GMG Sample Submission Portal Client Instructions QS 15 · SOP No.: QS.19 Title: GMG SAMPLE...

STANDARD OPERATING PROTOCOL ALL SERVICES

Title: GMG SAMPLE SUBMISSION PORTAL CLIENT INSTRUCTIONS QS_15

SOP No.: QS.19_15 Version: 1 Effective Date: 27

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of 44 Z:\GMG\GMG\NATA\SOPs\QS_15_v1.docx

GMG Sample Submission Portal Client Instructions

QS_15




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Table of Contents 1. Login into GMG Sample Submission Portal ................................................................... 4

Create account procedure ....................................................................................... 4 1.1.

1.1.1. Confirmation email ........................................................................................... 5

Login procedure ...................................................................................................... 6 1.2.

Two step authentication .......................................................................................... 6 1.3.

Sequencing Sample Submission on GMGSSP software ................................................ 8 2.

New Sequencing Manifest ...................................................................................... 8 2.1.

2.1.1. What are “Manifests” ........................................................................................ 8

2.1.2. Submitting a Manifest ...................................................................................... 8

Premix SEQ & Fragment Analysis Module .............................................................. 9 2.2.

2.2.1. Urgent samples .............................................................................................. 10

2.2.2. For Premix SEQ module we prefer samples to be dried down ....................... 10

2.2.3. Sequencing Service or Fragment Analysis Service ........................................ 10

2.2.4. Dilution of Fragment Analysis samples .......................................................... 10

2.2.5. Size standard to be added or not to Fragment Analysis samples ................... 10

2.2.11. Submitting the manifest .............................................................................. 14

2.2.12. Error message when submitting ................................................................. 14

SEQ Other Module ................................................................................................ 15 2.3.

2.3.1. Project Sequencing with Analysis .................................................................. 15

2.3.2. Project Sequencing without Analysis ............................................................. 15

2.3.3. Plasmid Mix & SEQ........................................................................................ 15

2.3.4. PCR Mix & SEQ ............................................................................................. 15

2.3.5. Project Comments ......................................................................................... 16

2.3.6. Submitting the manifest ................................................................................. 18

2.3.7. Error message when submitting ..................................................................... 19

Clinical Sequencing Module .................................................................................. 20 2.4.

2.4.10. Submitting the manifest .............................................................................. 23

2.4.11. Error message when submitting ................................................................. 23

Nucleic Acid Extraction Sample Submission on GMGSSP software ............................. 24 3.

New Nucleic Acid Extraction Manifest ................................................................... 24 3.1.

High Throughput DNA Extraction Module ............................................................. 24 3.2.

3.2.1. QiaSymphony Extraction ............................................................................... 24

3.2.2. 96well Plate Spin Column Extraction ............................................................. 25



High Throughput RNA Extraction Module ............................................................. 29 3.3.




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3.3.1. QiaSymphony Extraction ............................................................................... 29

3.3.2. 96well Plate Spin Column Extraction ............................................................. 30



Manual Extraction Module ..................................................................................... 34 3.4.



Manifest Management.................................................................................................. 40 4.

Saved Manifests ................................................................................................... 40 4.1.

Pending Manifests ................................................................................................ 40 4.2.

Deleted and Released Manifests .......................................................................... 40 4.3.

Download of Results for submitted samples ................................................................. 41 5.

Automatic email for released manifests ................................................................. 41 5.1.

Downloading results .............................................................................................. 42 5.2.

Sending Samples to GMG ........................................................................................... 43 6.

Sending of samples .............................................................................................. 43 6.1.

Contact us ............................................................................................................ 44 6.2.

Pricing information ................................................................................................ 44 6.3.

Garvan Molecular Genetics Terms and Conditions ............................................... 44 6.4.




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1. Login into GMG Sample Submission Portal The GMG Sample Submission Portal LIMS (GMGSSP) is located on the Garvan Institute server and has the address https://gmg-submit.gimr.garvan.org.au/#/login.

Create account procedure 1.1.Once landed on the webpage the screen shown in figure 1 is displayed. Either login with an existing account see below or create a new account by clicking on the button called “Create Account” see figure 1. Once this button is clicked a new popup window will appear and all information for the new account that is to be created must be entered, see figure 2. In the Box called “Register” under Account Details there are two fields called “Client Details” and “Billing Details”. If the details for “Client details” are filled in the button called “Same as Client Details” can be clicked to transfer the data from the client details field to the billing details field.

Figure 1 GMG Sample Submission Portal landing page

Figure 2 Registering new client page (“Create Account”)

https://gmg-submit.gimr.garvan.org.au/#/login




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Once all fields marked with a star (*) have been entered and either the billing information is entered too or the “Same as Client details” button was clicked the button called “Create” needs to be clicked so the information is saved and the popup window is closed and disappears.

1.1.1. Confirmation email The software will then send an account validation email to your nominated email address, see figure 3 for an example. This email contains a link to validate the account and email address. If the link in the email is clicked a popup window opens, see figure 4.

Figure 3 Example of account validation email sent by the software

Figure 4 Popup window if link in validation email is clicked In this popup window you need to enter your email address and you can set a new password in the field called “New Password”. In the field called “Reenter Password” the new password




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must be re-entered. Finally, the box called “I have read and accept the GMG Privacy and Terms & Conditions” must be ticked and the button called “Set Password” clicked.

Login procedure 1.2.In the login screen you need to enter the account- linked- email address in the field called “Email:”, see figure 5.

Figure 5 Login screen with example email The password that was defined in the account setup procedure needs to be entered in the field called “Password”. Then the box called “I have read and accept the GMG Privacy and Terms & Conditions” must be ticked and the button called “Login” clicked.

