WO1999030167A1 - Systeme de gestion de donnees-echantillons - Google Patents

Systeme de gestion de donnees-echantillons Download PDF

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Publication number
WO1999030167A1
WO1999030167A1 PCT/JP1998/005502 JP9805502W WO9930167A1 WO 1999030167 A1 WO1999030167 A1 WO 1999030167A1 JP 9805502 W JP9805502 W JP 9805502W WO 9930167 A1 WO9930167 A1 WO 9930167A1
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WO
WIPO (PCT)
Prior art keywords
sample
data
identification information
stage
input
Prior art date
Application number
PCT/JP1998/005502
Other languages
English (en)
Japanese (ja)
Inventor
Takeshi Nagasu
Yuji Sugita
Tomoko Kashiwabara
Tadahiro Oshida
Masaya Obayashi
Shigemichi Gunji
Original Assignee
Genox Research, 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 Genox Research, Inc. filed Critical Genox Research, Inc.
Publication of WO1999030167A1 publication Critical patent/WO1999030167A1/fr

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/00584—Control arrangements for automatic analysers
    • G01N35/00722—Communications; Identification
    • G01N35/00732—Identification of carriers, materials or components in automatic analysers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00—Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/00584—Control arrangements for automatic analysers
    • G01N35/00722—Communications; Identification
    • G01N35/00732—Identification of carriers, materials or components in automatic analysers
    • G01N2035/00742—Type of codes
    • G01N2035/00752—Type of codes bar codes

