1. Centro Nacional de Análisis Genómico
Jornada TOX
Ivo Glynne Gut
1.02.2013

2. The genomehenge
Sequencing capacity
• >700 Gbases/day = 6-7 human genomes per day at
30x coverage
Equipment
• 2 Illumina GA2x
• 10 Illumina HiSeq2000
• 1 Illumina MiSeq
• 4 Illumina cBots
• 950 core cluster super computer
• FPGA dataflow processor
• 2.2 petabyte disc space
• Barcelona Supercomputing Center (10 x 10 Gb/s)

3. How we work – Our process
Biological
Sequencing Informatics
Resources
-Bioinformatic Analysis
- Reception - Sample Preparation o Production Bioinformatics
- Quality control - Sequencing Production o Data analysis
- Conditioning - Methods Development - Bioinformatic Development
- Storage o Statistical Genomics
o Algorithm Development
o Functional Bioinformatics
o Genome Annotation
- Genome Biology
LIMS + QC

4. Sample preparation pipeline
DNA
• Whole genome sequencing
• No PCR
• Double size selection
• Targeted sequencing
• Agilent – SureSelect, HaloPlex
• Nimblegen – SeqCap EZ
• Refined protocols
• BARseq
• RADseq (in preparation)
RNA
• Regular Illumina protocols
• polyA+, ncRNA, miRNA, ribo minus
• Directionality
DNA methylation
• Whole genome bisulphite sequencing

5. Automation

6. Compute Elements of Sequencing
• Human genome sequence 3.000.000.000 bases
• 30x coverage – 100.000.000.000 bases – 1.000.000.000 reads
• Base calling (Illumina)
• Alignment to reference
• Variant calling
• Joining data for interpretation of study
• Presentation of the data
• Verification of results
• Interpretation of results

7. Informatics Resources
Production Bioinformatics
• Primary run analysis and verification
• QC systems and LIMS
Analysis Production
• Data analysis and interpretation
Statistics
• Alignment and variant calling with high performance CNAG pipeline
• Proprietary GEM/BFAST alignment and SNAPE variant calling
Annotation
• Proprietary pipeline for genome annotation
• Annotation against genome databases with Ensembl API (mirror)
Algorithm Development
• Development and improvement of alignment and assembly methods
Functional Bioinformatics
• Establish models of functional effects of variants
• Establishment of networks
Genome Biology - Structural Genomics
• 3-d structure of genomes
Databases
• Storage and distribution of data in collaboration with the BSC

8. What we do
The CNAG focuses its research efforts on the analysis and interpretation of genome
information in five interconnected research areas:
Cancer Genomics
Disease Gene Identification
Infectious Disease Genomics
Model- and Agro-Genomics
Synthetic Genomics

9. SEQUENCING
APPLICATIONS
WG-Seq
Exome-Seq
BS-Seq
mRNA-Seq
Custom capture-Seq
ChIP-Seq
dirRNA-Seq
Cancer Genomics
RESEARCH AREAS
Disease Gene Identification
Infectious Disease Genomics
Model Organisms and Agrogenomics
Other
2012 Data

10. What we do?
47 Projects/16 Countries

12. Proposed model for a different cell of origin of CLL subtypes
(U-CLL from naive-like B cells and M-CLL from memory-like B cells)
Normal B cell differentiation
Activation Proliferation Differentiation
Plasma
23,052 hypoM / 3,231 hyperM cell
Naive Memory
Leukemic transformation
B cell B cell
66%
CpGs in 4,607 hypoM
1,246 hyperM
common
3,265
diffM M-CLL
U-CLL

13. What we do?
CNAG is a major contributor and driver in three large International Initiatives:
1.- International Cancer Genome Consortium (ICGC)
Spanish Project on Chronic Lymphocytic Leukaemia
French Project on Prostate Cancer
French Project on Ewing’s Sarcoma
2.- International Human Epigenome Consortium (IHEC)
EU-funded Project Blueprint
3.- International Rare Disorders Research Consortium (IRDiRC)
Spanish Project on Charcot-Marie-Tooth Disease
EU-funded C-Project on data analysis and coordination

15. baldiri reixac, 4
08028, barcelona
spain
t +34 93 4020542
f +34 93 4037279
www.cnag.eu