Illumina LIMS. Software Guide. For Research Use Only. Not for use in diagnostic procedures. Document # June 2017 ILLUMINA PROPRIETARY

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1 Illmina LIMS Software Gide Jne 2017 ILLUMINA PROPRIETARY

2 This docment and its contents are proprietary to Illmina, Inc. and its affiliates ("Illmina"), and are intended solely for the contractal se of its cstomer in connection with the se of the prodct(s) described herein and for no other prpose. This docment and its contents shall not be sed or distribted for any other prpose and/or otherwise commnicated, disclosed, or reprodced in any way whatsoever withot the prior written consent of Illmina. Illmina does not convey any license nder its patent, trademark, copyright, or common-law rights nor similar rights of any third parties by this docment. The instrctions in this docment mst be strictly and explicitly followed by qalified and properly trained personnel in order to ensre the proper and safe se of the prodct(s) described herein. All of the contents of this docment mst be flly read and nderstood prior to sing sch prodct(s). FAILURE TO COMPLETELY READ AND EXPLICITLY FOLLOW ALL OF THE INSTRUCTIONS CONTAINED HEREIN MAY RESULT IN DAMAGE TO THE PRODUCT(S), INJURY TO PERSONS, INCLUDING TO USERS OR OTHERS, AND DAMAGE TO OTHER PROPERTY. ILLUMINA DOES NOT ASSUME ANY LIABILITY ARISING OUT OF THE IMPROPER USE OF THE PRODUCT(S) DESCRIBED HEREIN (INCLUDING PARTS THEREOF OR SOFTWARE) Illmina, Inc. All rights reserved. Illmina, and the streaming bases design are registered or pending trademarks of Illmina, Inc. and/or its affiliate(s) in the U.S. and/or other contries. All other names, logos, and other trademarks are the property of their respective owners. ii

3 Table of Contents Introdction 1 Access Featres 1 Chapter 1 Illmina LIMS Project Manager Software 2 Overview 2 Project Manager 7 Laboratory Manager 26 Resorces 27 Chapter 2 Illmina LIMS Web Client 30 Overview 30 Administrative Tools 30 Laboratory Management 34 Reports 35 Technical Assistance 53 iii

4 Introdction The Illmina Laboratory Information Management System (LIMS) software is comprised of two components: Illmina LIMS Project Manager, a server application that lets scientists or project managers: Set p instittes, projects, and investigators Accession samples Add global control sample plates Accession prodcts Add clster files For more information on sing the Project Manager, see Illmina LIMS Project Manager Software on page 2 Illmina LIMS web client that enables positive sample tracking throghot the laboratory workflow by providing: 100% sample tracking Real-time qality metrics from image scanning Project repository of sample data File management of decoding, image, intensity, and analytical data files For more information on sing the web client, see Illmina LIMS Web Client on page 30 Access Featres Access to the Illmina LIMS Project Manager or Illmina LIMS web client is done one of two ways: Windows athentication Database athentication Confirm yor log on method with yor system administrator. Yor lab manager or system administrator sets p ser acconts and determines the featres that are available to yo. To reqest changes to yor accont, contact yor system administrator. 1

5 Chapter 1 Illmina LIMS Project Manager Software Illmina LIMS Project Manager Software Overview 2 Project Manager 7 Laboratory Manager 26 Resorces 27 Overview The Illmina LIMS Project Manager lets yo easily accession experimental and control samples into the system sing familiar sample sheet definitions. When yo assign samples to an Infinim project, Project Manager atomatically qees them for processing in batches that match the Illmina reagent and BeadChip packages. Yo can also create cstomized Infinim batches manally. To se the Project Manager, yo mst have Management Client access. For more information on permissions, see Manage Users on page 30. Illmina LIMS Project Manager Workflow The following diagram illstrates the Project Manager workflow. For more detail on any of the steps, see the corresponding section. While prodcts can be accessioned into the system prior to adding instittes, there mst be a prodct in the system in order to create a project. Figre 1 Illmina LIMS Project Manager Workflow 2

6 Installing the Illmina LIMS Project Manager Client 1 In the URL field of yor web browser, type the address provided by the system administrator. The Illmina LIMS window opens. 2 Select Download Project Manager Client. The Illmina LIMS Project Manager client is installed. When complete, the Log into LIMS Project Manager window opens, and the Illmina lims-manager icon is added to yor desktop. 3 Set the Java Secrity configration by doing the following: In the Control Panel, select Java 32-bit. Select the Secrity tab. In the exception list, add the LIMS website address. Select OK and exit the Control Panel. Getting Started 1 Select the Illmina lims-manager icon. The Log into LIMS Project Manager window opens. The first time yo se the Project Manager yo mst configre the client server. a b c d Select Configre. Enter or edit the Display Name, Host, Port, and Context, then select OK. To add additional servers, select New Server then enter the Display Name, Host, Port, and Context. To delete a server, select the server from the list, and then select Delete. If yo do not know yor configration parameters, conslt yor Illmina LIMS system administrator. 2 Do one of the following: If yo are sing Windows athentication, enter yor Windows ser name and password in the Log into LIMS Project Manager window. If yo are sing database athentication, enter the ser name and password that were established for yor Illmina LIMS ser accont. If yo do not know what form of athentication is being sed, contact yor system administrator. 3 Select Login. The Illmina LIMS Project Manager window opens. The first time yo log in to the Project Manager, the Illmina LIMS Project Manager End-User Software License Agreement opens. Read the agreement, then select Agree to contine. The instrctions in this gide assme that yo are logged in to Project Manager. Configration Tools The configration of ,connection timeots, date and time formats, and log settings can be modified. To access these configration options in the Project Manager window select Tools Options. The table that follows describes the options on each tab. Option Sets the SMTP Server sed for . 3