Definitions

  • a label in which the name of the sample, the name of the person in charge, etc. are entered is attached. Then, the result of each experiment is written in the experiment notebook by the researcher. Disclosure of the invention
  • the present invention has been made in view of the above-described problems of the related art, and an object of the present invention is to provide a method of easily managing a series of sample data generated at each predetermined stage. To provide an overnight management system. It is another object of the present invention to provide a sample data management system capable of easily managing sample data by effectively utilizing existing resources.
  • the sample data management system issues identification information unique to each sample and associates data of each sample.
  • a sample data management system for managing data of a series of samples generated at predetermined stages, wherein identification information unique to each sample is issued.
  • “every predetermined stage” means each inspection stage or each operation stage. Specifically, for example, when sample Y is generated by manipulating sample X and sample Z is generated by manipulating sample Y, generation of sample X ⁇ generation of experimental sample Y • generation of experimental sample Z 'Indicate each stage of the experiment. Further, “upper sample positioned at a higher level in the predetermined stage” means the original sample from which the sample originated. In the above example, for sample Y, sample X is the upper sample, and for sample Z, sample Y is the upper sample.
  • the downstream stage When the sample (upper sample) is passed from the upstream stage to the downstream stage, the downstream stage, for example, collects a part of the upper sample and performs a predetermined operation. By doing so, a lower sample is generated.
  • the upper sample has already been given unique identification information. For example, a bar code or the like can be used as the identification information.
  • the identification information management means issues identification information to be assigned to the lower sample based on the identification information of the upper sample.
  • FIG. 2 is a block diagram showing a functional configuration of the sample data management system.
  • FIG. 3 is a flowchart showing the menu processing.
  • FIG. 4 is a flowchart showing the ID issuing / label printing process.
  • sample X is generated from the starting materials, and data of sample X is collected.
  • Data DX1 and DX2 such as inspection results and remarks are stored in the specified location of the table TX.
  • the table TX stores unique identification information (hereinafter abbreviated as “ID”) X001 assigned to the sample X and data DX1 and DX2.
  • ID unique identification information
  • the parent ID in the figure indicates the ID of the sample generated at the upstream side of the stage, and the child ID indicates the ID assigned to the sample generated at the stage. In this embodiment, since the starting material located on the upstream side is not assigned an ID, No data is stored in the parent ID column.
  • sample Y is generated from sample X, and data of sample Y is collected.
  • the ID “Y 001” given to the sample Y is generated based on the ID “X 001” of the sample X.
  • the reading of the ID “X001” of the upper sample X is used as a trigger signal to generate a serial number “001”, and by adding the stage identification information “Y” to the serial number “001”, the sample ⁇ Generate ID "Y00 1" to be given to
  • sample ⁇ is generated from sample ⁇ , and the data of sample ⁇ is collected.
  • the ID “ ⁇ 001” assigned to sample ⁇ is generated based on the ID “Y001” of upper sample ⁇ , as in the above case.
  • the collected data DZ 1 and DZ 2 are stored in the table TZ together with the parent ID “Y001” and the child ID “Z 001”.
  • stage SX stage SY—stage SZ corresponds to “predetermined stage”, and one cycle is completed.
  • the management device 1 configured as a personal computer or a workstation includes an ID management unit 2 as “identification information management means” and a data management unit 3 as “data management means”. , A database 4, and an ID storage unit 5. In addition, a display unit 6, a data input unit 7, an ID detection unit 8, and a printing unit 9 are connected to the management device 1.
  • the ID management unit 2 manages issuance of an ID assigned to a sample, and includes an ID determination unit 10 and an ID issuing unit 11 as internal functions.
  • An ID determination unit 10 that can be expressed as identification information determination means determines the consistency of the ID between stages based on the ID of the upper sample. That is, the ID determination unit 10 determines whether or not the detected upper sample ID is the ID provided in the immediately upstream stage. This determination can be made based on the stage identification information included in the ID.
  • the ID issuing unit 11 issues a new ID by incrementing the latest serial number stored in the ID storage unit 5 by 1 and adding the stage identification information of the stage.
  • the data management unit 3 manages various data inputted in relation to the sample.
  • the data management unit 3 includes a registration unit 12 and a search unit 13 as internal functions. Tables TX, ⁇ , and ⁇ are set up for each stage in Data Base 4.
  • the registration unit 12 stores the data inputted in relation to the sample at a predetermined position of each table and registers it.
  • the search unit 13 searches each table in the database 4 based on the input search key.
  • the display unit 6 is configured as, for example, a CRT (Cathode-Ray Tube), a liquid crystal display, or the like.
  • the display unit 6 is configured to display all or a part of a table related to the sample.
  • the data input unit 7 includes, for example, a keyboard switch, a pointing device such as a mouse, and the like, and inputs data, a search key, and the like to the management device 1.
  • the printing unit 9 that can be expressed as an identification medium generating unit is configured as, for example, a barcode printer.
  • the printing unit 9 converts the ID into barcode information and prints it on the label 22.
  • ID “X 001” of sample X is read by ID detector 8. Is notified to the ID management unit 2.
  • the ID discrimination unit 10 confirms that the stage identification information “X” corresponds to the stage SY
  • the ID issuing unit 11 issues an ID “Y001” to be added to the sample Y.
  • the issued ID is printed as barcode information on the label 22 by the printing unit 9 and attached to the container 21 of the sample ⁇ .
  • the experimental data and the like of the sample ⁇ are input to the data management unit 3 via the data input unit 7.
  • the ID “X001” of the upper sample X read by the ID detector 8 and the ID “Y001” of the newly generated sample Y are input to the data management unit 3.
  • the data management unit 3 associates the related data with each ID and stores them in the predetermined table SY.
  • FIG. 3 is a flowchart showing the menu processing.
  • the flowchart in this specification Does not faithfully show the actual operation of the program, but shows an example of the processing flow related to the gist of the invention. Therefore, even if various steps not shown in the drawings are added, the steps fall within the scope of the present invention as long as they are included in the gist of the present invention.
  • step (hereinafter abbreviated as “S”) 1 the display unit 6 displays a menu screen.
  • step (hereinafter abbreviated as “S”)2 when a desired menu is input via the data input unit 7, in S3, which stage is selected is analyzed based on the input information.
  • the process shifts to a process for operating the table TX relating to the stage SX (S4).
  • the stage SY and SZ are selected, the process shifts to a process for operating the tables TY and ⁇ . Yes (S5, S6).
