WO2003006973A1 - System and method for differential protein expression and a diagnostic biomarker discovery system and method using same - Google Patents
System and method for differential protein expression and a diagnostic biomarker discovery system and method using same Download PDFInfo
- Publication number
- WO2003006973A1 WO2003006973A1 PCT/US2002/019813 US0219813W WO03006973A1 WO 2003006973 A1 WO2003006973 A1 WO 2003006973A1 US 0219813 W US0219813 W US 0219813W WO 03006973 A1 WO03006973 A1 WO 03006973A1
- Authority
- WO
- WIPO (PCT)
- Prior art keywords
- protein
- sample
- profile
- specimen
- data
- Prior art date
Links
Classifications
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
-
- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
- Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
- Y10T436/00—Chemistry: analytical and immunological testing
- Y10T436/24—Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
Definitions
- the data output from the mass spectrometry is an array, or spectrum, of peaks with each peak representing a protein or group of proteins present in a given sample.
- the location of any given peak on the x-axis is related to the molecular mass and charge of the protein, while the height of the peak is associated with the relative abundance of the protein ion.
- the spectrum represents a molecular profile of the protein sub-group or fraction of the expressed proteins in a given specimen.
- the subject characteristics are input to the cell protein data processing unit 130 with input unit 140.
- Input unit 140 is suitably a computer that stores subject information.
- ProteinChipTM One of the differences between SELDI and conventional MALDI-TOF is the ProteinChipTM technology for sample application.
- ProteinChips are available with a variety of chemical surfaces, which permits the capture and analysis of whole classes of proteins based on their charge, hydrophobicity, or metal binding capablity.
- the analysis of a biological specimen using just one surface may give information on 40-60 different proteins.
- sample preparation and analysis must be optimized for each ProteinChip surface and for each sample type.
Abstract
Description
Claims
Priority Applications (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP02744533A EP1415141A1 (en) | 2001-07-12 | 2002-07-12 | System and method for differential protein expression and a diagnostic biomarker discovery system and method using same |
CA002453546A CA2453546A1 (en) | 2001-07-12 | 2002-07-12 | System and method for differential protein expression and a diagnostic biomarker discovery system and method using same |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US09/902,786 | 2001-07-12 | ||
US09/902,786 US20030013120A1 (en) | 2001-07-12 | 2001-07-12 | System and method for differential protein expression and a diagnostic biomarker discovery system and method using same |
Publications (1)
Publication Number | Publication Date |
---|---|
WO2003006973A1 true WO2003006973A1 (en) | 2003-01-23 |
Family
ID=25416390
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
PCT/US2002/019813 WO2003006973A1 (en) | 2001-07-12 | 2002-07-12 | System and method for differential protein expression and a diagnostic biomarker discovery system and method using same |
Country Status (4)
Country | Link |
---|---|
US (2) | US20030013120A1 (en) |
EP (1) | EP1415141A1 (en) |
CA (1) | CA2453546A1 (en) |
WO (1) | WO2003006973A1 (en) |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1685259A2 (en) * | 2003-10-23 | 2006-08-02 | University Of Pittsburgh Of The Commonwealth System Of Higher Education | Biomarkers for amyotrophic lateral sclerosis |
US8700335B2 (en) | 2006-05-18 | 2014-04-15 | Caris Mpi, Inc. | System and method for determining individualized medical intervention for a disease state |
US8768629B2 (en) | 2009-02-11 | 2014-07-01 | Caris Mpi, Inc. | Molecular profiling of tumors |