Two step authentication 1.3.After the successful entry of the email address and password there will be a new popup window shown in figure 6.

Figure 6 Two step authentication screen with barcode




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You need to download on your phone or tablet an application called “Authenticator” from Apple’s App Store or Google’s Play Store. Once installed on your phone or tablet the barcode shown on the screen needs to be scanned with the phone’s camera, see figure 7. As soon as the barcode is recognised by the Authenticator software it will show a GMG Sample Submission Portal specific code on the display of the phone, see figure 8.

Figure 7 Authenticator software on phone scanning the barcode displayed on GMGSSP Once this code of 6 digits is entered into the field of the GMGSSP software called “Authentication Code” the button called “Authenticate” can be clicked. If the code matches the code the software expects the next window shown on the screen will be the GMG Sample Submission Portal home screen. If the authentication fails there will be an error message and you will need to repeat the process. The most likely reason for a failed authentication is that the authenticator code is timed out. Each authenticator password refreshes after 30sec. there is a little icon on your phone’s screen indicating how much time of the 30sec is left for this code to be active. In case this icon is already very small, just wait a few seconds until a new code is produced and then authenticate.

Figure 8 Entering the Authentication Code from the Authenticator software into GMGSSP

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Sequencing Sample Submission on GMGSSP 2.software Once successfully logged on the first screen shown is the home screen of the software, see figure 9. In the home screen window the current information for billing & shipping details are shown. Samples can be submitted and the pending manifests can be accessed and the status checked. You can edit your account information with the “Edit account information “ button.

Figure 9 Example of GMGSSP software home screen

New Sequencing Manifest 2.1.

2.1.1. What are “Manifests” Samples are submitted in so called “Manifests”. Manifests are the virtual entities which contain the sample information and establish a collection of one to many samples that are treated as a unity in processing, progression, resulting and billing.

2.1.2. Submitting a Manifest By clicking on the button called “New Sequencing Manifest” a new manifest for the Sequencing and Fragment Analysis services is generated. There are 3 service modules you can choose from: -Premix Sequencing & Fragment Analysis -Other Sequencing (which includes PCR Setup & Cleanup and Project Sequencing) -Clinical Diagnostic Sequencing After clicking the button called “New Sequencing Manifest” a popup window will appear that looks like figure 10.




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Figure 10 Popup Window to select the module for creating the manifest By clicking on the buttons called “Premix SEQ & Fragment Analysis” or “SEQ Other” or “Clinical” you can choose the module for which you want to submit samples. In the field called “Number of Samples” the number of samples to be submitted can be entered. After selecting the module you need to click on the button called “Create”.

Premix SEQ & Fragment Analysis Module 2.2.The Premix SEQ service module is selected for samples for which you have premixed the right amount of DNA (between 20 to 100ng of DNA depending on the size of your DNA fragment) and the primer (always at 3.2pmol of primer).

There is no perfect DNA amount we can recommend as the DNA amount depends on the quality of your DNA (degradation, buffer or other contaminants etc) and the length of the fragments (the rule is: the longer, the more DNA). Please dilute your stock primer on the day of sample preparation to 3.2pmol/ul (freeze thawing the primer at this concentration will unavoidably lead to poor sequencing data). After the module “Premix SEQ & Fragment Analysis” has been selected and the “Create” button was clicked a new window appears, see figure 12. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but certain fields need to be updated using drop down menus, see figure 11.

Figure 11 Premix SEQ & Fragment Analysis screen Client fields that need client input




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2.2.1. Urgent samples If you send urgent samples you can choose between 24h and 8h urgency levels in the drop down menu in the field called “Urgency”. 24h urgency will incur a service fee increase of 50% and the 8h turnaround time increase the service fee by 200%. Our regular turnaround time is 48h. For all sample submissions please be aware that the cut-off time for sample submission is 10.30am. If you select 24h urgency level please make sure your samples are in the facility sample reception fridge (level 8 behind lifts) before 10.30am.

2.2.2. For Premix SEQ module we prefer samples to be dried down The field called “Samples dried down” is a mandatory field and must be filled in by you. The option is “Yes” or “No” from the drop down menu. We prefer if you dry down the samples but if you are in a hurry we can do this for you without extra charge. If you want to dry down your samples just place them into a thermocycler at a constant temperature of 80C for 10min with the lids of the tubes removed so all liquid can evaporate. DNA is stable at these temperatures and this incubation will not affect the products. After all liquid is dried out close the tubes with the lids.

2.2.3. Sequencing Service or Fragment Analysis Service The next field down is called “Samples are submitted Sequencing or Fragment Analysis Service” and is also mandatory. The option for sample submission is either Sequencing Service or Fragment Analysis Service. If you select Fragment Analysis service there are a few more questions in the next fields down.

2.2.4. Dilution of Fragment Analysis samples The next field down is called “Do the fragment separation samples need dilution?” and is not mandatory. The option is “Yes” or “No” from the drop down menu. If your samples can be run directly (without dilution) select “No”. If your samples need to be diluted before loading on the instrument select “Yes” and in the sample comment field instruct us on how to dilute your samples (for example 1:10 or 1:20).

2.2.5. Size standard to be added or not to Fragment Analysis samples The next field down is called “Do the fragment separation samples need a size standard?” and is not mandatory. The option is “Yes” or “No” from the drop down menu. If your samples can be run directly (without size standard) select “No”. If your samples need a size standard before loading on the instrument select “Yes” and in the sample comment field instruct us on which size standard to add (we have GS500 or GS600).

Figure GS600




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Figure GS500

2.2.6. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 12 lower half of the figure.