7 Option Connection Date/Time Format Log Settings Sets connection parameters. Server Commnication Select the nmber of seconds of lost connection time before server commnications timeot. A 0 setting indicates no time ots. Atomatic Logoff Select the nmber of seconds of inactivity before the ser is atomatically logged off. A 0 setting indicates that the sers are never logged off atomatically. Select whether to display a warning message prior to logoff and whether to reactivate the prior task after re-login. Sets the date and time format to be sed. Enables or disables logs. View Events and Commnications View Event Logs Project Manager logs all events that occr dring a session. These logs are often sed when trobleshooting system isses. The first time yo log in, the Event Log is atomatically displayed. The Event Log lists the events that have occrred in the crrent session. To remove the Event Log pane, from the Illmina LIMS Project Manager men bar select View Event Log. To redisplay the Event Log, from the Illmina LIMS Project Manager men bar select View Event Log. Select to increase or decrease the Max Lines (maximm nmber of lines) in the Event Log pane as needed. Select Clear in the Event Log pane to delete the contents of the list. View Reqest/Response Exchanges Yo can view all the reqests and responses between the server and the local client. If yo call technical spport, a technical spport scientist may reqest that yo trn this on. The first time yo log in, the Reqest/Response pane is atomatically displayed. The Reqest/Response pane shows the code that is being exected. To remove the Reqest/Response pane, from the Illmina LIMS Project Manager men bar select View Reqest/Response. To redisplay the Reqest/Response pane, from the Illmina LIMS Project Manager men bar select View Reqest/Response. Select Clear in the Reqest/Response pane to delete the contents of the list. the Reqest/Response Log 1 In the Reqest/Response pane, select Save to File. 2 Name the file with a.txt (text file) extension. 3 In the Reqest/Response pane, Select Mail. An dialog box opens poplated with the address for technical spport. 4 Enter yor address in the From box. 5 [Optional] Enter a sbject line or comments. Comments will appear in the body of the message. 4

8 6 Select Add, and then navigate to the location of the text file yo created and select it. 7 Select Send. Manage Display Project Manager lets yo modify the viewing options. Reset All Windows Yo can reset the Illmina LIMS Project Manager window to display the viewing panes in the defalt configration. From the men bar select View Reset All Windows so that all the viewing panes will be displayed and in their defalt location. The changes takes effect the next time yo open and log in to Project Manager. Manage Table Contents The contents of most tables can be copied for pasting into a spreadsheet or text file. Additionally, the order in which the rows of data are displayed can be sorted by a specified colmn. Copy table contents by placing the crsor within any table display, right-click, and select Copy. Open the destination application (for example, an Excel spreadsheet) where yo want to paste the table contents, right-click, and select Paste Click the colmn header to toggle the sort order between ascending, descending, or original order based on the contents of the colmn selected. Manage Forms A form can be saved, loaded, or saved as an image in the Project Manager. Using the form options lets yo save the inpt data and later load that data withot having to manally reenter it. To save a form, select Save Form. Name and save the selected workflow form to an XML format. To load a form, select Load Form. Locate and select the form that yo want to view. To captre an image of a workflow pane, select Form Screen Shot. Enter a name for the image of the workflow pane, and select Save to save the image in PNG format. Report Bgs 1 In the Project Manager window, select Report Bg. The window opens. The following information is atomatically inclded in the Yor address Sbject Comments abot the last event yo performed A screen shot of the last event yo performed 2 In the To field, enter the address of yor Illmina LIMS system administrator. 3 Enter additional comments if necessary. 4 Add or remove attachments if necessary. To add a file to the attachment list, select the add icon, choose the file to add, and then select Open. To remove a file from the attachments list, select the file from the list, then select the delete icon. 5 Select Send to send the bg report. 5

9 Administrator Tools The system administrator controls ser access and application vales from the Administration page. From the men bar select Tools Administrator. User Manager Illmina LIMS sers can be added and their permissions can be controlled throgh the User Manager. In the Administration page, select User Manager. A list of existing sers is displayed. Add User 1 In the Administration window, select the Add User icon. 2 Enter the ser name and password information, and then select Save. See Add User on page 6 to set p ser permissions. Edit Password Use this featre to edit passwords for sers logging in sing database athentication. 1 Select a ser from the list. 2 Select the Edit User icon. 3 Enter the new password information, and then select Save. Edit Permissions 1 Select a ser from the list. The ser s permissions are displayed for each Illmina LIMS task. A check in the Allowed colmn indicates that the ser has permission to perform that task. 2 To modify the ser s permissions do one of the following: Select Allow All to allow the ser to perform all Illmina LIMS tasks. Select Select Individal Tasks to allow the ser to perform only selected Illmina LIMS tasks and do one of the following: Check the box in the Allowed colmn next to each individal task that yo want the ser to have permission to perform. Select Check All to allow the ser to perform all Illmina LIMS tasks. Select Uncheck All to disallow the ser to perform any Illmina LIMS tasks. Select Copy Permissions of to copy the permissions of another ser. Select a ser whose permissions are to be copied from the drop-down men. 3 Select Save. App Vales This featre lets yo create and edit application vales, and create new categories. In the Administration window, select App Vales. The list of application vales is displayed in alphabetical order. 6

