WO2003069534A2 - Analyse et gestion de donnees et sequences moleculaires - Google Patents

Analyse et gestion de donnees et sequences moleculaires Download PDF

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Publication number
WO2003069534A2
WO2003069534A2 PCT/EP2003/001586 EP0301586W WO03069534A2 WO 2003069534 A2 WO2003069534 A2 WO 2003069534A2 EP 0301586 W EP0301586 W EP 0301586W WO 03069534 A2 WO03069534 A2 WO 03069534A2
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WIPO (PCT)
Prior art keywords
computer system
data set
user
central computer
database
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PCT/EP2003/001586
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English (en)
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WO2003069534A3 (fr
Inventor
Stefan Emler
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Smartgene Gmbh
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Application filed by Smartgene Gmbh filed Critical Smartgene Gmbh
Priority to EP03739496A priority Critical patent/EP1479027A2/fr
Priority to DE20316651U priority patent/DE20316651U1/de
Priority to AU2003210293A priority patent/AU2003210293A1/en
Publication of WO2003069534A2 publication Critical patent/WO2003069534A2/fr
Publication of WO2003069534A3 publication Critical patent/WO2003069534A3/fr

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    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Definitions

  • the present invention relates to the field of analysis and management of molecular data and DNA/RNA/protein sequences.
  • HIV HIV
  • This treatment is in general started during early stages of the infection, in order to prevent or reverse immunodeficiency caused by HIV.
  • a "cocktail" of several drugs with different active components is prescribed. The drugs are administered every day and the overall duration of the treatment depends on its efficiency and has yet not been defined. Parameters to monitor the treatment are: the general status of the patient, the viral load in blood, the CD4 cell count and - for reasons of side-effects, liver and other parameters.
  • anti-HIV treatment can be very successful, the virus by itself has a great ability to mutate and can convert into a drug-resistant genotype by simply changing its target genes for the respective drug.
  • the Reverse Transcriptase or the Protease are targeted by drugs, however new drugs for other targets are now appearing on the market. Mutations of the target gene sequences can occur under treatment pressure and would then render the virus isolate resistant to the drug used. As mutation of HIV into a resistant variant may be followed by an increase of viral replication and therefore by a decrease of the patients immune defense and possibly lead to a fatal outcome, doctors carefully monitor treatment with the parameters mentioned above, plus with the viral resistance profile obtained by genotyping.
  • HIV genotyping is becoming an increasingly important tool in HIV patient care and therefore physicians all over the world order it as a routine test, performed by experienced hospital and private- owned labs. Handling of genotyping data however is quite cumbersome for the laboratory as for the connected physicians, they normally lack of an adequate IT infrastructure for sequence management and handling of complex data and analyses.
  • the object of the present invention is to provide solutions enhancing analysis of molecular data and sequences.
  • the present invention provides an environment according to claim 1 and a method according to claim 12.
  • Fig. 1 illustrates a functional arrangement of the system according to the present invention
  • Figs. 2 to 19 illustrate exemplary graphical user interfaces of the environment according to the present invention.
  • HIV genotyping and resistance analysis In the following desciption of preferred embodiments, reference is made to HIV genotyping and resistance analysis. It has to be noted that these embodiments, in particular software features, hardware features, related configurations and implemetations, shown grapgical user interfaces, presented sequences, mutations, targets and molucular structures are only of illustrative purpose, but are not intented to limit the present invention in any way. Further, as illustrative example, reference is made to the Integrated Database Network System IDNSTM for HIV genotyping without intending any limitation of the present invention.
  • IDNSTM Integrated Database Network System
  • IDNSTM the Integrated Database Network System provides the following features:
  • the IDNS is a service for data-management and data-analysis provided through the Web. Its backbone consists of three basic modules: a server based SQL database, a user-management module and an application-defining module. Through these three modules,the IDNS can provide an application (disease)-specific platform to any user worldwide; the platform can be specifically adapted to the customer requirements and passwords protect the access and retrict it to the customers data (user-management). Via flags, set on data-sets, the IDNS can enable customers to network together and enables them to share selected data and communicate online.
  • the IDNS is an ideal tool for multi-center studies, data gathering, long-distance collaboration between research centers, while providing each participant with the specific tools and data formats required.
  • the IDNS also provides with reference databases derived from proprietary or public datasets.