Figure 12 Premix SEQ & Fragment Analysis sample submission screen There are two options for entering the location of the sample in the submitted Strip of tubes (0.2ml strip tubes) or the 96x well plate. If a 96x well plate is used the blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If you have a different way of submitting samples (other than the autofill positions) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number” for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.

2.2.7. Filling in sample information: Location in Strips If you want to submit samples in strip tubes please use 0.2ml 8x strip tubes from Interpath Services Pty. Ltd. (Cat# 3131-00; 0.2mL 8-Strip PCR Tubes with Caps pkt/ 1000).




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If you have more than 50 samples we recommend using 96-well semi skirted PCR plates covered with a seal (recommended Bio-Rad Cat # HSS-9901). The location of the samples in the strips can be entered in the second column called “Strip Position”. Using the black down button will prefill the fields for each sample. If you have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “SX:Y” where X = strip number and Y= sample number; for example S1:1, S1:2, S1:3 etc or S2:1, S2:2, S2:3 etc., see figure 12_1 below. All fields must be entered, meaning no sample can be without location information in the correct format.

Figure 12-1 How to label your strip tubes

2.2.8. Filling in sample information: sample names You have to enter sample names in the fields under the heading called “Sample Name”. This is the only mandatory field in the Premix SEQ service. There are no rules around sample names other that they must contain more than 1 letter or number and no special characters can be used like , . ; : ” + = @ $ % ^ & * ( ) < > ? ! or – (hyphen). The only permitted character is an underscore ( _ ). All samples need to have a name, names can be repetitive. Sample names can also be copied and pasted from Excel sheets by clicking on the little table button, see figure 12a, yellow highlighted. A popup window will appear, see figure 12b, and sample names can be copied from any source file into this window, see figure 12c. Clicking on the button called “Save will apply the sample names into the sample name fields of the software, see figure 12d. If you leave a field without a name the software will create an error message. So, if you have selected more samples then you later realize you want to submit, cancel this submission and create a new manifest.




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Figure 12a Click on the table button to enter names from an excel sheet

Figure 12b Popup window to enter same names for example from Excel

Figure 12c Copying process for sample names into the popup window

Figure 12d Sample names have been transferred into the sample submission software

2.2.9. Filling in sample information: optional fields You can enter more information like comments, primers used, sample material DNA amount or Primer amount. These fields are not mandatory and the information will be associated to the submitted sample.

COPY

PASTE




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2.2.10. Saving the information of the manifest After all information is entered the manifest can be saved for future submission by clicking on the button called “Save”, see figure 13.

Figure 13 Premix SEQ & Fragment Analysis screen manifest Save and Submit buttons

2.2.11. Submitting the manifest You can finally submit your manifest by clicking on the button called “Submit”, see figure 13. If there is no error (see heading below) in the manifest the submission will be confirmed by a popup window displayed in figure 14. This window can be confirmed by clicking on the button called “ok”.

Figure 14 Premix SEQ & Fragment Analysis screen popup window after submission

2.2.12. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 15. After the button called “ok” was clicked the popup window disappears and the Premix SEQ & Fragment Analysis screen shows the manifest with the fields in which the error occurred in red, see figure 16. After correcting the errors you can press the button called “Submit” again.

Figure 15 Premix SEQ & Fragment Analysis screen error popup window

Figure 16 Premix SEQ & Fragment Analysis screen with errors highlighted red




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SEQ Other Module 2.3.After the module “SEQ Other” has been selected and the create button was clicked a new window appears, see figure 17. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but certain fields need to be updated using drop down menus, see figure 18. If you send urgent samples you can choose between 24h and 8h urgency levels in the drop down menu in the field called “Urgency”. The field called “Project name” is a non- mandatory field and you can fill this field with a project name of your choice. The next field down is called “Internal or External Project” and is also a non- mandatory field. The option is either “internal” for internal clients or “external” for external clients. These options can be selected from the dropdown menu. The next field down is called “Requested Sequencing Service” and is a mandatory field. The options are:

2.3.1. Project Sequencing with Analysis You send us DNA and let us know what mutation (location) you are interested in and we design primers and perform PCR and sequence the product and perform an analysis (align the data against a reference gene and find the mutations) and send you a technical report. Please send at least 50ul of DNA of at least a concentration of 50ng/ul. Alternatively you can send us blood or tissue or any other material and we will extract DNA before we sequence the DNA.

2.3.2. Project Sequencing without Analysis You send us DNA and let us know what mutation (location) you are interested in and we design primers and perform PCR and sequence the product and but you perform the analysis and we just send you the raw data (abi) files. Please send at least 50ul of DNA of at least a concentration of 50ng/ul. Alternatively you can send us blood or tissue or any other material and we will extract DNA before we sequence the DNA.

2.3.3. Plasmid Mix & SEQ You send us plasmid DNA (at least 100ng) and we mix the DNA with primers at the right concentrations and sequence the mix and send you the raw data (abi) files. Please check your plasmid prep on a gel to see that there are no side products present. You should see only one clean band on the gel. If you have picked two colonies you will receive an overlay of two sequences which cannot be interpreted. Rule: the better your submitted DNA quality, the better the out-coming abi files.

2.3.4. PCR Mix & SEQ You send us your PCR product (at least 100ng) and we clean it up and mix it with primers at the right concentrations and sequence the mix and send you the raw data (abi) files. Please check your PCR product on a gel to see that there are no side products present. You should see only one clean band on the gel. Side products might sequence and you will receive an overlay of two sequences which cannot be interpreted. Rule: the better your submitted DNA quality, the better the out-coming abi files.




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2.3.5. Project Comments The next field down is called “Comments” and is non-mandatory. You can enter comments you think are relevant for the project you are submitting and will be good to know for the operator and in regards to analysis or billing.

