FULL APPLICATION - BY INVITATION ONLY
OFFICE FOR HEALTH AND MEDICAL RESEARCH
APPLICATION FORM
GENOMICS COLLABORATIVE GRANTS PROGRAM 2015-16
DEADLINE 5PM Wednesday 16th December 2015
SECTION A – ADMINISTRATIVE SUMMARY
A.1
Application Title
Provide a short descriptive title (maximum 200 characters including spaces).
A.2
Administering Institution
Administering Institution Details
Institute Name
A.3
Administering Institution Contact
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
NSW Genomics Collaborative Grants Program 2015-16
A.4
Chief Investigator A (1st Chief Investigator) Details
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
Are you an Australian Citizen/ Permanent Resident?
Are you located in New South Wales?
YES
YES
☐
☐
NO
NO
☐
☐
YES
YES
☐
☐
NO
NO
☐
☐
A.5
Chief Investigator B Details
Select a Title: Choose a Title
Family Name:
Given Name:
Postal Address:
Telephone:
Mobile:
Email:
Are you an Australian Citizen/ Permanent Resident?
Are you located in New South Wales?
[add in information on all Chief Investigators as required by copying the section above here]
SECTION B – APPLICANT TEAM AND CHIEF INVESTIGATOR
B.1
Qualifications and professional experience
Please attach a brief CV (maximum 2 pages) for the chief investigator(s) of your team. This
should specify PhD qualification, other educational qualifications, academic research, clinical,
professional and industrial experience and any career achievement and awards.
Please outline also the skills of the research team, their collaborative potential, potential
collaborators and, if possible, success in obtaining and delivering grant funding.
B.2
Publications
Please provide a list of all publications, reports, patents or conference presentations,
providing full references in the last 3 years produced by the chief investigator(s). All
publications relevant to this project should be highlighted.
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NSW Genomics Collaborative Grants Program 2015-16
B.3
Title
Associate Investigator/s
An Associate Investigator is a participant of the grant who provides intellectual input into the
project and whose participation warrants inclusion of their name on publications.
First Name
Last Name
Organisation
Contribution (max 400
characters)
Located
in NSW
(Y/N)
Title
Title
Title
Title
Title
Add more rows as needed.
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NSW Genomics Collaborative Grants Program 2015-16
SECTION C - RESEARCH STRATEGY
This section is modelled on the NHMRC application template for ease of cross-application for grants.
Please outline your research strategy using the three weighted sections listed below (maximum 10
pages, excluding references. References may be up to an additional 10 pages)
C.1.
Objectives, design and expected outputs and outcomes (50%)
This should include an outline of the study design under the following headings: Aims and
Objectives, Background, Research Plan, Analysis, Specific Outputs, Expected Outcomes.
Responses should correspond with the Eligibility and Assessment Criteria. The details of
whole genome sequencing to be purchased from the Garvan Institute for Medical
Research with the Grant. Applications should detail the minimum number of sequences
required to address the research question, and, if relevant a discussion of the value of
undertaking larger numbers than the minimum. A description of the nature and number
of bio-specimen samples to be sequenced, any tests already done, patient information
linkages, subject selection criteria and any other relevant information. This section should
also propose measureable milestones for the project.
C.2.
Significance of the Expected Outcomes and/or Innovation of the Concept (25%)
Proposals should focus on areas of substantial research need and benefit, where the
outcomes are anticipated to be feasible for adoption into the health system. Research
should be congruent with current NSW Government policies, strategies and priorities. A
description of where the project is situated in the ‘bench to bedside’ continuum for
research translation acknowledging NSW Health’s preference for projects that seek to
overcome the barriers at ‘T1’, ‘T2’ and ‘T3’ for translating existing research outcomes into
either population-scale outcomes, clinically targeted therapies and/or other interventions
that can be utilised in the health-system. This section should also detail how the project
will provide value for money for the health system. This section should also address the
Eligibility and Assessment criteria, where appropriate, especially around delineation of a
likely outcome for a defined patient group.
C.3.
Team Quality and Capability, relative to opportunity (25%)
The expertise and experience of the research team relevant to the project, their
collaborative potential and potential collaborators and success in obtaining and delivering
past grant funding. Demonstration of previous achievements of the team and
collaborative effort should be provided. An outline of the high level governance of the
project including nomination of Chief Investigator/s. Evidence of institutional support
should also be provided.
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NSW Genomics Collaborative Grants Program 2015-16
SECTION D – BUDGET
Maximum, 2 pages
D.1
Requested Budget for Sequencing and Bioinformatics
Applicants are asked to demonstrate that the project is financially viable. Information should
indicate sufficient funding support to make effective use of the sequences and bioinformatics
requested. This information will include researcher time and other funding for all other
necessary parts of the project, aside from the sequencing and bioinformatics.
Please also provide administrative certification for the grants and budget for the project. NB:
a reminder that funding under the NSW Genomics Collaborative Grants is for whole genome
sequencing and bioinformatics only.
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NSW Genomics Collaborative Grants Program 2015-16
SECTION E – CERTIFICATION
Privacy Notice
Applicants (researchers/ clinicians and administering institutions) consent to the information supplied as part of their
application being disclosed for the purposes of their application and for purposes connected with the making and
administration of the grant. Such disclosure includes, but is not limited to, disclosure to members of the independent panel
assessing applications, the Garvan Institute of Medical Research, independent researchers, assessors and relevant
representatives and employees of NSW Health. NSW Health may publicise and report on the awarding to, and the use of,
the funds including media releases, general announcements and reports.
