WO2001026029A2 - Procede et systeme permettant de fournir sur un reseau informatique des renseignements cliniques sur le genotype - Google Patents

Procede et systeme permettant de fournir sur un reseau informatique des renseignements cliniques sur le genotype Download PDF

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Publication number
WO2001026029A2
WO2001026029A2 PCT/US2000/040999 US0040999W WO0126029A2 WO 2001026029 A2 WO2001026029 A2 WO 2001026029A2 US 0040999 W US0040999 W US 0040999W WO 0126029 A2 WO0126029 A2 WO 0126029A2
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WO
WIPO (PCT)
Prior art keywords
snp
clinical profile
profile information
genotype clinical
computer
Prior art date
Application number
PCT/US2000/040999
Other languages
English (en)
Other versions
WO2001026029A3 (fr
Inventor
Michael Boyce-Jacino
Russell T. Granzow
Dale R. Pfost
Donald R. Marvin
Original Assignee
Orchid Biosciences, Inc.
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 Orchid Biosciences, Inc. filed Critical Orchid Biosciences, Inc.
Priority to AU13672/01A priority Critical patent/AU1367201A/en
Publication of WO2001026029A2 publication Critical patent/WO2001026029A2/fr
Publication of WO2001026029A3 publication Critical patent/WO2001026029A3/fr

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Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06Q—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL OR SUPERVISORY PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL OR SUPERVISORY PURPOSES, NOT OTHERWISE PROVIDED FOR
    • G06Q10/00—Administration; Management
    • G06Q10/10—Office automation; Time management
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/20—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for electronic clinical trials or questionnaires

