OMICS (Ivo gut)


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OMICS (Ivo gut)

  1. 1. Centro Nacional de Análisis Genómico Jornada TOX Ivo Glynne Gut 1.02.2013
  2. 2. The genomehengeSequencing capacity• >700 Gbases/day = 6-7 human genomes per day at 30x coverageEquipment• 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. 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. 4. Sample preparation pipelineDNA• 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• DirectionalityDNA methylation• Whole genome bisulphite sequencing
  5. 5. Automation
  6. 6. Compute Elements of Sequencing • Human genome sequence bases • 30x coverage – bases – 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. 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. 8. What we doThe CNAG focuses its research efforts on the analysis and interpretation of genomeinformation in five interconnected research areas: Cancer Genomics Disease Gene Identification Infectious Disease Genomics Model- and Agro-Genomics Synthetic Genomics
  9. 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 Other2012 Data
  10. 10. What we do? 47 Projects/16 Countries
  11. 11. 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
  12. 12. 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 Sarcoma2.- International Human Epigenome Consortium (IHEC) EU-funded Project Blueprint3.- International Rare Disorders Research Consortium (IRDiRC) Spanish Project on Charcot-Marie-Tooth Disease EU-funded C-Project on data analysis and coordination
  13. 13. baldiri reixac, 408028, barcelonaspaint +34 93 4020542f +34 93