Sequencing submission guidelines

Sequencing services are offered by the Garvan Institute of Medical Research’s Kinghorn Centre for Clinical Genomics, through its Sequencing Laboratory (KCCGSL). Through KCCGSL, local and international customers can access clinically-accredited, scalable sequencing and expert genomic analysis.

Download a copy of these guidelines.

Overview of Sample submission process

  1. Contact the Project Management  team to discuss project via:
    1. Email: kccgseq@garvan.org.au
    2. Phone: +61 2 9355 5763; or
    3. In person: on Level 6 of The Kinghorn Cancer Centre
  2. Receive quote and login details to the KCCGSL 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 KCCGSL Customer Portal: https://apps.kccg.garvan.org.au/sample-submission-x/#/home
  6. Receive email with link to manifest 
  7. KCCGSL-supplied FluidX barcoded  tubes will be posted to you 
  8. Fill in and submit manifest 
  9. Wait for ‘Manifest Accepted’ email 
  10. Aliquot your samples into the KCCGSL-supplied FluidX barcoded tubes 
  11. Submit samples to KCCGSL along with manifest label as per shipping requirements below.

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 KCCGSL 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

400 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

300 bp

>=1.8

>=1ug

WGBS: ACCEL – NGS Methyl-Seq DNA Library Kit

100

>=10

350 bp

>=1.8

>=0.5 ug

RNA  (Total  RNA,  mRNA)

  • Samples should be extracted using Qiagen RNeasy Extraction Kits or similar. Please contact KCCGSL 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

KAPA RNA HyperPrep Kit with RiboErase* / KAPA mRNA HyperPrep Kit

20 - 30

100 - 150

>=8.0

>=2.0

>=3 ug

* Only compatible with Human, Mouse and Rat

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, please contact KCCGSL to discuss available options.

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. (nM)

S1, S2 or S4 Flowcell (per library)

20

20

Pooled  libraries

Minimum Vol. (uL)

Minimum Conc. (nM)

S1 Flowcell (per flow cell)

30

20

S2 Flowcell (per flow cell)

50

20

S4 Flowcell (per flow cell)

100

20

*If your library does not meet the minimum requirements, please contact KCCGSL to discuss available options.

Customers  must fill in the  online electronic manifest via the  KCCGSL 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.
  • KCCGSL 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, KCCGSL will contact the Customer to seek the agreement  of the Customer for KCCGSL to issue a revised Quote  (which may be subject to Special Conditions which will be specified in the revised Quote).
  • If KCCGSL accepts the manifest, it will notify the Customer and request the Samples be sent to KCCGSL. 
  • KCCGSL 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,  KCCGSL may decline to accept the Samples and cancel the Order).
  • Samples sent in any container other than the FluidX 2D barcoded  tubes provided  by KCCGSL 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.

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.

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 (Retention Period). 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 Data File (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). 

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

  • 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
  • KCCGSL 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 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 5763

  • 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.

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

  • AQIS Import Permit (supplied by KCCGSL)
  • Manufacturer’s Declaration (supplied by KCCGSL)
  • 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.