2.3.6. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 17 lower half of the figure. The blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If you have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number” for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.

2.3.1. Filling in sample information: Sample Name You have to enter sample names in the fields under the heading called “Sample Name”. This is the a mandatory field. There are no rules around sample names other that they must contain more than 1 letter or number and no special characters can be used like , . ; : ” + = @ $ % ^ & * ( ) < > ? ! or – (hyphen). The only permitted character is an underscore ( _ ). All samples need to have a name, names can be repetitive. Sample names can also be copied and pasted from excel sheets by clicking on the little table button, see figure 19, yellow highlighted. A popup window will appear, see figure 20, and sample names can be copied from any source file into this window. Clicking on the button called “Save will apply the sample names into the sample name fields of the software. If you leave a field without a name the software will create an error message. So, if you have selected more samples then you later realize you want to submit, cancel this submission and create a new manifest.

Figure 17 SEQ Other sample submission screen




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Figure 18 SEQ Other sample submission screen fields that need client input

Figure 19 SEQ Other sample submission screen table fill and downfill options

Figure 20 SEQ Other sample submission screen excel input

2.3.2. Filling in sample information: Sample Material You have to enter the material of the samples you are sending in the field called “Sample Material”. This is a mandatory field. There are several options to choose from in the dropdown menu like “Blood”, “Cells”, “Buffy Coat”, “DNA”, “cDNA”, “Tissue”, etc. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 20, red highlighted.

2.3.3. Filling in sample information: Primer to be used You have to enter the primer that you want to be used with the submitted samples in the field called “Primer to be used”. This is a mandatory field. There are several options to choose from in the dropdown menu: -submitted with sample This option means you just send with your samples the primer you want us to use with the samples. You can either give us a stock primer tube (lypophilised or liquid) or the diluted primer at a concentration of 10uM.

-to be designed by GMG from your submitted SEQ file We will design the primer for you and order it from IDT and use it with your DNA samples. Please be specific what region of a sequence you are interested in. Call us in case of doubt. Any of the following primers is already available in our primer library. This means we have these primers in house and they can be used immediately without delay of ordering in primers:




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- The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 20, red highlighted.

2.3.4. Filling in sample information: non-mandatory fields You can enter further information about your samples in several non-mandatory fields which are called “Sample Concentration (ng/ul)”, “Reference Sequence”, “Gene of Interest”, Organism” and “Comments”. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 20, red highlighted.

2.3.5. Saving the manifest After all information is entered the manifest can be saved for future submission by clicking on the button called “Save”, see figure 21.

Figure 21 SEQ Other sample submission screen manifest Save and Submit buttons





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Figure 22 SEQ Other sample submission screen popup window after submission

2.3.7. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 23. After the button called “ok” was clicked the popup window disappears and the SEQ other module screen shows the manifest with the fields in which the error occurred in red, see figure 24. After correcting the errors you can press the button called “Submit” again.

Figure 23 SEQ Other sample submission screen error popup window

Figure 24 SEQ Other sample submission screen with errors highlighted red




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Clinical Sequencing Module 2.4.You can choose the clinical sequencing module for patient samples that need confirmatory Sanger Sequencing. Please make sure you submit at least 3 sample identifying information items with your sample (patient name, ID, DOB, address etc). Please also submit a patient consent form (which can be found on our webpage) with your sample. As part of Australian legislation including the Australian Privacy Principles set out in the Privacy Act 1988 and in accordance with Garvan Institute’s general privacy regulations Garvan Molecular Genetics is committed to ensure and enforce the maintenance of patient’s privacy at all times. Our privacy policy details how we maintain the privacy of patient related data. Please find a copy of the Patient Consent Form and GMG’s Privacy Policy at: http://www.garvan.org.au/research/capabilities/molecular-genetics/diagnostic-clinical-services

Finally make sure you fill in the information of the mutation that was identified and needs to be confirmed. Please submit the mutation to be identified in one of the following 3 possible formats:

1) NM_004643.3:c.476C>T

2) NC_000002.11:g.166211155G>A

3) ChrX(GRCh37):g.48932540G>T

Please also submit the gene name (for example PBN1 or OPN1A).

2.4.1. Filling in the online Sample Submission Form After the module “Clinical” has been selected and the create button was clicked a new window appears, see figure 25. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but one field needs to be updated using a drop down menu, see figure 25. The field called “Client Request” is a mandatory field and two options can be selected via the dropdown menu. The selection can either be “Clinical Diagnostic SEQ with Technical Report” or “Clinical Diagnostic SEQ with Genetic Pathology Report”. The next field down is called “Comments” and is non-mandatory. You can enter comments you think are relevant for the project you are submitting and will be good to know for the operator and in regards to analysis or billing.

2.4.2. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 25 lower half of the figure. The blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If you have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number” for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.

2.4.3. Filling in sample information: Patient Name You have to enter patient names in the fields under the heading called “Patient Name”. This is a mandatory field. There are no rules around patient names other that they must contain more than 1 letter or number and no special characters can be used like , . ; : ” + = @ $ % ^ & * ( ) < > ? ! or – (hyphen). The only permitted characters are space ( ) or underscore

http://www.garvan.org.au/research/capabilities/molecular-genetics/oligo-ordering




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( _ ). All patient name fields must have a name. If you leave a field without a name the software will create an error message. So, if you have selected more samples then you later realize you want to submit, cancel this submission and create a new manifest. Patient names can also be copied and pasted from excel sheets by clicking on the little table button, see figure 26, yellow highlighted. A popup window will appear, see figure 27, and patient names can be copied from any source file into this window. Clicking on the button called “Save will apply the patient names into the patient name fields of the software.