10 Edit Application Vales 1 Doble-click on the parent type folder that contains the application (app) vale type yo want to edit. 2 Select the + sign beside any folder to view more information, drilling down ntil yo see the app vale that yo want to edit. 3 Select the vale that yo want to edit. 4 Select Edit App Vale. 5 Enter the new App Vale and select Save. Add Category 1 Select New Category. 2 Enter the new Parent Type category and select Save. Add Application Vale 1 Doble-click on the folder that contains the parent type yo want to pdate. 2 Select the + sign beside any folder to view more information, drilling down ntil yo see the folder where yo want to add the app vale. 3 Select the folder that will contain the new app vale. 4 Select New App Vale. 5 Enter the new label or name in the App Vale Type field. 6 Enter specific information abot the App Vale Type in the App Vale field, sch as the directory path, vale, or setting. Active and inactive settings are defined as follows: Active: Anyone can do work associated with the application. Inactive: No one can do any work associated with the project. 7 Select Save. The new app vale and its type are added to the parent category folder. Exit Project Manager To exit Project Manager do one of the following from the Illmina LIMS Project Manager window: Select Logoff. Select File Exit. Select in the pper right corner. Project Manager The Project Manager area provides tools for creating and managing individal projects for each institte. Every project, investigator, sample, and batch is associated with a single institte. Prodcts are available to all instittes. 7

11 Adding and Managing Instittes An institte is a grop, instittion, department, or other entity that has projects in Illmina LIMS. Every project mst be associated with an institte. Adding an Institte 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 Select New Institte. The Add New Institte pane opens. 3 Enter the institte name and any ancillary contact information that yo wish to inclde. The only reqired information is the institte name. 4 If the institte has a system ID that allows the LIMS data to connect to its own backend database, enter the ID here. This ID appears on all institte-based reports as I-SSID (institte secondary system ID). 5 Select Save. Modifying an Institte 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the appropriate institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte and select Institte Detail, or doble-click the institte. The Institte Detail pane opens. 4 Select the institte name. The institte details are displayed. 5 Make any changes to the institte s contact information, and then select Save. Yo cannot change the name of the institte. Searching for an Institte 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 In the Search By drop-down list, select the type of information yo want to search by: Institte Name Project Name Investigator Name Sample Container Barcode (ie, DNA plate barcode) 3 In the Search Criteria field, type the text to search on (eg, RMS Lab, or WG DNA). The field is not case-sensitive. 4 [Optional] If yo do not know the fll name, enter a wild card (*) to represent the missing text. 8

12 For example (assming that yo are searching by institte): e* searches for all instittes whose names begin with e *e* searches for all instittes whose names contain e *e searches for all instittes whose names end in e To list all instittes, leave the field empty. 5 Select Search. The reslts of the search appear at the bottom of the pane. Sample Manifest The sample manifest defines the DNA or BCD samples that are rn throgh the lab. It can contain data for any nmber of plates, each of which can contain from 1 to 96 samples. To accession the sample manifest data, see Accessioning Institte Samples on page 10. The data in a sample manifest are specific to a single institte. If yo import the sample manifest into an institte other than the one named in the file, yo are prompted to confirm. DNA and BCD Sample Manifests The sample manifest mst contain the following information in the specific cells as indicated: A1: Institte Name A2: Date Received A3: Comments B1: The institte name accessioned for the samples listed in this manifest The sample manifest mst contain the colmns listed in the following table. The colmns can be in any order. DNA Inpt (ng) and Institte Sample Grop shold be sed only in the BCD manifest. Table 1 DNA and BCD Sample Manifest s Comments* Conc (ng/µl) DNA Inpt (ng) Extraction Method Institte Plate Label Institte Sample Grop Institte Sample Label Is Control Mass of DNA sed in WGA Parent 1* Parent 2* Replicate(s)* Row Any spplementary data abot the sample. The concentration of DNA in the sample, in nanograms per microliter. (BCD manifests only) DNA inpt in Bislfite conversion. The method by which the DNA was extracted from the tisse. The WG#-DNA barcode for the sample plate. (BCD manifest only) Reqired for methylation projects (for example, Disease vs. Normal). The name assigned by the institte to identify this sample. 0: Experimental sample 1: Control sample The mass of DNA sed for this sample in WGA, if WGA was the extraction method. The sample name or plate well of the parent, if known. The sample name or plate well of the other parent, if known. The name or barcode of any dplicate sample in the same plate. (Optional) The row nmber of the sample in the sample manifest. Integers only. These nmbers enable yo to make sre that yo have entered all the data for each plate (eg, 96 samples for the first plate and 72 samples for the second). 9