  • ID issuing processing and the like described later with reference to FIGS. 4 to 6 can be performed.
  • a comprehensive menu process may be constructed on the menu process shown in FIG.
  • the comprehensive menu can be configured to select, for example, each process such as ID issue / print process, data input / update process, data search / registration process, and the like.
  • FIG. 4 is a flowchart showing an ID issuing / label printing process executable in each stage.
  • the ID (parent ID) of the upper sample passed from the upstream stage is read by the ID detector 8 (S ll), and it is determined whether or not the parent ID matches the child ID to be issued in the stage. The judgment is made (S12). If there is no consistency between the IDs, an error message is displayed on the display unit 6 (S13).
  • the read parent ID is set in the parent ID column of the table relating to the stage (S14).
  • a new serial number is generated by incrementing the previously issued serial number by 1 (S15), and the stage identification information is added to this serial number to obtain the relevant serial number.
  • This child ID is set in the child ID column of the table (S17).
  • the print button has been operated (S18), and when the print button has been operated, the barcode of the child ID is printed on the label 22 (S19).
  • the printed label 22 is affixed to the container of the sample prepared from the upper sample.
  • FIG. 5 is a flowchart showing data input processing that can be executed in each stage.
  • the ID (child ID) of the sample relating to the stage is read by the ID detection unit 8 (S31), and then it is determined whether the read ID is correct (S32).
  • the ID is incorrect, for example, the stage identification information in the ID does not correspond to the corresponding stage, or the data on the read ID has already been input.
  • the ID may be duplicated, or the ID may be related to a discarded sample. If the ID is incorrect, an error message is displayed (S33).
  • the table relating to the read ID is read out from Data 4 overnight (S34).
  • data on the sample is input via the data input unit 7 (S35).
  • the relevant data may include various experimental data in the relevant stage, names of persons in charge, remarks, and the like.
  • a search key is input (S41).
  • a search key for example, each Species ID can be mentioned.
  • the database 4 is searched based on the search key (S42), and it is determined whether or not the corresponding data has been extracted (S43).
  • the data is displayed (S444). If there is no corresponding data, an error message is displayed (S45).
  • the ID may be read, the corresponding table may be read, and data may be added or corrected.
  • the ID of the sample related to the stage is issued based on the ID of the sample passed from the upstream stage, a series of steps generated for each predetermined stage is performed.
  • the sample can be accurately identified. That is, since a unique ID can be issued along the flow of sample generation, it is possible to prevent an ID issuance error or the like, and to accurately manage sample data.
  • the parent ID and the child ID are registered in each table along with the sample data, the tables between adjacent stages can be correlated. Therefore, it is possible to easily search for a table and easily know which sample the data is derived from, thereby improving the efficiency of research work.
  • FIGS. 1 and 2 The feature of this embodiment is that it is applied to a networked system as a sample data overnight management system.
  • the same components as those in the above-described first embodiment are denoted by the same reference numerals, and description thereof will be omitted.
  • FIG. 7 shows a schematic flow of a gene expression data management system using blood cells as an example according to the present embodiment.
  • a sample can be generated and data can be collected according to the following procedure.
  • Figure 7 shows only the main parts.
  • Sample I for blood samples D (BL nnnnn, where BL indicates a blood sample. N is a sequential number. Similarly, each of the following IDs also starts with an uppercase alphabetic letter and the sample type (stage). The following n indicates a serial number.) Is added and registered in the table Sm together with related data.
  • a plasma ID (PL nnnnn) is assigned to the plasma, and information such as the sample ID, the person in charge, the yield (ml), and the cryocontainer is recorded in the table PL.
  • Plasma is stored in a designated freezer with the plasma ID printed on a barcode label and affixed. Samples and data stored with a barcode label attached are not limited to this plasma sample, but their IDs must be detected with a wireless barcode reader, and the necessary information can be retrieved from the database and displayed. Can be.
  • RNA total RNA
  • RNA extraction solution for each T cell, etc., add an RNA extraction solution, and store at 180 ° C when proceeding to the stage before RNA extraction.
  • B cells are not subjected to RNA extraction and proceed to preparation of immortalized B cells.
  • Each type of cell is assigned a cell ID consisting of cell identification information (indicating the cell type) such as CT and CB and a 5-digit serial number.
  • Sample ID, contact person, date of separation, number of cells, It is stored in the table Cell together with the relevant data such as the cell storage box.
  • the cell ID is printed on a barco label, affixed, and stored at a predetermined location at -80 ° C. Proceed to the next stage without storing the B cells.
  • Each isolated B cell sample is used as an immortalized B cell line using EB virus.
  • immortalized B cell lines information such as cell ID, contact person, immortalized cell ID (IMnnn), date of freezing, number of cells, and storage location are recorded. Note that a barcode reader can be used to input the cell ID in this part.
  • the immortalized cell ID is printed on a barcode label, attached, and stored in liquid nitrogen.
  • RNA—ID This ID is configured as, for example, RXnnnn.
  • R represents RNA
  • X represents cell type (T etc.)
  • n represents serial number.
  • a barcode reader can be used to input the cell ID in this portion. For this sample, print the total RNA-ID on a barcode label, affix it, and store it at a designated place at 180 ° C for a short period of time.
  • RNA is type II
  • RNA reverse transcriptase
  • An enzyme that synthesizes complementary DNA starting from A) (Note: cDNA means complementary DNA, that is, complementary DNA.)
  • the bases complementary to each other form a pair between RNAs, between DNAs, and between RNA and DNA.
  • RNA prepared from the liquid cells was converted into type III, and three types of anchor primers complementary to the 3'-terminal polyA sequence of the mRNA sequence (GT15A, GT15C, GT15G; ⁇ ⁇ ⁇ has 15 consecutive sequences) to generate cDN ⁇ ⁇ ⁇ by reverse transcriptase reaction.
  • a cDNA-ID consisting of DXnnnn is assigned to the prepared cDNA.
  • D represents DNA
  • X represents one of A, C, and G indicating the type of anchor / primer used
  • n represents a serial number.
  • a barcode reader can be used for the input of the total RNA-ID.
  • the prepared cDNA is subjected to Differential 'display to analyze the abundance of various mRNAs in the original sample.
  • Differential display is a method in which cDNA is amplified by a PCR reaction under special conditions using an arbitrary primer and an anchor primer, and separated by precision acrylamide gel electrophoresis. This is to visualize (display) the fingerprint images of DNAs of various sizes amplified from the mRNA present in the sample.
  • cDNA sample into a 96-well PCR plate and dispense it.Add the optional primers, the same anchor primer as used for cDNA preparation, PCR reaction buffer, and PCR polymerase for PCR. Perform PCR reaction (T7). Then, the dispensed cDNA—ID, person in charge, date of creation, ID stored in the freezer, the type of arbitrary primer used, the location of the cDNA sample on the 96-well plate, etc., and the PCR plate ID (Qnnnn) Record in one bull Pp.