Families Citing this family (34)
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GB9808836D0 (en) * | 1998-04-27 | 1998-06-24 | Amersham Pharm Biotech Uk Ltd | Microfabricated apparatus for cell based assays |
US7261859B2 (en) | 1998-12-30 | 2007-08-28 | Gyros Ab | Microanalysis device |
SE0001790D0 (en) * | 2000-05-12 | 2000-05-12 | Aamic Ab | Hydrophobic barrier |
CA2441206A1 (en) | 2001-03-19 | 2002-09-26 | Gyros Ab | Characterization of reaction variables |
US6919058B2 (en) * | 2001-08-28 | 2005-07-19 | Gyros Ab | Retaining microfluidic microcavity and other microfluidic structures |
EP1490292A1 (en) * | 2002-03-31 | 2004-12-29 | Gyros AB | Efficient mmicrofluidic devices |
EP1614140A4 (en) * | 2003-04-02 | 2008-05-07 | Merck & Co Inc | Mass spectrometry data analysis techniques |
US20040236603A1 (en) * | 2003-05-22 | 2004-11-25 | Biospect, Inc. | System of analyzing complex mixtures of biological and other fluids to identify biological state information |
US7425700B2 (en) * | 2003-05-22 | 2008-09-16 | Stults John T | Systems and methods for discovery and analysis of markers |
JP4717810B2 (en) * | 2003-06-20 | 2011-07-06 | ユニバーシティ オブ フロリダ リサーチ ファウンデーション インコーポレイテッド | Biomarkers for distinguishing between type 1 diabetes and type 2 diabetes |
US20090010819A1 (en) * | 2004-01-17 | 2009-01-08 | Gyros Patent Ab | Versatile flow path |
EP1756578A2 (en) * | 2004-04-20 | 2007-02-28 | Board of Regents, The University of Texas System | Using plasma proteomic pattern for diagnosis, classification, prediction of response to therapy and clinical behavior, stratification of therapy, and monitoring disease in hematologic malignancies |
US20050244973A1 (en) * | 2004-04-29 | 2005-11-03 | Predicant Biosciences, Inc. | Biological patterns for diagnosis and treatment of cancer |
WO2006044946A2 (en) * | 2004-10-20 | 2006-04-27 | Onco Detectors International, Llc | Migration inhibitory factor in serum as a tumor marker for prostate, bladder, breast, ovarian, kidney and lung cancer |
JP5006800B2 (en) * | 2005-01-17 | 2012-08-22 | ユィロス・パテント・アクチボラグ | Method for detecting at least divalent analyte using two affinity reactants |
US8518926B2 (en) * | 2006-04-10 | 2013-08-27 | Knopp Neurosciences, Inc. | Compositions and methods of using (R)-pramipexole |
ES2379117T3 (en) | 2006-05-16 | 2012-04-20 | Knopp Neurosciences, Inc. | Compositions of R (+) and S (-) pramipexole and methods of use thereof |
US8524695B2 (en) * | 2006-12-14 | 2013-09-03 | Knopp Neurosciences, Inc. | Modified release formulations of (6R)-4,5,6,7-tetrahydro-N6-propyl-2,6-benzothiazole-diamine and methods of using the same |
US8519148B2 (en) | 2007-03-14 | 2013-08-27 | Knopp Neurosciences, Inc. | Synthesis of chirally purified substituted benzothiazole diamines |
US20110190356A1 (en) * | 2008-08-19 | 2011-08-04 | Knopp Neurosciences Inc. | Compositions and Methods of Using (R)- Pramipexole |
US20100099135A1 (en) * | 2008-10-22 | 2010-04-22 | Mandy Katz-Jaffe | Methods and assays for assessing the quality of embryos in assisted reproduction technology protocols |
KR101114228B1 (en) | 2009-06-01 | 2012-03-05 | 한국기초과학지원연구원 | Protein identification and their validation method based on the data independent analysis |
KR101135048B1 (en) | 2011-05-19 | 2012-04-13 | 한국기초과학지원연구원 | Protein identification and their validation method based on the data independent analysis |
US9512096B2 (en) | 2011-12-22 | 2016-12-06 | Knopp Biosciences, LLP | Synthesis of amine substituted 4,5,6,7-tetrahydrobenzothiazole compounds |
US9662313B2 (en) | 2013-02-28 | 2017-05-30 | Knopp Biosciences Llc | Compositions and methods for treating amyotrophic lateral sclerosis in responders |
SI3019167T1 (en) | 2013-07-12 | 2021-04-30 | Knopp Biosciences Llc | Treating elevated levels of eosinophils and/or basophils |
US9468630B2 (en) | 2013-07-12 | 2016-10-18 | Knopp Biosciences Llc | Compositions and methods for treating conditions related to increased eosinophils |
