Heidelberg Center for Personalized Oncology
DKFZ-HIPO
Project ID:
(Provided by HIPO)
1.
1.1
Project Overview
Applicant(s)
Name:
Title:
(Please include all applicants).
Department:
Address:
Tel.-Nr.:
Fax:
Email:
Name:
Title:
Department:
Address:
Tel.-Nr.:
Fax:
Email:
1.2
Project Title
1.3
Summary of Project
1.4
High-Throughput
Technologies (Sample
Numbers)
HIPO
Whole Genome
Exome
Transcriptome
Bisulfite Seq (WGBS)
ChIP
POP
SNP
Expression Profiling
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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Heidelberg Center for Personalized Oncology
DKFZ-HIPO
450K
Others, please
specify:
1.5
Matching Funds from
External Sources
2.
Project Information
2.1
Background and Significance
€
(0.5 -1 page)
2.2
Rationale
( 0.5- 1 page)
2.3
Research Design
(0.5 - 1 page). Please state your
detailed work plan!
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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DKFZ-HIPO
Heidelberg Center for Personalized Oncology
3.
Workflow
NCT MASTER Informed Consent
available for all Samples
3A
Sample Preparation
3A.1
Number of Provided
Samples or Analytes
Yes
Others
Please specify:
Tumor Samples
Number of Samples
Type (e.g. tissue, DNA, blood, FFPE)
Min. Tumor Cell Content
Germline Control
Number of Samples
Type (e.g. tissue, DNA, blood)
Others
Number of Samples
Type (e.g. liquid biopsy)
3A.2
Histological Diagnosis
Provided by HIPO/POP
Yes
No
(Institute of Pathology)
3A.3
Analytes Isolation in SPL*
required
No
DNA
Number of Samples
RNA
Number of Samples
Others , please specify:
Number of Samples
*QC and Submission of Samples have to be done exclusively by the Sample Processing Lab (SPL).
3B
Molecular and Bioinformatics Analysis
3B.1
Whole Genome
Number of Samples
Number of Lanes
HIPO-STD (3 lanes/sample)
other:
Person Responsible for
Bioinformatic Analysis
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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DKFZ-HIPO
Heidelberg Center for Personalized Oncology
3B.2
Exome
Number of Samples
Number of Lanes
HIPO-STD (3 s.p.l. (tumor), 4 s.p.l. (ctrl))
other:
incl. UTR
No
Kit
Yes
HIPO-STD (Agilent SureSelect XT Version 5)
other:
Person Responsible for
Bioinformatic Analysis
3B.3
Transcriptome
Number of Samples
Technique
polyA-RNA Seq.
other:
incl. small RNA
Number of Reads
No
Yes
please specify:
polyA-STD (40 Mio./ 2,5 samples/lane)
other:
Person Responsible for
Bioinformatic Analysis
3B.4
SNP Genotyping
Number of Samples
Array-Type
Human CytoSNP-12
other:
Person Responsible for
Bioinformatic Analysis
3B.5
Expression Profiling
Number of Samples
Array-Type
Human HT-12 beadarray
other:
Person Responsible for
Bioinformatic Analysis
3B.6
Epigenomes
Number of Samples
Technique
450K
Whole Genome Bisulfite Sequencing
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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DKFZ-HIPO
Heidelberg Center for Personalized Oncology
Number of Lanes (if
applicable)
Person Responsible for
Bioinformatic Analysis
3B.7
ChIP
Number of Samples
Tumor:
Marks
H3
(HIPO-Standard Marks are
highlighted)
H3K4me1
Control:
H3K4me3
H3K9ac
H3K9me3
H3S10p
H3K14ac
H3K27ac
H3K27me3
H3K36me3
H4
H4K16ac
H4K20me3
other (Please specify):
TOTAL ChIPs:
TOTAL Lanes:
Sequencing Type
HIPO-STD (50 bp Single Read, 5 s.p.l.)
other (Please specify)
Person Responsible for
Bioinformatic Analysis
3B.8
Others
Number of Samples
Technique
Additional Information
(e.g. estimated cost per
sample)
Person Responsible for
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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Heidelberg Center for Personalized Oncology
DKFZ-HIPO
Bioinformatic Analysis
3C
Data Access (Bioinformatics, PIs)
3C.1
Request for Data Access
Please list all scientists getting
access to data (including E-Mail
addresses)
3D
Clinical Data
3D.1
Patient, Diagnostic, Clinical
and Treatment Data
Contact Person (including E-Mail address):
Follow up:
4. Additional Comments
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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DKFZ-HIPO
Heidelberg Center for Personalized Oncology
Signatures
□ I have read the HIPO Code of Conduct and agree to the stated terms and conditions.
□ I agree to inform the HIPO board of directors about the intention to submit publications 10 days in
advance. Publication criteria should be agreed upon within the respective project team. It is
expected that the HIPO/POP organizing parties are considered in the usual academic manner.
Date:
Name:
Signature:
Date:
Name:
Signature:
□
I am aware that I am responsible to ensure that all patients included in this study have signed the
NCT-MASTER consent or an equivalent other consent form that allows for the applied genetic and
bioinformatics analyses as well as the storage of data.
□ If the study uses a patient consent other than NCT MASTER, I am responsible to ensure the
compliance with data storage guidelines, especially time limitations of stored data. I will inform
the HIPO Data Management Group (hipo-dtmg@dkfz.de) about approaching deadlines 3 months
in advance.
Date:
Name:
Signature:
Date:
Name:
Signature:
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
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Heidelberg Center for Personalized Oncology
DKFZ-HIPO
Guidelines
Please submit
1. Electronically as WORD-document to one of the coordinators (see contact details below)
2. After official acceptance send a signed version of the proposal to one of the coordinators
3. Please note: QC and Submission of Samples have to be done exclusively by the Sample Processing
Lab (spl@nct-heidelberg.de) or CHARM (for ChIP) (j.mallm@dkfz-heidelberg.de).
Contacts
HIPO-Coordinators:
POP-Coordinator:
Dr. Katja Beck
Dr. Janna Kirchhof
DKFZ - German Cancer Research Center
Abteilung Molekulare Genetik (Prof. Lichter)
Im Neuenheimer Feld 280
69120 Heidelberg
Dr. Daniela Richter
Phone: ++49 6221 42 4579
Fax: ++49 6221 42 4639
Email: j.kirchhof@dkfz.de
k.beck@dkfz.de
Phone: +49 (0) 6221 56-37819
Fax: +49 (0) 6221 56-6967
Email: daniela.richter@nct-heidelberg.de
Heidelberg Center for Personalized Oncology
Proposal_Version 5.0
Nationales Centrum für Tumorerkrankungen (NCT)
Abteilung Translationale Onkologie (Prof. von Kalle)
Im Neuenheimer Feld 460
69120 Heidelberg
8