Submission guidelines

Submission guidelines

An overview of the process for submitting samples :

  1. Contact the Project Management  team to discuss project via:
    1. Email: kccgseq@garvan.org.au
    2. Phone: +61 2 9355 5767; or
    3. In person: on Level 6 of The Kinghorn Cancer Centre
  2. Receive quote and login details to the KCCGCF billing  system: https://books.zoho.com/app#/home/
  3. Login and accept quote 
  4. Submit a Purchase Order to kccgseq@garvan.org.au 
  5. Receive login details to the KCCGCF Customer Portal: https://apps.kccg.garvan.org.au/sample-submission-x/#/home
  6. Receive email with link to manifest 
  7. KCCGCF-supplied FluidX barcoded  tubes will be posted to you 
  8. Fill in and submit manifest 
  9. Wait for ‘manifest accepted’  email 
  10. Aliquot your aamples into the KCCGCF-supplied FluidX barcoded tubes 
  11. Submit samples to KCCGCF along with manifest label as per shipping requirements below.

Sample preparation requirements

The  quality  and  quantity  of  input  Sample  (DNA/RNA or library)  are  critical  determinants  of  the success of a sequencing run and the generation  of robust sequencing data.

Please notify  the  Project  Management   team  if  the  below  requirements  cannot  be  met  by  your Samples, and/or if there are special requirements for the handling of your Samples.

Samples that do not pass the following  requirements,  as assessed using our in-house QC protocols, will be removed from further processing and the Customer will be notified of next steps. 

We cannot  guarantee QC performance and sequencing metrics for FFPE-derived, bisulphite converted Samples or submitted libraries.

Genomic DNA 

  • DNA should be extracted  using Qiagen  DNeasy / Tissue Extraction  kits or equivalent.  Please contact KCCGCF to ensure compatibility of the extraction protocol  prior to extraction.
  • Samples must be pure, intact and of high molecular weight. 
  • Samples must be free of contaminating nucleic acids. 
  • Samples must not be amplified (PCR, WGA, MDA etc.). 
  • DNA should be submitted in Qiagen  Elution Buffer (EB), Illumina Resuspension Buffer (RSB) or similar (10mM Tris/1 mM EDTA). 
  • Sample concentration must be completed using a fluorometric assay specific to  dsDNA  (e.g. Picogreen, Qubit  BR assay). 
  • Sample quality must be assessed prior to submission, preferably  using a Bioanalyzer, LabChip GX (or similar). 
  • Samples must meet the following specifications (QC Metrics):

Protocol

Vol. (uL)

Conc. (ng /uL)

Insert size

A260:280

Total

WGS: TruSeq Nano DNA Library Preparation Kit

100

10 - 40

450 bp

>1.8

>1 ug

WGS: KAPA Hyper PCR- Free Library Preparation Kit

100

12 - 100

450 bp

>1.8

>1.2 ug

WGS: Chromium Genome Solution Library Preparation Kit

100

5 - 20

Input gDNA with a mean length >50 Kb

>1.8

>0.5 ug

WES: Agilent Sure Select

Capture Exome

100

10-40

350 bp

>1.8

>1.2ug

RNA  (Total  RNA,  mRNA)

  • Samples should be extracted  using Qiagen  RNeasy Extraction  Kits or similar. Please contact KCCGCF prior to extraction to ensure compatibility and suitability of the extraction protocol. 
  • RNA must be submitted in DNase / RNase Free Water. 
  • Sample quantity   and  quality   must  be  assessed prior   to  submission,  preferably   using  a Bioanalyzer, LabChip GX (or similar). 
  • Samples may additionally be quantified via Picogreen Assay (or Qubit) 
  • Samples must meet the following specifications (QC Metrics):

Protocol

Vol. (uL)

Conc. (ng/uL)

RIN

A260:280

Total

TruSeq Stranded Total / mRNA Library Preparation Kit

20 - 30

100 - 150

>8.0

>2.0

>3 ug

Submitted  libraries

HiSeq X Platform

Protocol

Vol. (uL)

Conc. (ng/uL)

Insert size

A260:280

Total

Customer Submitted

Library for WGS

30

 

Expected library size:

580 – 850 bp*

 

20 nM

Customer Submitted Chromium Library for WGS (HiSeq X)

30

 

Expected library size:

580 – 850 bp*

 

10 nM

*If libraries fall outside of these parameters, the Customer will be contacted  for a decision as to how they would like to proceed.