  • the Integrated Database Network System is a database service with a web- based user interface. It is accessed through the Internet via personalized passwords. The transmission of the login and of the password is encrypted and passwords can be changed regularly. Login, access time, duration, actions and - if required - the IP address of the computer where the access came from, are all recorded for a desired or given period of time, e.g. up to 1 year.
  • a user-specific login and a personal password permit direct access to all data- platforms of the IDNSTM-system for which the user has entitled access authorization.
  • the personal password delivers maximum security by utilizing encryption technology. This password is never to be shared. Standard license agreement can in- clude,e.g., up to three users with personal passwords and can be expanded to accommodate more users.
  • the IDNSTM-system registers every access made by a user.
  • the users executed activities, modifications or analysis made during the session are recorded and stored for 1 year.
  • the access computer can be retraced and IP addresses of servers or access computers can be recorded as well.
  • the access to the IDNSTM can be limited to certain computers, if the user requires higher standards of security.
  • the IDNSTM secured access allows in the aftermath to generate a complete documentation of the steps accomplished in order to obtain a result and indispensable for quality management or when submitting study results obtained with IDNSTM to supervising authorities, such as the FDA, where a record of progress is required.
  • IDNSTM- system Besides security, personal passwords in the IDNSTM- system are also intended to grant access authorization that is custom fit specifically to the user's role and to his level of expertise.
  • a lab technician for example, would be allowed to add and analyze sequences, but could not be enabled to modify or delete sequences in order to avoid errors.
  • An epidemiologist would be entitled to analyze existing data statistically, but could not modify them.
  • the head of the project and other authorized personnel are able to add, modify and delete entries without restriction. Levels of access to certain fields can be adapted to fit specific needs of the research project and of the staff involved.
  • IDNSTM permits to grant access to shared study- data for outside collaborators, while access to other non-shared lab-data is restricted to entitled inside lab staff.
  • Access to the IDNSTM over the Internet is guaranteed 24 hours 7 days a week and users can access it easily and conveniently from any computer that is connected to the Internet. It is moreover possible to work in an institute at several computers simultaneously, thus avoiding waiting lists for analyses to be accomplished by different persons. This creates a more efficient means of acquiring data in a timely manner. Accesses are not limited in numbers or duration; this enables users to manage their data in a convenient manner without restriction and render the IDNSTM - system particularly convenient and cost-efficient.
  • IDNSTM After a given number of failed consecutive login attempts (e.g. three failed consecutive login attempts), IDNSTM will automatically block all subsequent logins. The user then has the possibility to reactivate the Login by sending an email to system operator. This function is designed to prevent that an unauthorized user, through multiple tries, accesses the data-platform. 3 IDNS 3.0 USER MANAGER AND APPLICATION MANAGER
  • the IDNS 3.0 User Manager and Application Manager provide the following features:
  • Each user's access to the IDNS database is controlled by the Application Manager and the User Manager.
  • the Application Manager defines which applications a user can access (HIV, Bacteria 16s, Orthopox, etc.) as well as the tools, reference databases and tool parameters relevant to that particular user.
  • the User Manager defines the access rights, datasets (i.e. sample datasets) available, affiliations, and data sharing rights for each user.
  • Fig. 1 The functional arrangement of the User Manager and Application Manager as regards the database and system users and end user computer system accessing the system is illustrated in Fig. 1.
  • the IDNS 3.0 User Manager is a highly secure, web-based system (see figure 1) for managing IDNS 3.0 user rights. Through this tool new IDNS 3.0 databases can be implemented quickly and effectively, as well as modify those already existing, and monitor IDNS 3.0 use. For initial access to the system, a user interacts with the User Manager entrance illustrated in Fig. 2
  • the target menu allows the labelling of the IDNS 3.0 reference databases to be controlled as illustrated by the by User Manager Target Screen shown in Fig. 4. 3.4 Data sets menu
  • the various reference and private data sets are managed via the Data Sets Menu shown in Fig. 5.
  • the data sets can be either private or shared, depending on inter-group collaborations.
  • the Data Set Groups Screen allows the various data sets to be grouped together allowing users to access a group of data sets as illustrated in Fig. 6.
  • IDNS 3.0 platforms, reference wesites, tools and tool parameters are defined via the Applications Screen (see Fig. 7). Also initial settings are included for the definition of the reference and sample data set access.
  • the companies section contains details of the IDNS 3.0 client companies. For disaply towards a user, the system uses the User Manager Companies Screen shown in Fig. 8.