Definitions

  • the present invention broadly concerns a method and system for providing personal genotype clinical profile information, and more particularly concerns a method and system for securely providing such information to individuals over the Internet.
  • Biomedical research is providing new insights into how a person's specific genetic make ⁇
  • HGP Human Genome Project
  • polymorphisms can effect a person's susceptibility to disease and/or response to drugs.
  • Single nucleotide differences in DNA known as “single nucleotide polymorphisms” (“SNPs”), are known as single nucleotide polymorphisms.
  • Pharmacogenetic effects on a person include various undesirable reactions to administered drugs. As a consequence, it is common practice for medical practitioners to question patients as to
  • ADR is responsible for up to 500,000 hospitalizations and 50,000 deaths per year. Yet, many others
  • ADR represents a leading cause of hospitalization and death.
  • New drugs can take from ten to fifteen years to reach the market and can
  • Genotypes and Haplotypes are the lexicon of correlations between patterns of genetic variability and the medical condition and treatment response of
  • test results may be used to discriminate against the individual. For example, if test results are such that the
  • Numerous types of medical data collection, storage, and display systems are available for use by individuals seeking medical information regarding their health. Examples include the
  • a client takes a biological sample of himself or herself at a location of their choice, sends the biological sample to a laboratory for single nucleotide polymorphisms (SNP) analysis, and securely accesses the results of the analysis over a computer network, such as the Internet.
  • SNP single nucleotide polymorphisms
  • the present invention satisfies the above described needs by providing a secure network- accessible personal genotype clinical profile system and method.
  • a client submits a biological sample containing the client's DNA to a laboratory, and thereafter is provided secure access over a computer network, such as the
  • the client extracts a biological sample which contains the client's DNA (some e.gs. blood, hair,
  • SNP single nucleotide polymorphism
  • the genotype clinical profile information for the client is securely stored in a database that is accessible over a computer network such as the Internet.
  • the client is provided with a user name and a password to permit only the client to access his or her genotype clinical profile information.
  • the client can permit others, such as a physician, to access all or part of the client's genotype clinical profile information over the computer network.
  • the biological sample is sent to a laboratory where DNA is extracted from the sample and the DNA is analyzed for single nucleotide polymorphism (SNP) data.
  • SNP data is entered into a computer system where it is analyzed for genotype clinical profile information, such as an adverse response to certain drugs or a predisposition to certain diseases.
  • genotype clinical profile information such as an adverse response to certain drugs or a predisposition to certain diseases.
  • the results of the analysis are securely stored in a database and are made available to the client over a computer network, such as the Internet.
  • Internet is used in the preferred embodiment, the invention is applicable to any computer network
  • topology where secure transactions between interconnected computers are provided.
  • the client remotely accesses a server computer system that is coupled to the database.
  • the client can access his or her genotype clinical profile information securely stored in the database.
  • FIG. 1 is a block diagram of a preferred personal genotype clinical profile system.
  • FIG. 2 is a flowchart outlining the preferred method for accessing the system.
  • FIG. 3 illustrates a preferred home Web page.
  • FIG. 4 illustrates a preferred user name and password Web page.
  • FIG. 5 is a flowchart outlining the preferred method for generating and receiving broadly grouped genotype clinical information.
  • FIGS. 6-7 are flowcharts outlining the preferred method for generating and receiving personal
  • a preferred embodiment of the present invention is directed to a secure network- accessible personal genotype clinical profile system and method.
  • the system and method is configured such that a client can submit a biological sample which contains his or her DNA to a
  • SNP single nucleotide polymorphism
  • the personal genotype clinical profile system includes: a server computer system 2, a plurality of client computer systems 4, a database server system 6, a SNP
  • the Internet 14 a laboratory 16
  • an optical detector 18 an e-mail server system 20.
  • the Internet 14 is a global network of interrelated computer networks allowing interchange of information between network accessible computers.
  • Each client computer system is a global network of interrelated computer networks allowing interchange of information between network accessible computers.
  • Each of the client computer systems 4, designated as Client 1, Client 2, ... Client n, in FIG. 1, is interconnected to the Internet 14 by various means known in the art, such as a dial-up modem connection to an Internet Service Provider (ISP) or a direct connection to a network that ISP is a service provider.
  • ISP Internet Service Provider
  • the client computer system 4 is a computer (an e.g.
  • Typical browser interfaces include a window frame which encompasses a control region and a viewing region.
  • the control region typically includes page controls which allow users to navigate between various pages of data
  • the viewing region typically includes a viewing area
  • the server computer system 2 is also connected to the Internet 14 as shown in FIG. 1 , and
  • the server computer system 2 includes computer hardware and software to serve up Web pages from the
  • the server computer system 2 manages the communications protocols and houses the pages and related software required to create the Web site on the Internet 14.
  • the server computer system 2 also provides data and software that is accessible to the various clients which
  • the server computer system 2 provides services such as searching for information and sending it back to the client computer system 4, such as when the database server system 6 or the general information database server system 12 at
