OMICS (Ivo gut)
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    OMICS (Ivo gut) OMICS (Ivo gut) Presentation Transcript

    • Centro Nacional de Análisis Genómico Jornada TOX Ivo Glynne Gut 1.02.2013
    • 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)
    • 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
    • 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
    • Automation
    • 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
    • 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
    • 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
    • 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
    • What we do? 47 Projects/16 Countries
    • 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
    • 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
    • baldiri reixac, 408028, barcelonaspaint +34 93 4020542f +34 93 4037279www.cnag.eu