Timing of work packages and their components

Year 1 Year 2 Year 3 Year 4
D Deliverable name 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D1.1 Establishment of a Steering Committee
D1.2 Establishment of a Management Office
D1.3 Kick off meeting
D1.4 Signed consortium agreement
D1.5 Project presentation produced
D1.6 Establishment of a Scientific Advisory
Group
D1.7 Establishment of a webpage with
password-protected info
D1.8 Establishment of Technology Transfer
Work Group
D1.9 Establishment of Ethical Review Work
Group.
D1.10 Annual Report #1, reviews from the
Technological Transfer Work and
Ethical Review Work groups..
D1.11 Annual meeting of the General
Assembly
D1.12 Update of Annex I according to State-of-
the-art
D1.13 Report from the meeting of the Scientific
Advisory Board.
D1.14 Annual Report #2, reviews from the
Technological Transfer Work and
Ethical Review Work groups..
D1.15 Annual meeting of the General
Assembly
D1.16 Annual Report #3 reviews from the
Technological Transfer Work and
Ethical Review Work groups..
D1.17 Report from the meeting of the Scientific
Advisory Board.
D1.18 Annual meeting of the General
Assembly
D1.19 Final Report, reviews from the
Technological Transfer Work and
Ethical Review Work groups..
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D2.1 Construction of central databases for
each cancer to hold individual
phenotype and SNP data from the
GWAS to be used in stage I
D2.2 Integration of SNP data from GWAS
into the SNP database
D2.3 Complete analysis of existing GWA data
for breast , ovarian and prostate cancer
– novel loci identified to be followed up
by WP4/5/6/7
D2.4 Define set of SNPs for breast, ovarian
and prostate cancer, for genotyping in
phase II (WP3)
D2.5 Incorporate individual SNP genotype
data generated in stage II (WP3, task
3.2) into the central databases
D2.6 First reports describing main effect
association analyses for each cancer
D2.7 Define set of SNPs to be typed for each
cancer in WP3
D2.8 Integration of gene expression data for
breast cancer into the gene expression
database.
D2.9 Website giving access to combined
analyses
D2.10 Incorporate data from WP3 into
database
D2.11 Report describing main effect
association analyses for subtypes (with
WP7)
D2.12 Reports on final main effects analysis
for each cancer
D2.13 Report on main effects of SNPs in
BRCA1/2 carriers
D2.14 Reports describing gene-gene
interaction analyses in each cancer
D2.15 Report of risk models for breast and
ovarian cancer
D2.16 Report of risk model for prostate cancer
D2.17 Report describing mapping of
expression subtypes to
histopathological equivalents for breast
cancer
D2.18 Website for the risk models for
estimating the risk of breast, ovarian
and prostate cancer.
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D3.1 Samples shipment to CNIO from other
groups
D3.2 Samples preparation for shipping and
genotyping
D3.3 Design and synthesis of Illumina
Custom Arrays
D3.4 Generation of genotypes (stage II) of
the three diseases (50,000 samples)
D3.5 Evaluation of assays for
Taqman/iPlex/Veracode
D3.6 Data replication and generation of
genotypes (stage III)
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D4.1 Manuscript describing the fine-scale
mapping process and results in one
breast cancer locus
D4.2 Report describing initial loci submitted
for fine-scale mapping
D4.3 Website cataloguing the candidate
causative variants at each locus,
identified by WP4 Task 1
D4.4 Report describing any additional loci.
identified as suitable for fine-scale
mapping if costs permit, from the
confirmed loci listed in D2.7
D4.5 Update of D4.3
D4.6 Report presenting the list of candidate
cancer-causing mutations defined by
WP4 Task 2 and listing planned papers
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D5.1 Questionnaires from consortia members
collected and posted on COGS website
D5.2 Data dictionary of established and
suspected lifestyle/environmental risk
factors for each cancer site, including
variable definition and coding, finalized
and placed on COGS website
D5.3 A database with harmonized
epidemiologic data established for each
of the different cancers and for
BRCA1/2 mutation carriers
D5.4 Results posted on the COGS website
from analysis of gene and environment
(GxE) performed for the already
established susceptibility loci of breast
cancer
D5.5 List of selected lifestyle/environmental
variables used for exploratory analysis
of GxE analyses for breast cancer with
all 1536 SNPs genotyped to be placed