Figure 25 Clinical module sample submission screen

Figure 26 Clinical module sample submission screen table fill and downfill options

Figure 27 Clinical module sample submission screen excel input

2.4.4. Filling in sample information: Submitted Sample ID You have to enter the sample IDs of the samples you are sending in the field called “Submitted Sample ID”. This is a mandatory field. There are no rules around Sample IDs other that they must contain more than 1 letter or number and no special characters can be used like: space , . ; : ” + = @ $ % ^ & * ( ) < > ? ! or – (hyphen). The only permitted character is an underscore ( _ ). All samples need to have a Submitted Sample ID, IDs can be repetitive. Sample IDs can also be copied and pasted from excel sheets by clicking on the little table button, see figure 26, yellow highlighted. A popup window will appear, see




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figure 27, and sample IDs can be copied from any source file into this window. Clicking on the button called “Save will apply the Sample IDs into the Sample IDs fields of the software.

2.4.5. Filling in sample information: Patient Date of Birth You have to enter the Date of Birth of the patient for the sample(s) you are sending in the field called “Patient Date of Birth”. This is a mandatory field. The date of birth of the patient can either be entered by typing the date of birth in the field in the format DD/MM/YYYY, so for a patient with a date of birth on the 2nd of August 2000 the correct entry would be “02/08/2000” or the entry can be done via a popdown calendar, see figure 28. Navigation in the calendar window occurs with the left and right arrows for selection of the month and year and by clicking on the number of the day for selection of the day.

Figure 28 Clinical module sample submission screen Patient Date of Birth dropdown

calendar entry

2.4.6. Filling in sample information: Sample Material You have to enter the material of the samples you are sending in the field called “Sample Material”. This is a mandatory field. There are several options to choose from in the dropdown menu like “Blood”, “Cells”, “Buffy Coat”, “DNA”, “cDNA”, “Tissue”, etc. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 26, red highlighted. If you send us genomic DNA, please send us at least 50ul of DNA with a concentration of at least 50ng/ul. If you send us blood samples please make sure they are sent cooled on ice and are not coagulated (ideally you send us 5ml EDTA blood tubes).

2.4.7. Filling in sample information: Confirmatory You have to confirm that the sample submission is a confirmatory testing not a predictive testing. Therefore in the drop down menu for the field called “Confirmatory” there is only one selection called “Yes” yet this field is mandatory and you need to select this option to legally state that this is a confirmatory diagnostic submission. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 26, red highlighted.

2.4.8. Filling in sample information: non-mandatory fields You can enter further information about your patient samples in several non-mandatory fields which are called “Patient ID”, “Patient Address”, “Date Sample Taken”, “Sample Concentration (ng/ul)”, “Sample Volume (ul)”, “Disease/Syndrome”, “Mutation”, Gene of Interest”, “Reference Sequence Number”, Primer to be used”, “Referring Clinician”, “Referring Laboratory Name”, “Referring Laboratory Address” and “Comments”. The arrow




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down can be used to fill the entire column with the selected sample material of the first field, see figure 26, red highlighted.

2.4.9. Saving the manifest After all information is entered the manifest can be saved for future submission by clicking on the button called “Save”, see figure 29.

Figure 29 Clinical module sample submission screen manifest Save and Submit buttons


Figure 30 Clinical module sample submission screen popup window after submission

2.4.11. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 31. After the button called “ok” was clicked the popup window disappears and the Clinical module screen shows the manifest with the fields in which the error occurred in red, see figure 32. After correcting the errors you can press the button called “Submit” again.

Figure 31 Clinical module sample submission screen error popup window

Figure 32 Clinical module sample submission screen with errors highlighted red




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Nucleic Acid Extraction Sample Submission on 3.GMGSSP software Once successfully logged on the first screen shown is the home screen of the software, see figure 9. In the home screen window the current information for billing & shipping details are shown. Samples can be submitted and the pending manifests can be accessed and the status checked. Samples are submitted in so called “Manifests”. Manifests are the virtual entities which contain the sample information and establish a collection of 1 to many samples that are treated as a unity in processing, progression, resulting and billing.

New Nucleic Acid Extraction Manifest 3.1.By clicking on the button called “New DNA/RNA Manifest” a new manifest for the Nucleic Acid Extraction Service is generated. There are 3 service modules you can choose from: -High Throughput DNA Extraction -High Throughput RNA Extraction -Manual Extraction After clicking the button called “New DNA/RNA Manifest” a popup window will appear that looks like figure 33.

Figure 33 Popup Window to select the module for creating a manifest By clicking on the buttons called “High Throughput DNA Extraction” or “High Throughput RNA Extraction” or “Manual Extraction” you can choose the module. In the field called “Number of Samples” the number of samples to be submitted can be entered. After selecting the module you need to click on the button called “Create”.

High Throughput DNA Extraction Module 3.2.We have two high throughput extraction methods available:

3.2.1. QiaSymphony Extraction You can choose to have your samples extracted via our QiaSymphony which is a magnetic bead based extraction technology performed on an automated platform. Please submit your samples in 2ml screw cap tubes from Sarstedt (cat # 72.693.005). Please select in the field called “QiaSymphony or 96wellSpinColumns” the option “QiaSymphony” for the sample(s) that you wish the extraction to be performed on the QiaSymphony. Please also decide on the extraction volume. There are 3 extraction volumes you can choose from, 50ul, 100ul or




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200ul. If not specified in the field called “Extraction Volume (standard = 200ul)” the sample(s) will be eluted in 200ul volume which is our standard extraction volume.