  • the Web site is queried or delivering Web pages.
  • the browser on the client computer system 4 sends the server computer system 2 a request for a specific Web page.
  • the server computer system 2 processes that request and sends an answer back to the browser, most often in
  • server computer system 2 the form of a Web page.
  • the construction and operation of the server computer system 2 will be well known to those skilled in the art. In particular, the server computer system 2 will be
  • the server computer system 2 runs a Web server program that allows Web pages (in HTML format)
  • the server computer system 2 also executes other programs and
  • gateway programs used to provide access from the Web to the database server system 6 and the general information database server 12.
  • CGI Common Gateway Interface
  • CGI scripts are used in large part to produce from non-Hypertext Transfer Protocol (HTTP) objects, HTTP objects that a Web client can render, and also produce from
  • HTTP Hypertext Transfer Protocol
  • HTTP objects non-HTTP objects to be passed on to another program or separate server, such as the database server system 6 and the general information database server 12.
  • Another program or separate server such as the database server system 6 and the general information database server 12.
  • the server computer system 2 passes requests to run CGI scripts to the CGI applications. These scripts run external programs, such as database lookup or interactive forms processing.
  • the server computer system 2 sends the script to the application via
  • the client fills out a form on a Web page to register to use the Web site and then later receives a notification of registration.
  • the CGI script takes the information the client filled in on the form and stores the information in the database server system 6, and then sends the notification of the registration to the client's browser.
  • the database server system 6 includes computer hardware and software for
  • the general information database server system 12 includes
  • the preferred e-mail server system 20 is coupled to the server computer system 2 via a network and can receive and deliver e-mail messages addressed to users through the Internet.
  • the e-mail server system 20 includes computer hardware and software capable of receiving and delivering e-mail messages over a computer network.
  • the e-mail server system 20 communicates the e-mail to other servers on the Internet using the simple mail transfer protocol (SMTP).
  • SMTP simple mail transfer protocol
  • the e-mail server 20 is structured and functions following a standard format generally known and available within the art.
  • the preferred system is the Rivest - Shamir - Adelman algorithm (RSA)
  • the laboratory 16 is preferably structured to receive a biological sample kit from the
  • SNP single nucleotide polymorphism
  • the laboratory 16 also includes the SNP computer system 8, the optical detector 18, and the SNP database system 10, which stores genotype clinical information relevant to patient healthcare.
  • the SNP computer system 8 includes computer hardware and software for controlling and communicating with the optical detector 18, and to control and communicate with
  • the optical detector 18 produces SNP data for use in the SNP computer system.
  • the SNP database system 10 includes computer
  • the SNP computer system 8 includes a correlation algorithm that analyzes the SNP data.
  • the correlation algorithm searches through the data stored in the SNP database system 10 for genotype clinical profile information relevant to the client's SNP data.
  • the relevant genotype clinical profile information is relevant to the client's SNP data.
  • the detection of the SNP data and the correlation of the SNP data to relevant genotype clinical profile information can be accomplished by various means known within the art. An example of one such means is discussed in U.S. Pat. No. 5,762,876 to
  • the client can retrieve his or her genotype clinical profile information by accessing the server computer system 2, which is coupled to the
  • the database server system 6 stores the genotype clinical profile
  • the system preferably executes several distinct modules or
  • processes include a client sending a biological sample to a laboratory for SNP analysis and providing access to the results of the analysis over the Internet 14. The steps associated with these processes are described in connection with FIGS. 2-7.
  • FIGS. 2-7 show flow charts that illustrate a preferred embodiment of the invention.
  • a client using the client computer system 4 and a commercially
  • the client accesses the Web site that hosts the personal genotype clinical profile service (step 50).
  • the client achieves this by entering a uniform resource locator (URL) associated with the IP address of the server computer 2.
  • URL uniform resource locator
  • the client can be an individual seeking genotype clinical profile information; a
  • the server receiving genotype clinical information for use in medical research.
  • the server receiving genotype clinical information for use in medical research.
  • the server receiving genotype clinical information for use in medical research.
  • step 54 Such options can include subscribing to the personal genotype clinical profile service or accessing general genotype clinical information.
  • a user name and password window is displayed on the client's browser, as illustrated in FIG. 4. If the client has previously used the
  • the client can simply enter his or her user name and password, that were selected during the registration process, enter them into the Web page fields, and proceed to access the Web site, step 56 of FIG. 2. If the client has not previously
  • the client can return to the home Web page and click an embedded Web page control associated with registering with the Web site.
  • the client must register with the Web site before he or she can access the Web site features.
  • To register with the Web site the client opens an account resident in the server computer system 2 by clicking on an
  • a typical Web page screen for opening an account includes fields for client name, postal address, e- mail address, and user name and password.
  • the client selects a user name and password and the server computer system 2 processes the information following a standard format generally known