  • the barcode reader must be used to enter the cDNA-ID of the cDNA sample used. Can be used. Also, print and affix the PCR plate ID on the barcode label and store it at -80 ° C in the specified place.
  • the PCR plate ID the arrangement of each sample on electrophoresis (lane information), the person in charge, the date of creation, the image file ID (Gnnnnn, G indicates DD gel electrophoresis), etc. are recorded in the table DD.
  • the PCR plate ID can be registered with a barcode reader.
  • the image file ID is printed on a barcode label and affixed to the printed DD gel image, and it is stored after firing.
  • the analysis of the image reveals a band that shows an increase or decrease in the specific sample
  • return to the original RNA sample prepare the cDNA again, and perform a PCR reaction on the differential display under the same conditions.
  • the excised band is placed in an extraction buffer, and the DNA is recovered from the band. Record the data such as the person in charge, the date of creation, the image file ID, the lane number containing the collected DNA band, the position on the lane, the ID in the freezer, and the DNA band ID in Table Bn.
  • a barco reader can be used to input the image file ID.
  • This system also includes an ID management unit 2, a data management unit 3, a data base 4, and the like, as in the first embodiment described above.
  • a management device is a first management device 3 having an ID management unit 2. 1 and a second management device 41 having a data management unit 3.
  • Each of the management devices 31 and 41 is connected to a network 100 such as a LAN via the communication control units 33 and 43, and performs two-way data communication between the management devices 31 and 41. It is configured as follows.
  • a web browser 32 as a “browsing / input means” is mounted on the first management device 31, and a web browser as a “hypertext information processing environment” is mounted on the second management device 41.
  • a server function 42 is provided.
  • the data on the side of the second management device 41 is provided via the web server function 42. Therefore, the first management device 31 can view the data on the second management device 41 side via the web browser 32 and the like.
  • the network 100 is connected to the Internet, by inputting a predetermined URL, it is possible to seamlessly access external information resources such as web pages and net news.
  • FIGS. 9 and 10 show an example of a screen configuration of the gene expression data management system.
  • Fig. 9 (a) shows the configuration of the menu screen.
  • the menu screens include “Experimental sample management” for managing a series of samples generated from blood samples, “Freezer management” for managing the frozen state of samples, and “General-purpose data search / update tool ".
  • a bar code display column G1 for displaying the read ID.
  • a link column G for jumping to each menu is provided. 2 are provided.
  • a URL input field G3 is provided at the top of the screen. By inputting the URL of the information resource provided by the second management device 41 in the URL input field G3, the gene expression data can be displayed. Distributed management is possible.
  • Fig. 9 (b) shows the screen configuration for each cell separated and generated from a blood sample.
  • the system is configured to allow input of sample IDs as parent IDs and cell IDs as child IDs, as well as related data such as cell numbers and separation dates.
  • FIG. 10 shows a screen configuration regarding immortalized B cells generated from a B cell sample.
  • the cell ID parent ID
  • the immortalized B cell ID child ID
  • the related data can be input.
  • a unique ID can be issued to a series of samples generated by performing a predetermined operation on a blood sample, and the data of each sample is stored in association with each other Therefore, the efficiency of the experimental work can be improved.
  • the present invention is preferably used.
  • the system is divided into a plurality of management devices 31 and 41 and the management devices 31 and 41 are connected via a network 100, relatively few convenience resources such as personal computers are used. By interconnecting, a distributed sample data management system can be obtained.
  • a web browser 32 is mounted on the first management device 31, and the second management device 41 is connected to a network because it is configured to provide information via the web server function 42. Browsing of web pages and the like and browsing of gene expression data can be performed seamlessly.
  • a web browser is actually a standard function of a personal computer, various types of computers can participate in the gene expression data management system without depending on the platform.
  • the present invention is not limited to the above embodiments, and various additions, deletions, modifications, and the like can be made.
  • the ID storage unit 5 can be abolished and the latest serial number can be generated by referring to the database 4.
  • a sample data management system for managing data of a series of samples generated for each predetermined stage, comprising: detection means (8) for detecting identification information given to each sample; Determining means (10) for determining whether or not the identification information of the upper sample located at the position corresponds to the stage; and determining means (10) If it is determined that the stage is more compatible, a serial number is added to the stage identification information indicating the stage, and identification information issuing means (11) for issuing identification information given to the sample related to the stage. And a data management means (3) for associating the identification information of the upper sample with the identification information of the lower sample, and managing data inputted in relation to the lower sample. De-night management system.
  • a program recording medium storing a sample data management program for managing data of a series of samples generated at each predetermined stage.
  • Identification information for issuing identification information of a lower sample generated following the upper sample based on the correspondence management function (for example, S12, S32) to be performed and the identification information set for the upper sample.
  • a data management function e.g., S15, S16
  • S15, S16 that associates the identification information of the upper sample with the identification information of the lower sample, and manages data input in connection with the lower sample.
  • a program recording medium in which a data management program for causing a computer to realize is stored in a form that can be read and understood by a computer.
  • the program recording medium for example, various recording media such as a floppy disk, a hard disk, and a memory can be adopted. Also, by downloading a program via a communication line, the gist of the present invention can be realized on a computer. Industrial applicability
  • the identification information of the lower sample related to the stage is issued based on the identification information of the upper sample passed from the upstream stage.
  • a series of samples generated each time can be accurately identified.
  • sample data between adjacent stages can be stored in association with each other, thereby improving work efficiency.
  • identification information and data are provided in a hypertext type information processing environment and browsing work is performed through browsing and input means, other network search work and sample data overnight management work can be performed seamlessly. It can be switched, and the resources of the existing convenience store can be used effectively.