EP3038467B1 (en) | 2013-08-13 | 2020-07-29 | Knopp Biosciences LLC | Compositions and methods for treating plasma cell disorders and b-cell prolymphocytic disorders |
DK3033081T3 (en) | 2013-08-13 | 2021-05-31 | Knopp Biosciences Llc | Compositions and methods of treatment of chronic urticaria |
US10274496B2 (en) | 2014-01-17 | 2019-04-30 | University Of Washington | Biomarkers for detecting and monitoring colon cancer |
CN106021988A (en) * | 2016-05-26 | 2016-10-12 | 河南城建学院 | Recognition method of protein complexes |
US10837970B2 (en) | 2017-09-01 | 2020-11-17 | Venn Biosciences Corporation | Identification and use of glycopeptides as biomarkers for diagnosis and treatment monitoring |
MX2022001519A (en) | 2019-08-05 | 2022-04-06 | Seer Inc | Systems and methods for sample preparation, data generation, and protein corona analysis. |
CN112485322B (en) * | 2020-12-01 | 2022-02-11 | 南京医科大学 | Application of seminal plasma extracellular vesicle SLC5A12 protein |
Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
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WO1997005553A1 (en) * | 1995-07-25 | 1997-02-13 | Horus Therapeutics, Inc. | Computer assisted methods for diagnosing diseases |
US5687716A (en) * | 1995-11-15 | 1997-11-18 | Kaufmann; Peter | Selective differentiating diagnostic process based on broad data bases |
Family Cites Families (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5856112A (en) * | 1994-06-16 | 1999-01-05 | Urocor, Inc. | Method for selectively inducing biomarker expression in urologic tumor tissue for diagnosis and treatment thereof |
US6218529B1 (en) * | 1995-07-31 | 2001-04-17 | Urocor, Inc. | Biomarkers and targets for diagnosis, prognosis and management of prostate, breast and bladder cancer |
US6043044A (en) * | 1997-07-15 | 2000-03-28 | Hudson; Perry B. | Macrophage migration inhibitory factor as diagnostic and prognostic marker for metastatic adenocarcinoma |
-
2001
- 2001-07-12 US US09/902,786 patent/US20030013120A1/en not_active Abandoned
-
2002
- 2002-07-12 WO PCT/US2002/019813 patent/WO2003006973A1/en not_active Application Discontinuation
- 2002-07-12 CA CA002453546A patent/CA2453546A1/en not_active Abandoned
- 2002-07-12 EP EP02744533A patent/EP1415141A1/en not_active Withdrawn
-
2003
- 2003-03-31 US US10/402,138 patent/US20040005634A1/en not_active Abandoned
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1997005553A1 (en) * | 1995-07-25 | 1997-02-13 | Horus Therapeutics, Inc. | Computer assisted methods for diagnosing diseases |
US5687716A (en) * | 1995-11-15 | 1997-11-18 | Kaufmann; Peter | Selective differentiating diagnostic process based on broad data bases |
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP1685259A2 (en) * | 2003-10-23 | 2006-08-02 | University Of Pittsburgh Of The Commonwealth System Of Higher Education | Biomarkers for amyotrophic lateral sclerosis |
EP1685259A4 (en) * | 2003-10-23 | 2007-12-12 | Univ Pittsburgh | Biomarkers for amyotrophic lateral sclerosis |
US7858071B2 (en) | 2003-10-23 | 2010-12-28 | University of Pittsburgh—of the Commonwealth System of Higher Education | Biomarkers for amyotrophic lateral sclerosis |
US8202510B2 (en) | 2003-10-23 | 2012-06-19 | University of Pittsburgh—of the Commonwealth System of Higher Education | Biomarkers for amyotrophic lateral sclerosis |
US8700335B2 (en) | 2006-05-18 | 2014-04-15 | Caris Mpi, Inc. | System and method for determining individualized medical intervention for a disease state |
US8768629B2 (en) | 2009-02-11 | 2014-07-01 | Caris Mpi, Inc. | Molecular profiling of tumors |
Also Published As
Publication number | Publication date |
---|---|
EP1415141A1 (en) | 2004-05-06 |
US20040005634A1 (en) | 2004-01-08 |
CA2453546A1 (en) | 2003-01-23 |
US20030013120A1 (en) | 2003-01-16 |
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