APPENDIX A – FULL APPLICATION
OFFICE FOR HEALTH AND MEDICAL RESEARCH
APPLICATION FORM
GENOMICS COLLABORATIVE GRANTS PROGRAM 2014
DEADLINE 5PM 3 November 2014
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:
Genomics Collaborative Grants Program 2014
A.4
Chief Investigator A 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.
B.3
Associate Investigator
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.
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Genomics Collaborative Grants Program 2014
Title
First Name
Last Name
Organisation
Contribution (max 400
characters)
Located
in NSW
(Y/N)
Title
Title
Title
Title
Title
Add more rows as needed.
SECTION C - RESEARCH STRATEGY
This section is modelled on the NHRMC 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 Selection 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.
C.3.
Team Quality and Capability, relative to opportunity (25%)
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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.
SECTION D – BUDGET
Maximum, 2 pages
D.1
Requested Budget
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.
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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 selection panel,
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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APPENDIX B – SPECIFICATIONS
Sydney Genomics Collaborative
Sydney 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 Sydney Genomics Collaborative Grants Program. KCCG is
equipped with the Illumina HiSeq X Ten platform, which has the capacity to sequence up to 350 genomes per
week.
Sequencing service specification
 Sequencing services are for research purposes only.
 Applicants should budget $1,600+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).
Sample quality and quantity specifications
 Minimum of 1.0 μg of purified DNA
 Maximum of 20 μL volume
 Concentration >50 ng/μL
DNA extraction and quantification
 DNA extraction by column purification is recommended (Qiagen or any other supplier)
 Spectrophotometry (A260) is not a recommended quantification method for whole genome sequencing.
 Fluorometric-based methods for quantification including Qubit or PicoGreen are recommended to provide
accurate quantification of dsDNA.
 It is recommended to avoid the use of samples prepared by Real-Time PCR for library preparation,
because residual ROX and DNA laser-damage diminishes the quality of the resulting sample.
Shipping instructions
 DNA should be suspended in water or EB (10 mM Tris-Cl, pH 8.5). For all sample submissions, an AMPure
bead purification will be performed.
 Samples should be sent in a 96-well fully-skirted plate for use in the automated pipeline.
 Samples should be shipped frozen on dry ice.
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 by [insert date] for submissions to be
considered in the first 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 either aligned reads (BAM) or FASTQ.
 Data will be made available via SFTP download (preferred) or shipped on external hard drive (additional
charges will apply).
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Terms and conditions
 Each project will need to agree to KCCG Terms and Conditions (attached).
Contact

For further information, contact:
Kerith-Rae Dias
Facility Manager, Kinghorn Centre for Clinical Genomics
Garvan Institute of Medical Research
P: (02) 9355 5846
E: kccgseq@garvan.org.au
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