13 Sex Species Tisse Sorce Volme (µl) Well WGA Method (if Applicable*) The sex of the individal from whom the sample was drawn. M: Male F: Female U: Unknown The species from which the DNA sample was drawn. The type of tisse from which the DNA was drawn. The amont of sample, in microliters. The coordinates of the well in the sample plate (eg, A01 or H10). The type of whole-genome amplification that was sed to extract the DNA, if WGA was the extraction method. *This colmn mst be present in the file bt does not need to contain any information. Accessioning Institte Samples To make samples available to projects within an institte, accession the sample manifest data into the institte. To begin, save the sample manifest as a comma-separated vale (*.csv) file. A manifest can contain any nmber of sample plates. For more information on the constrction of the sample manifest, see Sample Manifest on page 9. CAUTION If yo are generating the *.csv file from an Excel spreadsheet, before saving it as a *.csv file, review the Excel file to make sre that the final colmn has data in every row. If the last colmn is empty, Excel discards all commas after the last complete colmn in the row. This offsets the vales for the rest of the file and cases errors pon import. Projects only have access to samples that have been accessioned into the institte. Samples cannot be accessioned into more than one institte. This helps protect proprietary data. Accessioning Samples to an Institte 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the appropriate institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte, and then select Institte Detail. The Institte Detail pane opens. 4 Select Institte Samples. 5 Select Import Institte Samples. 6 Select a sample manifest file (*.csv), and then select Open. If yo import a sample manifest into an institte that is different from the institte name in the sample manifest, yo are prompted to confirm. The Import Manifest Detail pane opens and shows a row for each sample plate. For a detailed list of the colmns in the sample manifest, see Import Manifest Detail Fields on page

14 By defalt, the Qant Samples checkbox is selected for every sample plate. When yo save, the sample plates are qeed for the Make Qant task. Yo cannot assign sample plates to projects ntil they have completed the Read Qant task and are placed in the Available Sample Plates qee. 7 If yo do not want to qantify a sample plate, deselect that plate. When yo save, any sample plate that is not selected for Qant is immediately made available to assign to a project. 8 Select any sample plate in the Import Manifest Detail pane to view information abot each well in the plate. Table 2 Import Manifest Detail Fields IsControl Parent 1 Parent 2 Qant Samples Replicates Sample Sample Plate Sex Species Well 0: The well in this row contains an experimental sample. 1: The well in this row contains a control sample. The sample name or plate well of the parent, if known. The sample name or plate well of the other parent, if known. Indicates whether to qantify the samples in the sample plate. If the checkbox is selected, Project Manager atomatically qees the samples for Make Qant. Yo cannot add these samples to a project ntil Read Qant is complete. The name or barcode of any dplicate sample in the same plate. The sample name. The sample DNA plate barcode. The sex of the individal from which the sample was derived. M: Male F: Female U: Unknown The species from which the DNA sample was drawn. The coordinates of the well in the sample plate (eg, A01 or H10). 9 Make sre that the species cont specified on the Import Manifest Detail matches the nmber of species represented in the sample set. 10 Select Save to finish importing the samples into the institte. The imported samples appear at the bottom of the Institte Samples list. For more information, see the Sample Plate Fields table. Table 3 Sample Plate Fields IsControl Nmber of Samples Project Cont Sample Container Id Sample Plate 0: This plate is not a control plate. 1: This plate is a control plate. Control plates are visible to all instittes in Project Manager. The nmber of samples on the plate. The nmber of projects to which this plate has been assigned. System-generated database key. The sample plate name or barcode. 11

15 Validating Samples Project Manager atomatically validates all the fields in the manifest when it is saved. If all sample plate data are valid, the row appears in green. If there is an error in the sample plate data (eg, the IsControl colmn has a vale other than 0 or 1), the sample plate appears in red. Possible cases for errors inclde: A plate has the same ID as a sample plate that is already in the system There is a missing vale in one of the fields (eg, a blank volme) There is a character vale in a nmeric field If an error occrs, correct the data in the sample manifest *.csv file and reimport the samples. Viewing Institte Samples The Institte Samples pane lists sample plates that are available for all projects in the institte. Select a sample plate to show detailed information from the sample manifest in the Plate Detail pane. Table 4 Sample Plate Detail Fields Comment Conc (ng/µl) IsControl Parent 1 Parent 2 Replicate Sample Sex Species Tisse Type Volme (µl) Well Any comments from the sample manifest. The concentration of DNA in the sample, in nanograms per microliter. No: The well in this row contains an experimental sample. Yes: The well in this row contains a control sample. The sample name or plate well of the parent, if known. The sample name or plate well of the other parent, if known. The name or barcode of any dplicate sample in the same plate. The sample name. The sex of the individal from which the sample was derived. M: Male F: Female U: Unknown The species from which the DNA sample was drawn. The type of tisse from which the DNA sample was drawn. The amont of sample, in microliters. The coordinates of the well in the sample plate (eg, A01 or H10). Adding and Managing Investigators Investigators are the scientists associated with an institte. An investigator can only be associated with one institte. Every project mst have a principal investigator. Adding an Investigator 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the desired institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte, and then select Institte Detail. 12