3.2.2. 96well Plate Spin Column Extraction You can choose to have your samples extracted on 96x well spin column plates which is a silica membrane based extraction technology. Please select in the field called “QiaSymphony or 96wellSpinColumns” the option “96wellSpinColumns” for the sample(s) that you wish the extraction to be performed with 96well spin columns. Please also decide on the extraction volume. You can choose any volume between 30ul and 200ul. If not specified in the field called “Extraction Volume (standard = 200ul)” the sample(s) will be eluted in 200ul volume which is our standard extraction volume. After the module “High Throughput DNA Extraction” has been selected and the create button was clicked a new window appears, see figure 35. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but certain fields need to be updated using drop down menus, see figure 34.

Figure 34 High Throughput DNA Extraction screen Client fields that need client input If you send urgent samples you can choose between 24h and 8h urgency levels in the drop down menu in the field called “Urgency”. The field called “Sample Type” is a mandatory field and must be filled in. The options are “Tissue (excl. homogenization)”, “Tissue (incl. homogenization)”, “Buccal Swab (OraCollect)”, “Blood”, “Buffy Coat”, “Serum” or “Other”. The next field down is called “Qubit Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a fluorescent method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Nanodrop Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a photometeric method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Agilent Gel Analysis” and is not mandatory; you can choose whether you want your samples to be analysed after extraction by a quantitative gel analysis (Agilent Bio-analyser 2100 DNA gel) which will add a service fee to your extraction costs. The option is “Yes” or “No” from the drop down menu.

3.2.3. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 35 lower half of the figure.




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Figure 35 High Throughput DNA Extraction sample submission screen The blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If you have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number” for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.

3.2.1. Filling in sample information: sample names You have to enter sample names in the fields under the heading called “Sample Name”. This is the only mandatory field. There are no rules around sample names other that they must contain more than 1 letter or number and no special characters can be used like , . ; : ” + = @ $ % ^ & * ( ) < > ? ! or – (hyphen). The only permitted character is an underscore ( _ ). All samples need to have a name, names can be repetitive. Sample names can also be copied and pasted from Excel sheets by clicking on the little table button, see figure 35a, yellow highlighted. A popup window will appear, see figure 35b, and sample names can be copied from any source file into this window, see figure 35c. Clicking on the button called “Save will apply the sample names into the sample name fields of the software, see figure 35d. If you leave a field without a name the software will create an error message. So, if you have selected more samples then you later realize you want to submit, cancel this submission and create a new manifest.






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3.2.2. Filling in sample information: optional fields Especially for clinical samples that can also be submitted for this service you can enter patient information in the following fields: “Comments”, “Patient Name”, “Patient ID”, “Patient Date of Birth”, “Patient Address”, “Date Sample Taken”, “Referring Clinician”, “Referring Clinician Address”, “Referring Laboratory Name” and “Referring Laboratory Address”. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 36, red highlighted. The table icon can be used to import from excel sheets via a popup window that allows copy and paste, see figure 36, yellow highlight.

Figure 36 High Throughput DNA Extraction screen table fill and downfill options To enter the Date of Birth of the patient or when the sample was taken the date can either be entered by typing the date in the field in the format DD/MM/YYYY, so for a patient with a date of birth on the 2nd of August 2000 the correct entry would be “02/08/2000” or the entry can be done via a popdown calendar, see figure 37. Navigation in the calendar window occurs with the left and right arrows for selection of the month and year and by clicking on the number of the day for selection of the day.

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Figure 37 Patient Date of Birth or Sample Taken entry dropdown calendar entry


Figure 38 High Throughput DNA Extraction screen manifest Save and Submit buttons


Figure 39 High Throughput DNA Extraction screen popup window after submission

3.2.5. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 40. After the button called “ok” was clicked the popup window disappears and the High Throughput DNA Extraction screen shows the manifest with the fields in which the error occurred in red, see figure 41. After correcting the errors you can press the button called “Submit” again.

Figure 40 High Throughput DNA Extraction screen error popup window




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Figure 41 High Throughput DNA Extraction screen with errors highlighted red

High Throughput RNA Extraction Module 3.3.We have two high throughput extraction methods available:

3.3.1. QiaSymphony Extraction You can choose to have your samples extracted via our QiaSymphony which is a magnetic bead based extraction technology performed on an automated platform. Please submit your samples in 2ml screw cap tubes from Sarstedt (cat # 72.693.005). Please select in the field called “QiaSymphony or 96wellSpinColumns” the option “QiaSymphony” for the sample(s) that you wish the extraction to be performed on the QiaSymphony. Please also decide on




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the extraction volume. There are 3 extraction volumes you can choose from, 50ul, 100ul or 200ul. If not specified in the field called “Extraction Volume (standard = 200ul)” the sample(s) will be eluted in 200ul volume which is our standard extraction volume.

3.3.2. 96well Plate Spin Column Extraction You can choose to have your samples extracted on 96x well spin column plates which is a silica membrane based extraction technology. Please select in the field called “QiaSymphony or 96wellSpinColumns” the option “96wellSpinColumns” for the sample(s) that you wish the extraction to be performed with 96well spin columns. Please also decide on the extraction volume. You can choose any volume between 30ul and 200ul. If not specified in the field called “Extraction Volume (standard = 200ul)” the sample(s) will be eluted in 200ul volume which is our standard extraction volume. After the module “High Throughput RNA Extraction” has been selected and the create button was clicked a new window appears, see figure 43. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but certain fields need to be updated using drop down menus, see figure 42.