  • Definitions of the IDNS 3.0 individual users are stored in the users section and can be displayed via the User Manager User Screen illustrated in Fig. 9. Details include the user's name, login information, contact information, and the company a user belongs to.
  • the User Manager Activity Log Scree shown in Fig. 10 allows User Manager operatives to monitor IDNS 3.0 use. Each time the IDNS is accessed the relevant details such as the date, user, which application, the IP address of the computer used, etc., are added to the list on the right-hand side of the screen. The activity log can also be searched permitting a more precise display of information, for example, searching by company allows the details relevant to that particular company to be displayed. This is also illustrated in Fig. 10.
  • the entry page or so-called "home-page" of a user platform is the first Web-page which pops up after the login (see Fig. 11). Its design is kept simple in order to render the access to data and data-management functions easy. Only access to databases and functions that have been requested by the user are shown. The page is therefore not overloaded with unnecessary tools and items. Clear separation of reference data and user-owned sample data renders data-management and access to databases easy and reliable.
  • the design and logical structure of IDNSTM Web pages remain similar for different users and applications; this allows users to switch between different IDNSTM applications and platforms without loosing time for adaptation.
  • the platform's top section carries the user's logo and shows his name for the running session (see Fig. 12).
  • the bottom section shows common tools for administrative and communication purposes.
  • the central main menu which allows access to the reference and client databases will be discussed in Chapters 5 and 6.
  • IDNSTM users and laboratory manager can check for overall sequence- and/or sample- entry numbers; these functions allow give an overview of the respective data platform and of the laboratory's activities.
  • Hyperlinks Clicking the "link” button opens a webpage with customized hyperlinks which are directly accessible for the user. This function allows the user to organize and bookmark important websites with hyperlink connectivity. Hyperlinks and make these sites accessible quick and easily. The system operator takes care to update and evaluate those hyperlinks regularly and can integrate new sites on suggestion. Hyperlinks can be adapted and expanded according to platform profile and user needs.
  • This function allows to enter and store email-addresses of all individual users involved in a project, network or study and make their contact information available to all project participants. Through simple clicking on this email-address, the user can contact colleagues outside of its institute and can share problems or experiences.
  • the logout function the user can logoff himself from IDNSTM-platform when finished with his work. If there is no logoff after a longer period without no activity, the system will log-out automatically (the time-out can be defined specifically). This is another layer of database security and should avoid access of unauthorized personnel.
  • the respective logo of the user or his/her institution is displayed together with a hyperlink that directly connects to the respective home page of the institution, if available.
  • the logo of the system operator leads to the its Homepage.
  • the homepage will give you general information and on ongoing or accomplished development of with regard to IDNSTM and will provide you with links to customer service.
  • the homepage carries information on the services provided to the customers and presents new software tools which can be integrated on demand to existing IDNSTM platforms. 5 THE BLUE DATABASE - REFERENCE SEQUENCE DATABASE
  • the reference sequence databank in the IDNSTM the "Blue Database" contains reference sequences to which patient- or sample-sequences can be compared.
  • the NL43 consensus-sequence for HIV is used as a reference sequence as it is validated and updated regularly by different expert panels.
  • the NL43 sequences are updated with regard to the newest literature and highlights the positions susceptible for therapy resistances with blue coloring, in accordance to advice from expert panels.
  • the reference sequences determine the reading-frame and therefore the exact positions of possible mutations of analyzed sample sequences.
  • Other reference sequences representing regional dominant variants can also be added to the reference databank, after expert validation and may then be used for comparison.
  • New reference databases for new targets can be added at a later stage, thus enabling the user to keep his data-management up-to-date with his scientific proceedings.
  • IDNSTM-HIV platforms can vary with regard to specific user requirements and customization; user-specific application platforms show only analysis tools which have been requested by the user for his specific requirements. Below is a description of typical functions.
  • Search mutations will detect and identify mutations of a specific sample sequence, in comparison to the designated reference sequence (see Fig. 13). Any sequence which the user pastes into the "search mutations” field is compared to the reference sequence, already stored in the reference database.
  • This function enables experienced users to enter and store new, additional reference sequences, such as regionally dominant virus sub-types.