16 4 Select Investigators. 5 In the Investigators pane, select New Investigator and enter the reqired information. First name Last name address Phone #1 6 Select Save. The investigator appears in the Investigators list at the top of the pane. Updating an Investigator Yo can only modify investigator contact information, the name cannot be changed. 1 In the Institte Detail pane, select Investigators. 2 In the Investigators pane, select the investigator. The investigator s personal information appears at the bottom of the pane. 3 Modify the contact information as needed, and then select Save. Prodct Accessioning Accessioning is the process of adding new prodcts to the database. After a prodct is accessioned, it is available to projects in any institte. To accession a prodct, the following files are reqired: Prodct Definition file (*.xml): contains fields describing the specific prodct format. Bead Pool Manifest file (*.bpm): provides information abot every locs on the prodct. For mltispecies prodcts, all bead pool manifests associated with the prodct mst be imported. [Optional] Clster file (*.egt): Provide the clster positions reqired for generating genotype calls with Atocall. For more information, see Clster File Manager on page 14. Mltise prodcts (eg, HmanOmni1-qad Mlti-Use) mst be accessioned even if the single-se version of the same prodct is already in the database (eg, HmanOmni1-qad). Accessioning Prodcts 1 In the left pane, select Prodct Manager. 2 In the Prodct Manager frame, select Prodct Accession. The Prodct Accession window opens. 3 Select Browse, navigate to the definition file (*.xml), and select Open. The prodct information atomatically poplates. 4 For mltispecies prodcts, the nmber of species associated with the prodct is displayed, select Next. The BPM Import pane opens. 5 For each species associated with the imported prodct, select by species to add or modify the Bead Pool Manifest. 6 Navigate to the bead pool manifest file (*.bpm), and select Open. The selected manifest path and file name are displayed. 7 Select Next. 13

17 8 Review Prodct accession Detail, and then select Save. It can take a few moments for the prodct accession to complete. When accession is complete, the prodct appears in the Available Prodcts list. Following prodct accession, clster files can be added. For more information, see Clster File Manager on page 14. Accessioning Individal BeadChips In addition to accessioning prodct definitions into the system, yo mst accession each individally barcoded item. The information that needs to be accessioned can be downloaded via MyIllmina. For more information, see Technical Assistance on page 53. Before accessioning an individal BeadChip, yo mst have already accessioned its associated part nmber. 1 Access the BeadChip map data sing the Decode File Client. 2 Navigate to the data destination folder and save files. 3 Open a window to display the contents of the data destination folder. 4 Navigate to the AtoLoad folder defined for yor system. For more information abot configring system folders, see the Illmina LIMS Web Client on page Drag the BeadChip barcode folder into the AtoLoad folder. The next time that the Illmina Project Manager polls the AtoLoad folder, it accessions the items it finds there. If the accession is sccessfl, the BeadChip is qeed for the appropriate task. The prodct mst be accessioned before the individal item can be an accessioned. If the accession fails, the DMAP files are moved atomatically to the atoload_failre folder on the LIMS server, and an error appears in the AtoAccession Failre report. For more information abot reports, see the Illmina LIMS Web Client on page 30. Clster File Manager Clster files (*.egt, *.egtp) provide clster definitions. For the AtoCall program to generate genotype calls, yo mst link a clster file to each prodct. For single-species, each prodct can have one or more associated clster files, bt only one clster file can be active at any time. For mlti-species, each prodct can have one or more associated clster files, and only one clster file per species can be active at any time. For standard prodcts, import the clster file sing the Clster File Manager. Cstom BeadChips do not come with a clster file. To create the clster file, rn the BeadChip against yor samples, analyze the data in GenomeStdio, and export a clster file. Import the file into the Project Manager sing the Clster File Manager. Adding another clster file is also sefl if yo wish to change the clster definitions as yo gather more data. To do this, cstomize the clster file in GenomeStdio and export it. Importing mltiple clster files lets yo contine to refine the file as yo gather more data. After each modification, it is recommended that yo reqee the samples sing the latest clster file. 14

18 AtoCall does not work with Methylation prodcts. Viewing Clster Files 1 In the left pane, select Clster File Manager. 2 Select the Prodct Name, and then select Next. The active and inactive clster files are displayed. The active clster file appears in green. Adding a Clster File 1 In the Clster File Manager window, select the Prodct Name, and then select Next. 2 Select Add Clster File to add a file to the list. 3 Navigate to the clster file (*.egt, *.egtp), and then select Open. When the clster file finishes importing, it is added to the list in the Manage Clster Files window. The defalt stats is Inactive. More than one clster file can be added, however, only one can be active for a prodct or species at a given time. Activating a Clster File 1 In the Clster File Manager window, select the Prodct Name, and select Next. 2 Select the clster file that yo want to se for this prodct. 3 Select Activate Clster File. The file yo select applies to all revisions of the prodct. The active clster file appears in green. If yo activate a different clster file for this prodct, the previosly active clster file atomatically becomes inactive. Inactivating Clster Files 1 In the Clster File Manager window, select the Prodct Name, and then select Next. 2 Select Inactivate Clster Files. The stats of all listed files is set to inactive. Adding and Managing Projects Most of the work done in Illmina LIMS is associated with a project, which in trn is associated with an institte. The project defines the available prodcts, sample plates, and batches. Before adding a project, yo mst have already done the following: Added investigators (see Adding and Managing Investigators on page 12) Accessioned prodcts (see Prodct Accessioning on page 13) 15