Figure 42 High Throughput RNA Extraction screen Client fields that need client input If you send urgent samples you can choose between 24h and 8h urgency levels in the drop down menu in the field called “Urgency”. The field called “Sample Type” is a mandatory field and must be filled in by the client. The options are “Tissue (excl. homogenization)”, “Tissue (incl. homogenization)”, “Blood”, “Buffy Coat”, “Cells”, “FFPE”, “PAXgene” or “Other”. The next field down is called “Qubit Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a fluorescent method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Nanodrop Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a photometeric method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Agilent Gel Analysis” and is not mandatory; you can choose whether you want your samples to be analysed after extraction by a quantitative gel analysis (Agilent Bio-analyser 2100 DNA gel) which will add a service fee to your extraction costs. The option is “Yes” or “No” from the drop down menu.

3.3.3. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 42 lower half of the figure. The blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If clients have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number”




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for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.

Figure 43 High Throughput RNA Extraction sample submission screen







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3.3.5. Filling in sample information: optional fields Especially for clinical samples that can also be submitted for this service clients can enter patient information in the following fields: “Comments”, “Patient Name”, “Patient ID”, “Patient Date of Birth”, “Patient Address”, “Date Sample Taken”, “Referring Clinician”, “Referring Clinician Address”, “Referring Laboratory Name” and “Referring Laboratory Address”. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 44, red highlighted. The table icon can be used to import from excel sheets via a popup window that allows copy and paste, see figure 44, yellow highlight.

Figure 44 High Throughput RNA Extraction screen table fill and downfill options To enter the Date of Birth of the patient or when the sample was taken the date can either be entered by typing the date in the field in the format DD/MM/YYYY, so for a patient with a date of birth on the 2nd of August 2000 the correct entry would be “02/08/2000” or the entry can be done via a popdown calendar, see figure 45. Navigation in the calendar window occurs with the left and right arrows for selection of the month and year and by clicking on the number of the day for selection of the day.

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Figure 46 High Throughput RNA Extraction screen manifest Save and Submit buttons

3.3.7. Submitting the manifest You can finally submit your manifest by clicking on the button called “Submit”, see figure 46. If there is no error (see heading below) in the manifest the submission will be confirmed by a popup window displayed in figure 47 This window can be confirmed by clicking on the button called “ok”.

Figure 47 High Throughput RNA Extraction screen popup window after submission

3.3.8. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 48. After the button called “ok” was clicked the popup window disappears and the High Throughput RNA Extraction screen shows the manifest with the fields in which the error occurred in red, see figure 49. After correcting the errors you can press the button called “Submit” again.

Figure 48 High Throughput RNA Extraction screen error popup window




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Figure 49 High Throughput RNA Extraction screen with errors highlighted red

Manual Extraction Module 3.4.For our Manual Extraction Service module we use single spin columns which is a silica membrane based extraction technology. Please decide on the extraction volume. You can choose any extraction volume between 30ul and 200ul. We are flexible with the extraction volume. If not specified in the “Comment” field of the sample we will extract in 200ul which is our standard extraction volume.




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After the module “Manual Extraction” has been selected and the create button was clicked a new window appears, see figure 51. The fields for Billing Information should be prefilled by the software and can be overwritten if so needed or just accepted. The Client Information field has the name and email prefilled but certain fields need to be updated using drop down menus, see figure 50.

Figure 50 Manual Extraction screen Client fields that need client input If you send urgent samples you can choose between 24h and 8h urgency levels in the drop down menu in the field called “Urgency”. The field called “Sample Type” is a mandatory field and must be filled by you. The options are “Tissue (excl. homogenization)”, “Tissue (incl. homogenization)”, “Buccal Swab (OraCollect)”, “Blood”, “Buffy Coat”, “Cells”, “PAXgene”, “FFPE”, “Serum” or “Other”. The next field down is called “Qubit Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a fluorescent method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Nanodrop Concentration Measurement” and is not mandatory; you can choose whether you want your samples to be measured after extraction by a photometeric method which will add a service fee to your extraction costs. The option is either is “Yes” or “No” from the drop down menu. The next field down is called “Agilent Gel Analysis” and is not mandatory; you can choose whether you want your samples to be analysed after extraction by a quantitative gel analysis (Agilent Bio-analyser 2100 DNA gel) which will add a service fee to your extraction costs. The option is “Yes” or “No” from the drop down menu.

3.4.1. Filling in sample information: Location in plate In the rows below the Client and Billing Information fields is the area for entering sample related information, see figure 51 lower half of the figure. The blue arrow can be clicked and the software will automatically fill the location for the number of samples selected. If clients have a different way of submitting samples (other than the autofill position) the autofill can be overwritten or sample locations can be entered manually in the format “letter:number” for example A:1, A:2, A:3 etc or A:1, B:1, C:1 etc. All fields must be entered, meaning no sample can be without location information in the correct format.




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Figure 51 Manual Extraction sample submission screen







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3.4.3. Filling in sample information: optional fields Especially for clinical samples that can also be submitted for this service clients can enter patient information in the following fields: “Comments”, “Patient Name”, “Patient ID”, “Patient Date of Birth”, “Patient Address”, “Date Sample Taken”, “Referring Clinician”, “Referring Clinician Address”, “Referring Laboratory Name” and “Referring Laboratory Address”. The arrow down can be used to fill the entire column with the selected sample material of the first field, see figure 52, red highlighted. The table icon can be used to import from excel sheets via a popup window that allows copy and paste, see figure 52, yellow highlight.

Figure 52 Manual Extraction screen table fill and downfill options To enter the Date of Birth of the patient or when the sample was taken the date can either be entered by typing the date in the field in the format DD/MM/YYYY, so for a patient with a date of birth on the 2nd of August 2000 the correct entry would be “02/08/2000” or the entry can be done via a popdown calendar, see figure 53. Navigation in the calendar window occurs with the left and right arrows for selection of the month and year and by clicking on the number of the day for selection of the day.