  • Nonpayment services can be accessed by clicking an associated Web page control and may include access to genotype clinical information, journals, and/or other types of data and, publications, and services (step 60).
  • a client interested in receiving this healthcare information may answer a questionnaire relating to the client's health information, such as medical
  • the questionnaire is displayed in a Web page where the client can insert information into Web page fields and send the information to the server computer system 2, by following a standard format and process generally known and available within the art.
  • the client can click a Web page control associated with requesting the health information in the questionnaire to be correlated to genotype clinical profile information that is stored in the SNP database system 10 (step 64).
  • the health information is entered into the SNP computer system 8,
  • step 66 The algorithm is stored, as a report, in the database server system 6, under the appropriate client user name (step 66).
  • the client can later retrieve the relevant genotype clinical profile information,
  • step 68 by accessing the server computer system 2 using his or her client computer system 4 and Web browser (step 68).
  • the client is able to search through the general
  • the clients are electronically linked to the medical information relating to variability in human conditions, so that
  • the information can be collected, processed, stored, and transmitted to the client or a third party upon request.
  • the client can also be linked, via a Web page, to sites with a more detailed description of various medical conditions and recent discoveries to treatment and prognosis.
  • the client can select services requiring payment, which can be accessed after filling out Web page fields requiring credit card information, such as credit card name, name on the credit card, credit card number and expiration date (step 70).
  • credit card information such as credit card name, name on the credit card, credit card number and expiration date (step 70).
  • the client can be subscribing to the personal genotype clinical profile service.
  • this service requires the client to submit a
  • the client can elect to create a personal genotype clinical profile of himself or herself, by clicking an associated Web page control (step 72). Additionally, the client fills in Web page fields requiring the client to provide a second password that can be used by the client to access the client's personal genotype clinical profile information that can be
  • the second password is created following
  • the client can then request that a
  • biological sampling kit be sent to the client's postal address, which was provided when the client
  • the client may purchase the kit at a pharmacy or other retail outlet.
  • the client can also fill out Web page fields requiring his or her credit card information, such as credit card name, name on the credit card, credit card number, and credit card expiration date, so that the client may be charged a fee for the
  • the biological sampling kit contains a specimen container, such as a test card, a test tube, a lance, or a swab, for containing a biological sample or specimen for transportation to the laboratory 14.
  • the biological sample can be anything containing DNA, such as blood, hair, sputum, saliva, stool, urine, semen, or saliva.
  • the biological sample can be from a mammal, such
  • the sampling kit preferably includes a specimen test card that contains a space for the client to print his or her user name on the card, a space for depositing a drop of blood, and a lance to safely obtain blood from the client.
  • the client deposits a sample of blood on the test card and sends (an e.g. by mail) the
  • the client's DNA is extracted from the blood sample that was deposited on the specimen test card (step 80).
  • the client's DNA is then analyzed to determine single nucleotide polymorphism (SNP) data (step 78).
  • the SNP data is entered into the SNP computer system 8, where it is applied to a correlation algorithm that searches the SNP database system 10 for genotype clinical profile information
  • the relevant genotype clinical profile information accumulated
  • Such information can be an adverse response to certain drugs, lack of efficacy, and a predisposition to certain diseases.
  • the client's genotype clinical profile information is stored as a report in the SNP database system 10 that is accessible over the Internet 12 through
  • the client can retrieve his or her genotype clinical profile information by accessing the Web site.
  • the client logs on to the site by submitting his or her user name and password to verify that the client has registered with the Web site and is entitled to use the Web site features (step 86).
  • a Web page control associated with accessing this information (step 88). After clicking the Web page control, but before the requested Web page is displayed, a Web page presents the client with a user name field and a second password field, which the client must accurately fill out to gain access to his or her personal genotype clinical profile information file
  • step 90 If the user name and password is correct then the Web page containing the client's personal genotype information is displayed on the client's browser (step 92). This information is
  • the reports are preferably in a form that conform to industry standards of the Clinical Reference
  • the client also has the option of forwarding his or her general or personal genotype clinical profile information or subset of this information to third parties, such as physicians, healthcare providers, or family members, who have access to the Internet.
  • third parties such as physicians, healthcare providers, or family members, who have access to the Internet.
  • the client can select and remove text from a Web page displaying such information, using standard controls available on the client's browser.
  • the client can then click a Web page control associated with forwarding information to a third party, which results in a standard e-mail service being displayed on the browser.
  • the e-mail server 20 is structured and functions following a standard format generally known and available within the art. Using standard browser controls, the client inserts the selected text into an e-mail text window and enters an e-mail address to which the client would
  • the client clicks a button associated with sending the e-mail (step 94).