  • the RT gene sequence and the Protease gene sequence can be entered as separate sequences or as one stretch, plus the therewith-connected information such as origin and particularity. Entering and assignment of reference sequences is restricted to experts with specific access rights. By default, the international reference sequence "NL43" is accessible in the reference database.
  • authorized experts/users can delete reference sequences.
  • HIV drug target sequences can be entered either in a separate manner (RT and Protease) or as a continuous stretch; here, the separate entry is commented as an example.
  • Other sequence targets can be added such as gp41, pl7...
  • the IDNSTM-HIV platform can handle more than 8 different sequence targets; this renders it flexible for the ongoing evolution in drug resistance monitoring, patient care and for other aspects of clinical HIV research. 1.1.1 "Reference nb'V'Sequence date"
  • a publicly available reference sequence from Genbank, EMBL, or from other public databases comes with its accession number under which the sequence has been published. When a lab-internal reference sequence is entered, this will be the tag given by the laboratory, plus the date of entry registration.
  • Determination and “Last Update” indicate the origin of the reference sequence (e.g. sequence derived from isolate XY West- Africa) and the date of the last update.
  • Source is where the reference sequence entry originates from: e.g. laboratory XY or expert panel/publication/journal.
  • RT sequence of HIV encodes for the gene of the Reverse Transcriptase enzyme in HIV .
  • RT transcribes viral RNA in DNA after the entry of the virus into the cell. The transcription renders the viral genome compatible with the host DNA and permits integration in the host genome.
  • This enzyme is retro-virus- specific and is therefore a preferred target to many anti- viral drugs (RT-inhibitors, nu- cleoside-analogs).
  • the sequence can be pasted along with its associate information into the respective fields and will then be recorded when quitting the site.
  • Protease (PR) sequence of HIV codes for the gene of the HIV protease enzyme. This enzyme cleaves the HIV proteins after their reproduction within the host-cell and thus renders allows assembly of infectious virus particles.
  • Reference databases for all sequence targets can be designed and can integrate published or customer-owned sequences.
  • Regular - automated — updates of reference databases with regard to published data from public databases guarantee an up-to-date quality standard of the sequence analysis procedure and diminish the work-load of the laboratory staff considerably.
  • Customer-owned reference sequences would be an integral part of the respective reference database but will not be shared with other customers, unless the submitting laboratory decides otherwise.
  • the "Red database” is the customer-created sample database.
  • each laboratory has its own databases that are freely accessed by its lab personnel and non-accessible to other IDNSTM users. Upon request, this database or subsets of it (“study database”) can be connected to other laboratories' databases and can be integrated into a "collector" database for multi-center collaborations.
  • the sample database stores the sample-data and patient sequences that are produced in the laboratory and submitted to the IDNSTM.
  • Patient names, patient addresses or other data which may be used to retrieve patients, are not stored in the IDNSTM; for this purpose, a link to the hospital/laboratory internal data-system is created by a common key number.
  • the user is provided with individually adapted and application-optimized functions, designed to analyze the data, the sequences, to organize the database, to export data and to inform other users/collaborators on results etc.
  • the sample database fulfills the function of a data archive and provides the user with parts of this database can be shared with other institutes or laboratories.
  • switch-board central network node
  • mutations of the patient sample can be obtained quickly by comparing the patient sequence to NL43.
  • “Quick search mutations” see Fig. 14
  • the user can search for any sequence of an HIV-isolate with the sample- or patient-number and automatically compare them to the respectively active reference sequence (see reference “Blue Database”).
  • the function "Quick search mutations" separately examines the RT- and Protease- sequence of a sample. This function allows the selected sequence to align with the reference sequence, and any mutations will be identified, as well as any deletions and insertions. These variations will be recorded automatically (optional) or by the user and will be translated respectively to the reading frame in amino acids with the respective amino acid position. This will be displayed on a Clipboard. IUPAC- nucleotide-positions are also recognized and corresponding alternatively-amino acid through "/" separately indicated.
  • the function "Quick search mutations” reduces the once laborious preparation of a sequence to less than 1 minute, in utmost security (recognizes mutation that are al- ready stored, the cursor forgets no mutations and positions that are known for resistances, are blue underlined) and with total flexibility (the user selects relevant mutations). If all mutations are recognized and are itemized correspondingly in a Clipboard, they can be stored directly in the respective sample file; at the same time earlier mutation are deleted and therefore doubling or transmission mistakes avoided. Physicians, lab personnel or nurses, who does not need to possess knowledge in the virus genetics or the molecular biology, can also use the function "Quick search mutations". Therefore the user spectrum is considerably expanded. Common functions found in this section are described below.