19 Adding a Project 1 In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the desired institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte, and then select Institte Detail. 4 Select Projects. 5 Select New Project. 6 Enter the project name. 7 If the project has a system ID that allows the LIMS data to connect to its own backend database, enter the ID. This ID appears on all the project-based LIMS reports as P-SSID (project secondary system ID). 8 Select the principal investigator. If the investigator does not appear in the list, go to the Investigators pane and add a record for the investigator. For more information, see Adding and Managing Investigators on page 12. If a newly added investigator does not appear in the list, select Refresh Project to refresh the screen. 9 Enter or select a starting date (mm/dd/yyyy) and a de date (mm/dd/yyyy). The starting date and de date are for tracking prposes only, and have no effect on how the project is rn. 10 Select the prodcts that will be sed in the project. Yo can select mltiple prodcts at one time, except for MSI prodcts. If a prodct does not appear in the list, go to the Prodct Manager and accession the prodct into the system. For more information, see Prodct Accessioning on page 13. When yo assign sample plates to the project, a separate batch is created for each prodct. For more information on sample plates, see Viewing Sample Plates on page Select Save. The project appears in the Projects list at the top of the page. Adding Prodcts to an Existing Project Yo can add new prodcts to a Infinim project at any time. The prodct mst be accessioned into the system before it can be added to a project. For more information, see Accessioning Prodcts on page In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the desired institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte, and then select Institte Detail. 16

20 4 Select Projects. 5 Highlight a project in the Projects pane. The project data appears at the bottom of the pane. 6 Select Add Prodct. The Assign Prodcts to Project dialog box opens. 7 Assign prodcts to the project: Select one or more prodcts from the Available list and select > to move them to Assign to Project. Select < to move items from the Assign to Project list back to the Available list. 8 Select Add Prodct/Bild Batches. The prodcts are added to the Project Detail window. 9 When prompted, indicate whether yo want to create batches for all samples. If yo select No, yo can still batch old samples for the new prodct by sing the Import Manal Batch fnction. For more information, see Importing Manal Batches on page 17. When Project Manager finishes adding the prodcts, they appear on the list of prodcts for the project. 10 Select Save in the Project Detail window. 11 If yo chose to batch existing samples for the new prodct, select the Batches tab. The new batches appear on the list along with the prodct and batch creation date. Importing Manal Batches This featre lets yo create a cstomized batch of samples from a single project. By exporting sample data as a *.csv file and then sorting and filtering the data, yo can qickly assemble the batch regardless of how many samples the project contains. 1 Rn the Project Detail report from the Illmina LIMS web client, and export it to a *.csv file. 2 Edit the *.csv file to create a batch import file. 3 Import the file into the project. See the following sections for more detailed instrctions. Illmina LIMS can atomatically batch yor samples as well. For more information, see Assigning Sample Plates on page 21. Defining the Batch This section explains how to create the batch import file from an Illmina LIMS report. To create manal batches, yo mst have previosly accessioned the samples, qantified them if necessary, and assigned them to a project. For more information, see Accessioning Institte Samples on page 10. The samples shold be in one or more DNA plates. 1 Log in to the Illmina LIMS web client. 2 Select the Reports tab, and then in the left pane, select Lab Management Project Detail Report. 3 Select a project from the list. 4 Select Export to CSV, and then select Rn Report. Select to Save or Open the *.csv file. The *.csv file contains information abot every sample in the project. 17

21 5 Edit the information in the *.csv file to refine the list to only the samples yo want to batch. To import samples from one DNA sorce plate, prepare a batch import file as shown in Figre 2. To import samples from mltiple DNA sorce plates, prepare a batch import file as shown in Figre 3. 6 Save the edited Project Detail Report *.csv file to a new batch import *.csv file with the following strctre: The colmn field names mst exactly match the names listed below. Table 5 Cell A1 B1 A3 B3 Project Detail Report fields header Prodct Part Nmber The actal prodct nmber. The prodct part nmber can be fond sing the Prodct Inventory Report. Sample Plate colmn that lists the sample plate barcode(s). Yo can batch samples from more than one plate. Sample Wells colmn that lists the well for each sample yo want to batch. The maximm nmber of samples yo can batch is 96. Figre 2 Sample Batch Import File from One DNA Sorce Plate [ 18

22 Figre 3 Sample Batch Import File from Mltiple DNA Sorce Plates [ Importing the Batch 1 In the Institte Detail pane, select Projects. 2 Highlight a project in the Projects pane. The project data appears at the bottom of the pane. 3 Select the Batches tab. Batches that are crrently associated with the project are displayed. 4 Select Import Manal Batch. 5 Browse to the sample batch import file (*.csv), and then select Open. Project Manager imports the batch data and qees the batch for amplification. The new batches appear in the list with the date and time of import. Modifying Project Stats Projects can have one of for stats codes. Active Defalt state when a project is added. The project can be modified, and anyone can do work associated with the project. Inactive Set to Inactive to pt a project on hold. No one can do any work associated with the project. Yo can only change the stats to Active, or to Awaiting Archive. Awaiting Archive Set inactive projects to archive. No work can be done on the project, nor can the stats of the project be changed. A poller rns at set intervals and archives the data to an archive folder on the file server. 19