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Abstract

L'invention concerne un système et un procédé permettant de fournir à des personnes, de façon sûre par le biais d'Internet, des renseignements sur leur profil clinique. Lesdits système et procédé permettent d'extraire un échantillon biologique d'une personne, d'extraire dudit échantillon l'acide désoxyribonucléique (ADN), d'analyser cet ADN pour déterminer des données de polymorphisme nucléotidique simple (SNP), d'analyser les données SNP, et de donner un accès sécurisé sur l'Internet aux résultats de l'analyse.
PCT/US2000/040999 1999-10-01 2000-09-26 Procede et systeme permettant de fournir sur un reseau informatique des renseignements cliniques sur le genotype WO2001026029A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU13672/01A AU1367201A (en) 1999-10-01 2000-09-26 Method and system for providing genotype clinical information over a computer network

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US41114799A 1999-10-01 1999-10-01
US09/411,147 1999-10-01

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WO2001026029A2 true WO2001026029A2 (fr) 2001-04-12
WO2001026029A3 WO2001026029A3 (fr) 2002-03-07

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TW (1) TW473684B (fr)
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EP1260927A2 (fr) * 2001-05-25 2002-11-27 Hitachi, Ltd. Système de traitement d'information utilisant des informations relatives à des séquences nucléotidiques
WO2004111909A1 (fr) * 2003-06-12 2004-12-23 Hitachi, Ltd. Systeme de traitement de l'information reposant sur l'emploi d'informations en rapport avec des sequences de base
EP1553512A1 (fr) * 2002-07-15 2005-07-13 Hitachi Ltd. Systeme de traitement d'informations utilisant des informations relatives a des sequences de bases
EP1569154A1 (fr) * 2002-11-20 2005-08-31 Hitachi, Ltd. Systeme de traitement de donnees utilisant des donnees relatives a des sequences de base
EP1574982A1 (fr) * 2002-11-18 2005-09-14 Hitachi Ltd. Systeme de traitement de l'information utilisant une information se rapportant a une sequence de base
JP2007220141A (ja) * 2007-05-01 2007-08-30 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
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JP2010277601A (ja) * 2010-07-26 2010-12-09 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
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US9092391B2 (en) 2006-11-30 2015-07-28 Navigenics, Inc. Genetic analysis systems and methods
EP2636003B1 (fr) * 2010-11-01 2019-08-14 Koninklijke Philips N.V. Test de diagnostic in vitro comprenant le courtage automatisé de paiements de royalties pour des tests propriétaires

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TW201516725A (zh) * 2013-10-18 2015-05-01 Tci Gene Inc 單一核苷酸多型性疾病發生率預測系統

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US8103368B2 (en) 2001-05-25 2012-01-24 Hitachi, Ltd. Information processing system using nucleotide sequence-related information
JP2007157168A (ja) * 2001-05-25 2007-06-21 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
KR100832077B1 (ko) * 2001-05-25 2008-05-27 가부시끼가이샤 히다치 세이사꾸쇼 염기배열관련정보를 사용한 정보처리시스템
EP1260927A2 (fr) * 2001-05-25 2002-11-27 Hitachi, Ltd. Système de traitement d'information utilisant des informations relatives à des séquences nucléotidiques
US8571810B2 (en) 2001-05-25 2013-10-29 Hitachi, Ltd. Information processing system using nucleotide sequence-related information
JP2012234558A (ja) * 2001-05-25 2012-11-29 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
JP2004152316A (ja) * 2001-05-25 2004-05-27 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
US7912650B2 (en) 2001-05-25 2011-03-22 Hitachi, Ltd. Information processing system using nucleotide sequence-related information
CN102637245A (zh) * 2001-05-25 2012-08-15 株式会社日立制作所 使用核苷酸序列相关信息的信息处理系统
JP2010123132A (ja) * 2001-05-25 2010-06-03 Hitachi Ltd 塩基配列関連情報を用いた情報処理システム
EP1260927A3 (fr) * 2001-05-25 2006-06-21 Hitachi, Ltd. Système de traitement d'information utilisant des informations relatives à des séquences nucléotidiques
US7945389B2 (en) 2001-05-25 2011-05-17 Hitachi, Ltd. Information processing system using nucleotide sequence-related information
US8126655B2 (en) 2001-11-22 2012-02-28 Hitachi, Ltd. Information processing system using information on base sequence
US8639451B2 (en) 2001-11-22 2014-01-28 Hitachi, Ltd. Information processing system using nucleotide sequence-related information
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