIVERSAL NUCLEOSIDE FOR USE AT AMBIGOUS SITES IN DNA PRIMERS", NATURE,GB,MACMILLAN JOURNALS LTD. LONDON, vol. 369, no. 6480, 9 June 1994 (1994-06-09), pages 492 - 493, XP000560346, ISSN: 0028-0836 *
PEVZNER P A ET AL: "IMPROVED CHIPS FOR SEQUENCING BY HYBRIDIZATION", JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,US,ADENINE PRESS, NEW YORK, NY, vol. 9, no. 2, 1 October 1991 (1991-10-01), pages 399 - 410, XP000602036, ISSN: 0739-1102 *
PEVZNER P A: "1-TUPLE DNA SEQUENCING: COMPUTER ANALYSIS", JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,US,ADENINE PRESS, NEW YORK, NY, vol. 7, no. 1, 1 August 1989 (1989-08-01), pages 63 - 73, XP000602038, ISSN: 0739-1102 *
R. ARRATIA AND G. REINERT: "Poisson Process Approximation for Repeats in One Sequence and Its Application to Sequencing by Hybridization", PROCEEDINGS: COMBINATORIAL PATTERN MATCHING, 7TH ANNUAL SYMPOSIUM CPM 96, 10 June 1996 (1996-06-10) - 12 June 1996 (1996-06-12), Laguna Beach, USA, pages 209 - 219, XP000910364 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8882980B2 (en) 2008-09-03 2014-11-11 Nabsys, Inc. Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels

Also Published As

Publication number Publication date
ATE315106T1 (en) 2006-02-15
AU1204600A (en) 2000-05-01
DE69929365D1 (en) 2006-03-30
EP1121472A2 (en) 2001-08-08
WO2000022171A2 (en) 2000-04-20
EP1121472B1 (en) 2006-01-04
DE69929365T2 (en) 2006-09-21

Similar Documents

Publication Publication Date Title
WO2000022171A3 (en) Systems and methods for sequencing by hybridization
BR9407712A (en) Methods and compositions for effective nucleic acid sequencing
CA2370976A1 (en) Detection of nucleic acid reactions on bead arrays
CA2133956A1 (en) Dna sequencing method
AU2496900A (en) Enhanced sequencing by hybridization using pools of probes
AU3199699A (en) Modified nucleotides and methods useful for nucleic acid sequencing
ATE356221T1 (en) SEQUENCING BY LIGATION OF ENCODED ADAPTERS
WO2000040755A3 (en) Method for accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing
EP1961826A3 (en) A method for direct nucleic acid sequencing
WO2000024937A3 (en) Parallel methods for genomic analysis
ATE238434T1 (en) A CASCADED DUPLICATION REACTION OF NUCLEIC ACIDS
ATE269908T1 (en) METHOD FOR SEQUENCING NUCLEIC ACIDS
WO2003089906A3 (en) Functionalized nanoparticles and methods of use
WO2001088089A8 (en) Single copy genomic hybridization probes and method of generating same
ES2146309T3 (en) NUCLEIC ACID SEQUENCING.
WO1998054313A3 (en) Dna methyltransferase genomic sequences and antisense oligonucleotides
WO2004044164A3 (en) Method for identifying risk of melanoma and treatments thereof
DE69917636D1 (en) Polymerasesignalversuch
CA2142156A1 (en) Nucleic Acid Sequences Specific for Mycobacterium Kansasii
WO2001063543A8 (en) Method and system for the assembly of a whole genome using a shot-gun data set
WO1998013527A3 (en) Compositions and methods for enhancing hybridization specificity
ATE211180T1 (en) METHOD FOR THE NON-RADIOACTIVE DETECTION OF MEMBRANE-BONDED NUCLEIC ACIDS AND TEST KIT
WO1989002440A3 (en) Y-specific dna hybridization probes and uses therefor
AU2038500A (en) Method for the detection of specific nucleic acid sequences by polymerase nucleotide incorporation
WO2001007664A3 (en) Genome analysis

Legal Events

Date Code Title Description
ENP Entry into the national phase

Ref country code: AU

Ref document number: 2000 12046

Kind code of ref document: A

Format of ref document f/p: F

AK Designated states

Kind code of ref document: A2

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW SD SL SZ TZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

WWE Wipo information: entry into national phase

Ref document number: 1999970428

Country of ref document: EP

WWP Wipo information: published in national office

Ref document number: 1999970428

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWG Wipo information: grant in national office

Ref document number: 1999970428

Country of ref document: EP