  • search sample here represents the patient tag of the hospital of with a network. It also can be used as "Patient ID number”.
  • Another patient ID can also be named laboratory label or study label. All labels can be named and defined (number of positions) according to the customer's requirement. With the "Patient Label", the lab personnel can type in the patient number or unique identifier without revealing patient name and other private data.
  • Patient samples can be sorted by cohort number/sequence date/sample data and also for a certain time period (see above sample date from - to). This enables to retrieve samples specifically and to set samples in relation, e.g. all samples from 1 patient sorted by date.
  • search-sequence is copied by simple copy/paste into the assigned field, furnished with a reference number and then in second compared against the entire sample databank.
  • the sample- sequences that are similar to the search-sequence are itemized and organized according to the degree of similarity and are represented in pair wise alignment.
  • Additional sample sequence serves to input and to storage of new samples and its sequences into the IDNSTM- system (see Fig. 18).
  • New Samples are furnished with a patient number, a laboratory number, and a sample date and sequence date. These parameters can individually be customized and adapted to the laboratory condition. New sequences are copied directly out of the respective sequencing program as a text file and are inserted into the respective window.
  • a further important option is the comparisons of samples to particular studies, which can be freely defined by the user and are implemented by SmartGene on request. Studies create data sub-groups out of assigned inputs of the sample databank, which can be shared again with other laboratories or can be separately managed. This function serves for the compilation of research programs or multi-center studies, without the need for the user to manage data twice. Samples or sequences that are assigned to certain studies will be adapted automatically for all users if the first user who inputted the sequence changes it afterwards.
  • This function permits the user to sort samples and sequences according to certain criteria or to summarize them in groups (see Fig. 19). At the same time, samples can be organized into lists along different criteria, printed out and single samples if necessary can be edited and modified.
  • sample sequences also permits the specific administration of studies as a subgroup of the sample databank. Editing functions, e.g. the modification of samples and sequences can be restricted on certain user-groups; therewith can external users for clinical research purposes also use the databank without jeopardizing the data at the same time.
  • the "Delete sample sequence” function can be used to delete samples-entries and also the associated sequences. This function can be blocked for unauthorized users to prevent unintentional manipulation and deletion of entries.
  • Align sequences is used for the specific comparison of single sequences that are single itemized through the "Align Sequences" - function or in list and then selected through a mouse-click and therewith ready for alignment.
  • the alignment-sequence list can include several lists/pages and single sequences again can be deleted.
  • IDNSTM-server All sample data that is handled on the secured IDNSTM-server is automatically backed up on a second, separate hard-drive. After 12 hours, a safety back-up copy is generated on a secondary server. Monthly and on customer request (optional) a CD-ROM with the customer specific data is produced and sent to the customer. Several other options for increased data protection are available within the IDNSTM system.
  • the IDNSTM system automatically performs back-ups on a second server hard-disc on a different computer. Every 24h, a copy of the complete database system is made to a server within another building, thus avoiding data loss and damage in case of physical destruction of a server. On request, IDNSTM users can get copies of their sample databases on CD-ROM for a minimal fee.
  • the IDNSTM access protection via personalized passwords does not allow one user the general access to all data on the IDNSTM server, but restricts is access privileges to the data he is entitled to see. No person outside the technical staff from the system operator has larger access privileges; physical access to servers is restricted by safe server location in locked compartments and by specific passwords to the server maintenance staff.
  • Firewalls to the Swiss academic network at the EPFL (Eidjust Tech- nische Hochhoff Lausanne/CH) and several firewalls within the the system operator's network prevent unauthorized access to the internal network and its server management capabilities.
  • Sample data stored on IDNSTM servers belong to the client who has deposited it; issues on data-ownership with regard to patients and third-parties are not relevant to the system operator.
  • the system operator can access user data for database maintenance procedures and for internal technical development. SmartGene will not disclose data to third-parties.
  • users can only modify and access their own data; only in case of a data-collection platform in a multi-center set-up, specifically entitled users from the study monitoring team will acquaint access to the complete study subsets.
  • IDNSTM can offer the following solutions:

