1. Data and Hartwig Medical Foundation
December 2016

2. Eg: Primary Tumor location
Molecular and clinical data both required
Eg: Primary Tumor location
Genetic variants
Molecular data (WGS)
Clinical data (ECRF)
Patient Report
Data for Research
Treatment A/B/C
Genetic profiles

3. Biopsies per center
Note: stats from patients reported until 26 oct 2016 and ECRF data from 2nd of nov 2016 (total of 425 biopsies)

4. Clinical data: Primary tumor location
Note: "Other" includes 15 types (vaginal, skin, cervical, bladder, ovarian, lung (non NSCLC), gallbladder, stomach, pancreatic, small intestine, eye, urinary, salivary
gland, anal, oesophageal)
Note: stats from patients reported until 26 oct 2016 and ECRF data from 2nd of nov 2016 (total of 425 biopsies)

5. Clinical data: first documented treatment
Note: stats from patients reported until 26 oct 2016 and ECRF data from 2nd of nov 2016 (total of 425 biopsies)

6. The ‘pipeline’ Genomic Variants sequencing (lab) gVCF
GATK SNV + INDEL calling
bcl2fastq conversion
gVCF
FASTQ file collection for one sample
genotyping
read-mapping
variant filtering
SNP Check
Main msg: ready to share data (but start with only own center)
mark-duplicates
annotation
indel-realignment
VCF
BAM
Genomic Variants

7. somatic variant calling
The ‘pipeline’
TXT
somatic variant calling
Tumor / Normal pair?
CNV calling
annotate
VCF
merge
strelka
mutect
freeBayes
varscan
YES
filter
Kinship Check
Somatic Mutations

8. The ‘pipeline’
Goal: move from a molecular report to "treatment report"

9. Patient Report: time to report
Goal Hartwig Medical Foundation: report within 6 weeks (= 42 days)
Note: stats from patients reported until 26 oct 2016

10. Data sharing
Data will be stored centrally (partner Schuberg-Philis) Relevant clinical data retrieved from medical centers via ECRF
Only data from patients who sign informed consent form
Data is owned by patient and treating hospital
Supplying centre has access to its own data
Anonymised data (the database) accessible for research Data request handled by Data Access Board

11. Data sharing: Portal (currently in test phase)
Goal: allow healthcare professionals to access/download the relevant data from their own centre

12. Data quality
Central theme: Genome in a Bottle (GIAB) sample NA12878
Germline: periodically sequence single sample NA12878
Somatic: use artificially created "tumor" by mixing two GIAB samples
PrecisionFDA: DREAM challenge:
Germline
Somatic
Internal
GIAB NA12878
GIAB based 70/30 Mixin
External
precisionFDA
DREAM / Synapse
Main msg: ready to share data (but start with only own center)

13. Tumor coverage depth
Aim Hartwig Medical Foundation: minimal 90x when % tumor-cells = 30
Other metrics to add to our catalogue: mutational patterns, variant distributions
Note: stats from patients reported until 26 oct 2016 (total of 425 biopsies)