The Centro Nacional de Análisis Genómico (CNAG) has significant sequencing capacity, including multiple Illumina sequencers capable of sequencing over 700 gigabases per day. CNAG focuses on cancer genomics, disease gene identification, infectious disease genomics, model organism genomics, and synthetic genomics. In 2012, CNAG conducted 47 projects across 16 countries as a major contributor to international genome initiatives.
Two approaches (clone by clone & whole genome shotgun).
Types of DNA sequencing ( 1st, next and 3rd).
Crop genomes sequenced . (Example :Arabidopsis,Rice, Pigeon pea)
Microarray as one of recent biomedical technologies produce high dimensional data. This makes statistical analysis become challenging. I presented an overview of microarray analysis specifically in the use of gene expression profiling in a discussion.
Two approaches (clone by clone & whole genome shotgun).
Types of DNA sequencing ( 1st, next and 3rd).
Crop genomes sequenced . (Example :Arabidopsis,Rice, Pigeon pea)
Microarray as one of recent biomedical technologies produce high dimensional data. This makes statistical analysis become challenging. I presented an overview of microarray analysis specifically in the use of gene expression profiling in a discussion.
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
This presentation consists of topics related to oncogene, proto oncogene, Tumor suppresor gene, Ras gene family and structure and functions of tumor suppressor gene.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
High throughput next generation sequencing and robust transcriptome analysis help with gene expression profiling, gene annotation or discovery of non-coding RNA.
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.for more details please visit
www.indiandentalacademy.com
this is a presentation on gene expression vector that includes what is expression vector, how many types of expression vector and difference between cloning and expression vector
GRC Workshop at Churchill College on Sep 21, 2014. This is Paul Kitt's talk describing the NCBI approach to annotation the full human reference assembly.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Tag-based transcript sequencing: Comparison of SAGE and CAGEMatthias Harbers
Talk given at the European Meeting on Next Generation Sequencing, August 29 to September 1, 2010, at Leiden University Medical Center, The Netherland.
Data have been published in: Hestand et al.: “Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.” Nucleic Acids Res. 2010 Sep;38(16):e165.
PMID: 20615900
This presentation consists of topics related to oncogene, proto oncogene, Tumor suppresor gene, Ras gene family and structure and functions of tumor suppressor gene.
DNA SEQUENCING METHODS AND STRATEGIES FOR GENOME SEQUENCINGPuneet Kulyana
This presentation will give you a brief idea about the various DNA sequencing methods and various strategies used for genome sequencing and much more vital information related to gene expression and analysis
High throughput next generation sequencing and robust transcriptome analysis help with gene expression profiling, gene annotation or discovery of non-coding RNA.
The Indian Dental Academy is the Leader in continuing dental education , training dentists in all aspects of dentistry and
offering a wide range of dental certified courses in different formats.for more details please visit
www.indiandentalacademy.com
this is a presentation on gene expression vector that includes what is expression vector, how many types of expression vector and difference between cloning and expression vector
GRC Workshop at Churchill College on Sep 21, 2014. This is Paul Kitt's talk describing the NCBI approach to annotation the full human reference assembly.
After sequencing of the genome has been done, the first thing that comes to mind is "Where are the genes?". Genome annotation is the process of attaching information to the biological sequences. It is an active area of research and it would help scientists a lot to undergo with their wet lab projects once they know the coding parts of a genome.
Presentation carried out by CNAG's director, Ivo Gut, at the course: Identification and analysis of sequence variants in sequencing projects: fundamentals and tools.
Genomic Big Data Management, Integration and Mining - Emanuel WeitschekData Driven Innovation
Thanks to Next Generation Sequencing (NGS), a technology that is lowering the cost and time of reading DNA, we are faced with huge amounts of biomedical data. These data are continuously collected by research laboratories, and often organized through world-wide consortia, which are releasing many public data bases. One of the main aims of bioinformatics is to solve fundamental issues in biomedicine research (e.g., how cancer occurs) starting from big genomic data and their analysis. In this talk I will give an overview of big genomic data management, integration, and mining.
Applied StemCell Inc’s MAPK genomic DNA (gDNA) reference standards represent biologically-relevant controls that can be directly incorporated into your sample processing workflows in order to optimize your protocols, evaluate assay sensitivity and specificity, and analyze the impact of workflow changes on downstream analysis. They represent ideal materials for both assay development and routine monitoring of assay performance.
The MAPK Genomic DNA Reference Standards are extracted from ASC’s panel of isogenic MAPK mutation cell lines with 50 recurrent pathway-activating mutations in the EGFR, KRAS and BRAF genes, based on data from the Sanger Institute’s COSMIC database.
Key Features of the MAPK Series gDNA Reference Standards:
Most comprehensive MAPK mutation panel on the market
Well-characterized colorectal cancer cells lines: EGFR (RKO), KRAS (RKO), BRAF (HCT116)
Paired, isogenic wild-type cell lines to serve as an ideal control
Footprint-free, homozygous mutations
Reference cell lines are expanded from single-cells, ensuring maximum homogeneity
Available in multiple formats, including slides, scrolls, and full FFPE blocks
Why Use Reference Materials (DNA: Reference standadrds provide a consistent and reliable resource for evaluating and optimizing various stages in your sample processing workflow. Whether you’re starting from DNA extraction, assay design, or library preparation, our reference materials can help you to identify and eliminate sources of variability within your protocols.
@AppliedStemCell offers validated, cellular reference standards for direct incorporation into sample processing workflows or quality control processes.
Highlights:
Overview of molecular reference materials
Workflow and QC for ONCOREF™ cell line generation (#CRISPR)
Advantages of CRISPR-engineered molecular reference standards
Applications of reference materials in assay development
Q & A
#sangersequencing #ngs
REGLAMENTO (UE) N o 640/2012 DE LA COMISIÓN de 6 de julio de 2012 que modifica, con vistas a su adaptación al progreso técnico, el Reglamento (CE) n o 440/2008, por el que se establecen métodos de ensayo de acuerdo con el Reglamento (CE) n o 1907/2006 del Parlamento Europeo y del Consejo, relativo al registro, la evaluación, la autorización y la restricción de las sustancias y preparados químicos (REACH)
En UTOX hemos definido 6 fichas técnicas para los 6 sectores mayoritarios de actuación en toxicología, las cuales muestran nuestro ámbito de actuación para cada uno de ellos.
En UTOX hemos definido 6 fichas técnicas para los 6 sectores mayoritarios de actuación en toxicología, las cuales muestran nuestro ámbito de actuación para cada uno de ellos.
En UTOX hemos definido 6 fichas técnicas para los 6 sectores mayoritarios de actuación en toxicología, las cuales muestran nuestro ámbito de actuación para cada uno de ellos.
En UTOX hemos definido 6 fichas técnicas para los 6 sectores mayoritarios de actuación en toxicología, las cuales muestran nuestro ámbito de actuación para cada uno de ellos.
En UTOX hemos definido 6 fichas técnicas para los 6 sectores mayoritarios de actuación en toxicología, las cuales muestran nuestro ámbito de actuación para cada uno de ellos.
More from La unidad de Toxicología Experimental y Ecotoxicología (UTOX-PCB) (15)
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
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
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