NovaSeq 6000 platform

The following  requirements  apply for libraries prepared  with the above listed library preparation  kits. For any other library preparation or requirements,  please contact  the Project Management  team to discuss the best option.

Non-pooled (single libraries)

Minimum Vol. (uL)

Minimum Conc. (ng/uL)

S1, S2 or S4 Flowcell (per library)

20

20nM

 

Pooled  libraries

Minimum Vol. (uL)

Minimum Conc. (ng /uL)

S1 Flowcell (per lane)

30

20nM

S2 Flowcell (per lane)

50uL

20nM

S4 Flowcell (per lane)

100uL

20nM

 

Manifest and tubes

Customers  must  fill  in  the  online  electronic  manifest  via the  KCCGCF Customer  Portal  detailing several  Sample  characteristics.  Customers  must  transfer  Samples  into  the  provided   FluidX  2D barcoded  tubes and ensure the caps are sealed tightly.

  • The manifest is pre-filled with the associated tube barcode(s), providing a unique identification code for each submitted  Sample. Please ensure that Sample details for each barcode  matches the Sample aliquoted  into  that tube.  In addition,  ensure all the necessary details are filled  out prior to submitting the manifest.
  • KCCGCF will, within  a reasonable  period  of  receipt  of  the  manifest  submission,  review  the manifest against the Quote and either:
    • approve the manifest 
    • decline the manifest and cancel the Order; or 
    • if the manifest is identified as non-conforming, KCCGCF will contact the Customer  to seek the agreement  of the Customer for KCCGCF to issue a revised Quote  (which may be subject to Special Conditions  which will be specified in the revised Quote).
  • If KCCGCF accepts the manifest, it will notify the Customer and request the Samples be sent to KCCGCF. 
  • KCCGCF will, within  a reasonable  period  of  receipt  of  the  Samples, inspect  the  Samples in accordance with these guidelines and either: 
    • accept the Samples; 
    • decline to accept the Samples and cancel the Order: 
    • decline  to   accept   the   Samples  and  hold   the   Order   pending   receipt   of   further information  or further Samples; or 
    • if the  Samples are identified as non-conforming,  contact  the  Customer  to  seek the agreement  of the Customer to Sample Acceptance subject to Special Conditions  which will be specified in a revised Quote  (failing agreement,  KCCGCF may decline to accept the Samples and cancel the Order).
  • Samples sent in any container other than the FluidX 2D barcoded  tubes provided  by KCCGCF will not be accepted. 
  • We cannot accept Samples from you until we have received and approved your manifest. You will receive an email notification advising you to prepare your Samples for shipment.

Turnaround time and delivery

The turnaround  time, if any specified in a Quote, comprises of the period from the day of receipt and approval of Samples in the laboratory  until data delivery of all data files to the specified recipients. In the  event  of  failure  to  meet  the  required  QC  metrics,  the  Customer  will  be  notified  to  seek an agreement on whether/how to proceed and the turnaround  time revised.

Provision and retention of data files

A Data File is taken to be delivered  when the Data File is released by Garvan for shipping  on data storage media (if specified in the Quote) or is otherwise made available to the Customer on a cloud-based  platform.