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Figure 54 Manual Extraction screen manifest Save and Submit buttons


Figure 55 Manual Extraction screen popup window after submission

3.4.6. Error message when submitting If there are errors in the manifest there will be a popup window shown in figure 56. After the button called “ok” was clicked the popup window disappears and the Manual Extraction screen shows the manifest with the fields in which the error occurred in red, see figure 57. After correcting the errors the client can press the button called “Submit” again.

Figure 56 Manual Extraction screen error popup window




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Figure 57 Manual Extraction screen with errors highlighted red




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Manifest Management 4.You can view the status of your submitted sample manifests on the “Home” screen. Sample Manifests are shown in the lower half of the screen as either “Saved”, Deleted”, “Pending” or “Released”.

Saved Manifests 4.1.Saved Manifests have been saved but not submitted, see figure 58 for an example. These manifests can be reopened by clicking on the manifest and then you can continue completing the manifest and either save for a later submission or submit for these manifests to become a status “pending” manifest. As soon as the saved manifest is submitted it appears in GMG’s sample management software. Saved manifests can be deleted with the button called “Delete”. If you choose to click on the delete button a popup window will appear, see figure 59. In the popup window the action of deleting a manifest can be either confirmed by clicking the button called “Delete” or cancelled by clicking the button called “Cancel”. After clicking either one of these two options the popup window will disappear.

Pending Manifests 4.2.Pending Manifests have been submitted, see figure 58 for an example. These manifests are in progress in GMG’s sample management software. Pending manifests can be deleted with the button called “Delete”. If you choose to click on the delete button a popup window will appear, see figure 59. In the popup window the action of deleting a manifest can be either confirmed by clicking the button called “Delete” or cancelled by clicking the button called “Cancel”. After clicking either one of these two options the popup window will disappear.

Deleted and Released Manifests 4.3.Deleted and Released Manifests can only be viewed, see figure 58 for an example. These manifests are completed and cannot be altered after their completion. If clicked on the manifest or on the green button called “View” the manifest will open and show its content, see figure 60 for an example.

Figure 58 Sample Submission Portal Home Screen




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Figure 59 Delete Popup Window

Figure 60 Example Manifest that was opened after a release status update

Download of Results for submitted samples 5.Once manifests have been progressed in the GMG Sample Management Software to the status of released we will send you an automatic email to your nominated email address defined in your account. In this email is a link that enables you to download the results for the submitted samples as a ZIP file. Sample Manifests are shown in the Home screen of the sample submission portal as “Released” and they have a green button called “View” which you can click to access the manifest to download the results, see figure 60a.

Figure 60a Home Screen with several manifest examples shown

Automatic email for released manifests 5.1.The software will send an automatic email to the nominated email address defined in your account that looks like figure 61.You have to login into your account first and THEN you can download the data via the link in the email. If you click the link directly without logging in first the software will take you to the login screen. The email also contains the technical report according to NATA requirements as an attachment.




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Figure 61 Automatic email for released manifests

Downloading results 5.2.When the manifest for which results shall be downloaded is opened the screen shows the information for the results and also contains a button called “Download All Results (zip)”, see figure 63. If this button is clicked the software will create a ZIP folder in your download folder on the C: drive of your computer, see figure 62 for an example. In this ZIP folder are the actual .abi result files, the seq files with the sequence result as a text file and the summary of sample names and GMG IDs in an excel sheet.

Figure 62 Example of file content of opened ZIP folder after download




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Figure 63 Manifest screen with button called “Download All Results (zip)”

Sending Samples to GMG 6.

Sending of samples 6.1.Please use the below address to send samples to us. The samples should be sent in a padded envelope with Australia Mail or by courier: For Australia Mail Attn. Pavel Bitter Garvan Institute GMG/ Level 8 384 Victoria Street Darlinghurst, NSW, 2010 For Couriers Attn. Pavel Bitter Garvan Institute Loading Dock West Street (off Burton Street) Darlinghurst, NSW, 2010 Loading Dock phone: 02 9295 8640 Dock times: 8am to 4pm Alternatively you can drop off your samples in our sample reception fridge on level8 behind the lifts:




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Contact us 6.2.We have an all encompassing webpage, please have a look at: https://www.garvan.org.au/research/capabilities/molecular-genetics You can also call us on 02 92958384 Or email us at [email protected]

Garvan Molecular Genetics Pavel Bitter (Molecular Genetics Facility Manager) email: [email protected]

Pricing information 6.3.Please find our current pricing information on our webpage under: https://www.garvan.org.au/research/capabilities/molecular-genetics/shop

Garvan Molecular Genetics Terms and Conditions 6.4.Our Terms and Conditions apply to all services provided by Garvan Molecular Genetics (GMG), a service of the Garvan Institute of Medical Research, on request from Specialists or Researchers. The obligation of GMG to perform the Services is conditional on acceptance of a Request and the samples which need to pass acceptance to the service. For clinical diagnostic sequencing the request for service must be supported by the following documents:

-a completed Clinical Diagnostic Sequencing Sample Submission Form -a completed GMG Patient Consent Form

On acceptance of the Request, GMG will perform the Services in accordance with its Terms and Conditions detailed in the document GMG Terms and Conditions.

https://www.garvan.org.au/research/capabilities/molecular-genetics

mailto:[email protected]

mailto:[email protected]

https://www.garvan.org.au/research/capabilities/molecular-genetics/shop

GMG Sample Submission Portal Client Instructions QS 15 · SOP No.: QS.19 Title: GMG SAMPLE...

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Transcript of GMG Sample Submission Portal Client Instructions QS 15 · SOP No.: QS.19 Title: GMG SAMPLE...