Abstract

La présente invention porte sur un environnement permettant l'analyse de séquences moléculaires, et comprenant un système informatique central, au moins un système informatique utilisateur terminal, un réseau pour les communications de données entre le système informatique central et le système informatique utilisateur terminal, une base de données associée au système informatique central et comprenant au moins une séquence moléculaire de référence ou ensemble de données. Le système informatique central est conçu pour stocker au moins une séquence d'échantillons ou ensemble de données, communiquée depuis le système informatique utilisateur terminal de la base de données de façon à procéder à une analyse par rapport à au moins une séquence moléculaire de référence ou ensemble de données.
PCT/EP2003/001586 2002-02-15 2003-02-17 Analyse et gestion de donnees et sequences moleculaires WO2003069534A2 (fr)

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EP03739496A EP1479027A2 (fr) 2002-02-15 2003-02-17 Analyse et gestion de donnees et sequences moleculaires
DE20316651U DE20316651U1 (de) 2002-02-15 2003-02-17 Analyse und Verwaltung molekularer Daten und Sequenzen
AU2003210293A AU2003210293A1 (en) 2002-02-15 2003-02-17 Analysis and management of molecular data and sequences

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DE10206406A DE10206406A1 (de) 2002-02-15 2002-02-15 Vorrichtung und Verfahren zur Durchführung und Auswertung genetischer Analysen
DE10206406.7 2002-02-15

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Publication number Priority date Publication date Assignee Title
WO2007053962A1 (fr) * 2005-11-09 2007-05-18 Smartgene Gmbh Procede et systeme informatiques permettant d'identifier des organismes
US20120215724A1 (en) * 2011-02-18 2012-08-23 Bank Of America Corporation Institutional provided data share platform
US8548930B2 (en) 2011-02-18 2013-10-01 Bank Of America Corporation Institutional provided data share platform
US9026991B2 (en) 2011-02-18 2015-05-05 Bank Of America Corporation Customizable financial institution application interface

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DE10206406A1 (de) 2003-11-13
DE20316651U1 (de) 2004-02-12
WO2003069534A3 (fr) 2004-09-10
AU2003210293A1 (en) 2003-09-04
EP1479027A2 (fr) 2004-11-24

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