  • If the  Data  File  is  to  be  made  available  to  the  Customer  on  a  cloud-based   platform,   the Customer  authorises  Garvan  to  provide   the  Data  File  to  the  provider   of  that  cloud-based platform.
  • Garvan will retain the Data File for a period of 90 days from  the date  of delivery  (Re t e n t i on Per i od ). If the Customer does not receive the Data File or the Data File is otherwise unavailable to  the  Customer  on  the  relevant  Data  Delivery  Platform,  the  Customer  is  responsible   for contacting  Garvan within the Retention Period to request that the Data File be delivered  again. Garvan  may  not  be  able  to  provide   Data  Files  after  the  Retention  Period.  Any  Data  Files provided  after the Retention Period will be at an additional  cost to the Customer.
  • Delivery of the Data File is undertaken or facilitated  by third-parties  and Garvan is not liable to the Customer for the performance  or non-performance of any such third-party  in respect of the delivery of, or failure to deliver, the Data File.
  • Where the  Customer  selects  the  cloud-based  platform   option   for  delivery  of  the  Data  File, Garvan will be required  to disclose Personal Information  relating to the Customer's personnel to the  cloud-based  platform  provider  to  enable  delivery  of  the  Data  File  (for  example,  contact details necessary to create an account). The Customer must ensure that its personnel consent to such Personal Information  being  provided  (having been informed  that the cloud-based  platform provider  handles Personal Information  in accordance with its privacy policy and that Garvan has not taken steps to ensure that the cloud-based  platform  provider  does not breach the Australian Privacy Principles in relation to that information).
  • Data Delivery Platform means a cloud-based platform  for transfer and/or  storage of a DataFile (or physical data storage media if specified in the Quote).
  • Data File means FASTQ format of DNA sequence data (or such other available data file format agreed with the Customer and specified in the Quote).

Sample retention

As per clause 12 of the Terms and Conditions  unless agreed otherwise in a Quote.

Shipping requirements

  • Please ensure that the barcoded tubes sit securely in the rack (if provided) and the lid is locked using the orange clips on the side of the rack. Ensure the rack containing  the barcoded  tubes is packaged into an appropriately rigid shipping container.
  • If no rack is provided, prevent  damage  to  your  FluidX  2D tubes  in transit  by ensuring  your tubes are stored securely as follows:
    • Place the Primary Receptacle  (FluidX 2Dtube)  into  a Secondary  Receptacle  (tube rack, Falcon tube or BioBottle)
    • Place the Secondary Receptacle into a Tertiary Receptacle (padded outer packaging)
    • Package the Tertiary Receptacle into an appropriately rigid shipping container
  • KCCGCF provides a shipping label with the manifest ID inside the package with your FluidX 2D tubes.  Please affix this label to the outside of the shipping container.
  • DNA Samples can be shipped at ambient temperature or on dry ice.
  • RNA Samples must be shipped on dry ice.
  • Submitted library Samples must be shipped on dry ice.
  • Attach the provided shipping label addressed to KCCGCF as per below:  

ATTN: KCCG Core Facility Sequencing  Laboratory 
Garvan Institute of Medical Research 
The Kinghorn Cancer Centre 
Precinct Loading Dock 
West Street (off Burton Street)
Darlinghurst  NSW 2010 
Australia 
Phone: +61 2 9355 5846 

  • At the time of shipping, please send an email notification to  kccgseq@garvan.org.au with your express mail tracking number, as this will allow us to watch for your shipment.
  • We will notify you when the Samples have been received and approved (under these guidelines) in the laboratory.

For international customers

In  addition   to  the  above  instructions,  please  ensure  that  the  following   documents   are  clearly attached to the outer package:

  • AQIS Import Permit (supplied by KCCGCF)
  • Manufacturer’s Declaration (supplied by KCCGCF)
  • 4 copies of Customs Declaration (Customer to provide).

We recommend that you state a value of less than AUD$1,000 (or equivalent) on any paperwork you provide, so as to not trigger a requirement for a Tax Invoice. Please note this is not  the value of the sequencing project.

We currently recommend World  Courier, LabCabs, DGI and Logical  Freight Solutions. We strongly advise against the use of DHL or FedEx for shipment of Samples to Australia.