23 Archived When the archive completes, the project stats is atomatically pdated to Archived. Once the stats is set to Archived, the IT department can back p the files. Viewing Sample Plates The Sample Plates tab lists the sample plates that are assigned to yor project, by name or barcode. It indicates whether the plate is a control plate, and identifies the nmber of wells. Viewing Sample Plates Associated With the Project 1 In the Institte Detail pane, select Projects. 2 Highlight a project in the Projects pane. The project data appears at the bottom of the pane. 3 Select the Sample Plates tab. Plates that are crrently associated with the project are listed. Table 6 Project Sample Plate Fields Barcode Nmber of wells The barcode of the sample plate. The nmber of sample wells in the plate. Viewing Sample Plate Details for a Project 1 In the Projects pane, highlight a project. The project data appears at the bottom of the pane. 2 Select the Sample Plates tab. Plates that are crrently associated with the project are listed. 3 In the Institte Detail pane, select Projects. 4 Doble-click a plate name in the Sample Plates tab. The Displaying Plate Detail pane opens. It displays information abot every sample well on the plate. Table 7 Plate Detail Fields Comment IsControl Conc (ng/µl) Parent 1 Parent 2 Replicate Sample Sex Species Any comments regarding the samples. No: The well in this row contains an experimental sample. Yes: The well in this row contains a control sample. The concentration of DNA in the sample, in nanograms per microliter. The sample name or plate well of the parent, if known. The sample name or plate well of the other parent, if known. The name or barcode of any dplicate sample in the same plate. The sample name or barcode. The sex of the individal from which the sample was derived. M: Male F: Female U: Unknown The species from which the DNA sample was drawn. 20

24 Tisse Type Volme (µl) Well The type of tisse from which the DNA sample was drawn. The amont of sample, in microliters. The coordinates of the well in the sample plate (eg, A01 or H10). Assigning Sample Plates After yo have accessioned sample plates into the institte, yo can assign them to projects. When yo assign a sample plate to a project, the Project Manager atomatically batches the samples and starts the laboratory workflow. Yo can also add batches manally. For more information, see Importing Manal Batches on page 17. Atomatically generated batches consist of samples on a single plate. For mltise prodcts, Illmina LIMS assigns as many 24-sample batches as possible from each plate, with the remaining samples filling ot the last batch. For mltisample prodcts, the batches can contain 48 or 96 samples. For optimal processing, make sre that the sample plates contain mltiples of the nmber of samples per batch, which reslts in fll batches for every rn. Assigning Sample Plates to a Project 1 In the Projects pane, highlight a project. The project data appears at the bottom of the pane. 2 Select the Sample Plates tab. Plates that are crrently associated with the project are listed. 3 Select Assign Sample Plates. The Assign Samples to Project dialog box opens. It lists all the available sample plates in the institte. To add another plate to this list, see Accessioning Institte Samples on page Select one or more samples from the Available list and select > to assign them to the project. 5 Select Add Samples/Bild Batches. The sample plates appear in the Sample Plates tab. If the project contains one or more mltispecies prodcts, the Analysis Assignment Needed dialog box opens. Batches that reqire species assignments to associate the species name in the sample manifest with the species name in the bead pool manifest (*.bpm) are highlighted in red. 6 To set assignments, select Assign Species for each batch highlighted in red. The Set Analysis Assignment dialog box opens; nassigned samples are highlighted in red in the Sample pane. 7 Select one or more samples in the Sample pane, choose the appropriate species in the Prodct pane, and then select Assign. Alternatively, if all highlighted samples are assigned to a selected species in the Prodct pane, select Assign to all nassigned. 8 When all samples are assigned to the appropriate analysis species, select Set Batch Assignments. The Analysis Assignment Needed dialog opens and batches are highlighted in green if species assignment was sccessfl. 9 Select Bild Batches. 21

25 Viewing Project Samples Select a plate name in the Sample Plates tab to view sample plate details for a project. The Displaying Plate Detail pane displays information abot every sample well on the plate. For information abot the colmns in this table, see the following. Table 8 Plate Detail Fields Comment IsControl Conc (ng/µl) Parent 1 Parent 2 Replicate Sample Sex Species Tisse Type Volme (µl) Well Any comments regarding the samples. No: The well in this row contains an experimental sample. Yes: The well in this row contains a control sample. The concentration of DNA in the sample, in nanograms per microliter. The sample name or plate well of the parent, if known. The sample name or plate well of the other parent, if known. The name or barcode of any dplicate sample in the same plate. The sample name or barcode. The sex of the individal from which the sample was derived. M: Male F: Female U: Unknown The species from which the DNA sample was drawn. The type of tisse from which the DNA sample was drawn. The amont of sample, in microliters. The coordinates of the well in the sample plate (eg, A01 or H10). Batch Detail The Batch Detail tab provides detailed information abot the project batches. 1 In the Institte Detail pane, select Projects. 2 In the Projects pane, highlight a project. The project data appears at the bottom of the pane. 3 Select the Batch Detail tab. The batch detail appears. For information abot the colmns in this tab, see the table that follows. Table 9 Batch Detail Fields Amplification Plate Batch Prodct Name Sorce Plate Task The amplification plate ID. The batch nmber. The name of the prodct (eg, HmanHap300-Do). For mltise prodcts, this is the first BeadChip that is hybridized in the series. Make sre that the Prodct Name colmn is associated with the proper batch nmber for the prodct. Note: Mltise prodcts list mltiple batch nmbers for the same plate. It is important to note the batch nmber of the first BeadChip that is processed in the series. The sorce plate ID. The crrent qee of the batch. 22