on COGS website
D5.6 Results posted on the COGS website
from analysis of GxE performed for the
possible susceptibility loci of breast
cancer from previous GWAS
D5.7 Results posted on the COGS website
from analysis of GxE (using global
variables) performed for breast cancer
in BRCA1/2 mutation carriers and for
the established susceptibility loci from
GWAS for ovarian and prostate cancer
D5.8 List of selected detailed variables for
GxE analyses in breast, ovarian and
prostate cancer to be placed on COGS
website
D5.9 Results posted on the COGS website
from analysis of GxE analysis for
confirmed susceptibility loci for breast,
ovarian, and prostate cancer
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D6.1 Standardization of histopathological and
immunohisto data; codebook
D6.2 TMA scoring system for the different
immuno-histochemical analyses agreed
D6.3 Database for the incorporation of the
histopathological and
immunohistopathology data established
D6.4 Draft of two manuscript based on pre-
COGS data, i.e. tumour subtype
survival analyses, and genotype and
tumour subtype risk analyses.
D6.5 Existing data on tumour characteristics
coded and incorporated in developed
database
D6.6 The SNP data from Stage I of
genotyping from WP3 will be added to
the database including tumour
characteristics
D6.7 Standard risk and prognosis analyses
will be performed using genotype (G)
and tumour type (T)(standard
histopathology)
D6.8 Analyses of genotype/environment
interaction (GxE) and (T) will be
performed
D6.9 Draft manuscript deliverable 6.6
D6.10 New G data WP3/WP4 added to
database
D6.11 New G and T(standard histopathology)
analysis
D6.12 New GxE and T(standard
histopathology) analysis
D6.13 Draft manuscripts deliverable
6.7/6.10/6.11
D6.14 Coding of available TMA staining in
developed database
D6.15 Standard risk and prognosis analyses
will be performed using genotype (G)
and tumour type (T)(using TMA)
D6.16 Standard risk and prognosis analyses
will be performed using genotype (G)
and tumour type (T)(using CGH)
D6.17 Initial analysis GxE and T (TMA)
D6.18 Initial analysis GxE and T(expression or
CGH-array)
D6.19 New refined G & E data WP3/4/5 added
to database
D6.20 Draft manuscripts deliverable 6.14-16
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4
D7.1 Participant list and report of first
Steering Group meeting
D7.2 Draft terms of reference and agreed
participant list for main Working Group
D7.3 International Working Group Workshop
1 (programme/participants)
D7.4 First draft paper on risk stratification
using polygenic model
D7.5 Workshop 1 report outlining key issues
in targeted prevention
D7.6 Scientific paper on risk stratification
assuming a polygenic inheritance model
D7.7 First draft report on effectiveness/cost-
effectiveness of targeted screening
D7.8 Final report on effectiveness/ cost-
effectiveness of targeted screening
D7.9 International Working Group Workshop
2 (programme/participants)
D7.10 Workshop 2 report
D7.11 International Working Group Workshop
3 (programme/participants)
D7.12 Workshop 3 report
1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4

Timing. In Figure 1.3.2. the communication between WP in the course of the project has been depicted through consecutive steps. The three iterative phases imply the definition of novel sets of confirmed SNPs by WP2 to be evaluated in fine-scale mapping analyses in WP4, in gene-environment interaction analyses in WP5 and in tumour subclasses in WP6. In Phase 1 the WP2 SNP analyses will be conducted on existing (GWAS) data within the consortia (genotyping Stage I), while in Phase 2 and Phase 3 the analyses will be preceded by new genotyping in WP3 (genotyping Stage II and III). There will be cross-talk among WP4-6 before the results of these work packages will be returned to WP2 in order to be incorporated in risk prediction modelling. In the final Step 11 the overall risk prediction model will be transmitted to WP7 to be integrated into risk stratification models, which will be discussed in workshops for implementation in public health. In reality, most steps will be overlapping, because work in the next WP will start with existing/preliminary data from the data transmitting WP, for instance to further develop the statistical methods. Especially, data transmission by WP2 to WP7 will take place during the entire course of the project and not just following Phase 3.

Figure 1.3.2. Timing of the different WPs

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