Abstract

L'invention concerne des informations d'identification (telles qu'une identité) qu'on imprime sur une étiquette (22) comme données de code à barres, et cette étiquette (22) est collée sur un contenant d'échantillon (21). Une fois que l'identité d'un échantillon provenant d'une platine de support est lue par une section de détection d'identité, une section de détermination d'identité (10) détermine si l'identité (identité principale) d'un échantillon de niveau supérieur correspond ou non à la platine pertinente. Si elle correspond à la platine pertinente, une section d'établissement d'identité (11) établit une nouvelle identité (identité accessoire) en ajoutant à l'information d'identification de la platine un numéro de séquence indiquant le platine pertinente. Des données expérimentales de l'échantillon, etc, sont stockées dans une base de données (4) avec l'identité principale et l'identité accessoire. Les échantillons et les données générés au niveau d'une série de platines sont mutuellement rapprochés et peuvent être traités et stockés.
PCT/JP1998/005502 1997-12-06 1998-12-04 Systeme de gestion de donnees-echantillons WO1999030167A1 (fr)

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JP9/352130 1997-12-06
JP35213097 1997-12-06

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Cited By (5)

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JP2003519829A (ja) * 1999-10-13 2003-06-24 シークエノム・インコーポレーテツド データベースを作成する方法および多型遺伝的マーカーを同定するためのデータベース
WO2008108098A1 (fr) * 2007-03-08 2008-09-12 Hitachi Plant Technologies, Ltd. Procédé de gestion de la préparation de cellules dans le cadre de la préparation de cellules, et système de gestion de la préparation de cellules
US7860727B2 (en) 2003-07-17 2010-12-28 Ventana Medical Systems, Inc. Laboratory instrumentation information management and control network
US8719053B2 (en) 2003-07-17 2014-05-06 Ventana Medical Systems, Inc. Laboratory instrumentation information management and control network
JP2019194619A (ja) * 2019-07-12 2019-11-07 国立研究開発法人産業技術総合研究所 実験データ記録装置、コンピュータプログラム、実験データ、実験データ記録方法、実験データ表示装置及び実験データ表示方法

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