26 Monitoring Project Usage The Project Usage tab provides information abot the samples that have been hybridized to a BeadChip. If yo adjst the clster files dring a project, yo may wish to reanalyze all the project samples. The Project Usage tab has a Reqee Prodcts for AtoCall fnction that lets yo reqee the samples per prodct to AtoCall, to regenerate genotyping call files. 1 In the Institte Detail pane, select Projects. 2 In the Projects pane, highlight a project. The project data appears at the bottom of the pane. 3 Select the Project Usage tab. Sample information for the project appear. For information abot the colmns in this table, see Project Usage Fields on page To reqee all the samples for a prodct in this project to AtoCall, select Reqee Prodcts for AtoCall. A list of all prodcts in this project appears. 5 Select the prodcts that yo want to reanalyze, and then select Reqee. If yo are reanalyzing de to adjstments in a clster file, remember that each clster file is specific to a prodct. Therefore, yo may not need to reanalyze the samples for every prodct. Table 10 Project Usage Fields Barcode Date Completed Date Created Prodct Name Sample Name Sample Section Stats The barcode of the individal BeadChip. The date and time when the batch amplification was completed. The date and time when the batch was added to the project. The name of the prodct (eg, HmanHap300-Do). The sample name. The section of the BeadChip where the sample was hybridized. Active: The batch is qeed for amplification. Completed: The samples in the batch have been amplified. Deleted: The batch was deleted. Viewing Project Batches 1 In the Institte Detail pane, select Projects. 2 In the Projects pane, highlight a project. The project data appears at the bottom of the pane. 3 Select the Batches tab. Batch information appears. For information abot the colmns on this tab, see the tables that follow. Table 11 Batches Fields Completed Date The date and time when the samples were amplified. 23

27 Created Date Format LIMS Task Nmber of Transfers Prodct Name Sample Batch ID Stats The date and time when the batch was created. The format of the prodct (eg, 1x10, 1x12, 96x1). The task that is being performed for this batch: Mltise BeadChip options: Make AMP2 Single-se BeadChip options: Make MSA# (where # is the MSA version), Make AMP# (where # is the AMP version) The nmber of wells from the sample plate that have been assigned to this batch. The name of the prodct (eg, HmanHap300-Do). Project Manager atomatically assigns a nmber to each batch. Select the batch nmber to open the Batch Detail window. Active: The batch is qeed for amplification. Completed: The samples in the batch have been amplified. Deleted: The batch was deleted. 4 To view detailed information abot a batch, select the batch nmber. The Displaying Batch Detail window opens and shows information abot every sample well in the batch. Table 12 Batch Detail Fields Analysis Species BeadChip BeadChip Qee Id Institte Project Sample Sample Plate Sample Species Sample Well Stats The species of the associated analysis file. The barcode nmber of the BeadChip. The BeadChip stats. The sample plate identification nmber. The name of the institte. The name of the selected project. The name of the sample. The name or barcode of the original sample plate. The species of the sample. The coordinates of the well in the sample plate (eg, A01 or H10). Active: The batch is qeed for amplification. Completed: The samples in the batch have been amplified. Deleted: The batch was deleted. Deleting Project Batches 1 In the Institte Detail pane, select Projects. 2 Highlight a project in the Projects pane. The project data appears at the bottom of the pane. 3 Select the Batches tab 4 Highlight one or more batches in the list and select Delete. Completed batches cannot be delete, only active batches can be deleted. 24

28 Viewing Batch History The Batch History pane shows historical batch data for all projects in the institte. To view batch data for a single project, see Viewing Project Batches on page In the left pane, select Project Manager. The Institte Search pane opens. 2 Find the appropriate institte. For more information, see Searching for an Institte on page 8. 3 Highlight the institte and select Institte Detail. 4 Select Batch History. The batch history information appears. Table 13 Batch History Fields Assay Type Batch ID Nmber of Transfers Plate Qee Stats The assay type: WGGT or GGGT. Project Manager atomatically assigns a nmber to each batch. Select the batch nmber to open the Batch Detail window. The nmber of wells from the sample plate that were assigned to this batch. Barcode nmber for amplification plate. The crrent task the amplification plate is qeed for. Active: The batch is qeed for amplification. Completed: The samples in the batch have been amplified. Deleted: The batch was deleted. 5 Select any batch to open a Batch Detail window. The window shows information abot every sample in the batch. Table 14 Item Alpha Coordinate appvaletype Item Item Sample Container Id Task Batch History Detail Fields Reqee for Atocall The name or barcode of the original sample plate. The coordinates of the well in the sample plate (eg, A01 or H10). Active: The batch is qeed for amplification. Completed: The samples in the batch have been amplified. Deleted: The batch was deleted. The name or barcode of the sample inside the well. The Barcode nmber of the BeadChip. Project Manager atomatically assigns a nmber to each batch. The BeadChip stats. Reqee for Atocall allows samples for an institte to be reqeed via project, batch, or BeadChip. Select the attribte to reqee by and the detail pane poplates with items available for reqee. 1 In the Institte Detail pane, select Reqee for Atocall. 2 Select an attribte (Project, Batch, or BeadChip) from the Reqee for Atocall by drop-down men. The details display in the lower portion of the pane and vary depending pon the selected attribte. 25