Documents containing personal information are handled and protected in accordance with the provisions of the Privacy
and Personal Information Act 1998 which sets standards for the collection, storage, use and disclosure of, and access to,
personal information.
E.1
Certification by first named Chief Investigator
I certify that:
1.
To the best of my knowledge and belief, the information in this application is complete, true and
correct and I understand that the provision of false or misleading information may attract
substantial penalties;
2.
I consent to this application being peer-reviewed by persons who will remain anonymous;
3.
I have read and agreed to the Privacy notice above;
4.
All named applicants on this application have read this application in full and given their consent
to be included;
X
Name:
Title:
E.2
Date:
Certification by the Administering Institution
I certify that:
1.
I am authorised signatory on behalf of this Administering Institution;
2.
The resources described in Section D are available;
3.
I am prepared to have the Grant administered by this institution under the conditions as set out;
4.
All funds awarded for the Grant will be used only for the purpose for which they were awarded;
5.
Agreement has been reached with collaborators in this application, or will be reached prior to the
commencement of this Grant, about IP ownership, financial arrangements and any other support
specified in the form;
6.
The Administering institution will ensure that all ethical and other clearance(s) have been
obtained that may be necessary prior to the establishment of or during this Grant
X
Na me :
Title :
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Date:
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NSW Genomics Collaborative Grants Program 2015-16
APPENDIX B – SPECIFICATIONS
Sydney Genomics Collaborative
NSW Genomics Collaborative Grants Program
Technical Information – Whole Human Genome Sequencing
The Kinghorn Centre for Clinical Genomics (KCCG) at the Garvan Institute of Medical Research is the provider
of whole human genome sequencing for the NSW Genomics Collaborative Grants Program. KCCG is equipped
with the Illumina HiSeq X Ten platform, which has the capacity to sequence up to 350 human genomes per
week.
Sequencing service specification
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Sequencing services are for research purposes only.
Sequencing is for whole human genomes only (transcriptomic and epigenomic sequencing is not
permitted; non-human derived DNA is not permitted)
Applicants should budget $1,750+GST per DNA sample.
Genomes will be sequenced to a minimum mean coverage of 30X (minimum 100 Gbases, 2x150bp paired
end reads, >75% of bases with Q score > 30) in line with Illumina’s ‘Sequencing Coverage Calculation
Methods for Human Whole-Genome Sequencing’ documentation (http://tinyurl.com/o9bkmy7).
DNA extraction and quantification
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DNA should be extracted using Qiagen DNeasy Blood / Tissue Extraction Kits or similar. Please contact
KCCG prior to extraction to ensure compatibility and suitability of the extraction protocol.
DNA should be suspended in Qiagen Elution Buffer (EB - 10 mM Tris-Cl, pH 8.5) or Illumina Suspension
Buffer (RSB).
Fluorometric-based methods for quantification including Qubit or PicoGreen are recommended to provide
accurate quantification of dsDNA. Spectrophotometry is not a recommended quantification method for
whole genome sequencing.
DNA samples must meet the following specifications;
Protocol
Vol. (uL)
Conc. (ng/uL)
A260:280
Total
WGS v2.1 (TruSeq PCR-Free)
>50
50 - 100
>1.8
>2,500 ng
WGS v2.0 (TruSeq Nano)
>50
20 - 100
>1.8
>1,000 ng
DNA samples must not be amplified (i.e. DNA should not have been subjected to PCR, WGA, MDA) or
reverse transcribed from RNA.
DNA samples must be free of contaminating nucleic acids.
DNA samples cannot be derived from FFPE material.
DNA samples should not be modified prior to shipping (e.g. bisulphite conversion).
DNA samples must be pure, intact and of high molecular weight.
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NSW Genomics Collaborative Grants Program 2015-16
Samples submitted failing to meet any of the above criteria will be removed from further processing and the
submitter notified.
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Shipping instructions
Samples must be submitted in FluidX 2D Barcoded tubes associated with online submission forms
(provided by KCCG).
Online sample submission must be completed and submitted for validation prior to samples shipping.
Samples should be shipped Frozen on Dry Ice and tracking number provided to KCCG.
Ethics and consent
 DNA can only be accepted from studies governed by a recognised Human Research Ethics Committee
(HREC).
 DNA can only be accepted from individuals that have undergone informed consent for genetic testing.
 Study approval and consent will be required to be in place before sequencing commences for submissions
to be considered in the funding round.
Turnaround time and data delivery
 On sample acceptance following internal QC, data will be returned within 6 weeks (subject to capacity).
 Data will be supplied as FASTQ data files. Bioinformatic analysis (i.e. alignment and variant calling –BAM
and VCF files) can be performed at the KCCG at an additional cost of $250+GST per genome.
 Data will be made available via DNAnexus or shipped on external hard drive (additional charges will
apply).
Terms and conditions
 Each project will need to agree to KCCG Terms and Conditions (attached).
Contact

For further information, contact:
Kinghorn Centre for Clinical Genomics
Sequencing Facility,
Garvan Institute of Medical Research
P: (02) 9355 5846
E: kccgseq@garvan.org.au
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