Downloaded 23 times
![ Eukaryotes [2231]
◦ Animal
◦ Fungi
◦ Plants
◦ Protists
◦ Others
Prokaryotes [14268]
Viruses [3219]
Ref:
http://www.ncbi.nlm.nih.gov/genome/brows
e/](https://image.slidesharecdn.com/genomesequencingprojects-120926235720-phpapp02/85/Genome-sequencingprojects-6-320.jpg)
![ JGI – IMG [http://img.jgi.doe.gov/]
Broad
TIGR
WashU
VBI at Virginia Tech](https://image.slidesharecdn.com/genomesequencingprojects-120926235720-phpapp02/85/Genome-sequencingprojects-14-320.jpg)
![Key Findings:
• 80% of the human genome is active!!
– 70,000 promoters and 400,000 enhancers
• 75% of the genome transcribed in some tissue
or other during life time.
• Environment plays great role in switching on
or off of a lot many genes. [Epigenetics]
• Most of the diseases don’t lie with the genes
but the switches!!
• Dark matters controlling the genes are
physically close to the genes they control.](https://image.slidesharecdn.com/genomesequencingprojects-120926235720-phpapp02/85/Genome-sequencingprojects-22-320.jpg)
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Genome sequencingprojects
- 1. Sucheta Tripathy, 27th September 2012 https://sites.google.com/site/suchetalab/
- 2. Introduction. History of Genome Sequencing. Rationale behind genome sequencing. How genomes are sequenced. What happens next. ◦ Assembly and Annotation. ◦ Sequence Submissions. Microbial Genome Sequencing. Human Genome Project. ◦ Encode Project. ◦ 1000 genomes project.
- 3. Gene + Chromosome -> Genome A/T/G/C A/U/G/C
- 4. Determining the order of billions of chemical units that builds the genetic material. ◦ Secrets of life is locked up in the order of the 4 letters!!!! 5-100 million living species???
- 5. Organism Year Institute Genome Size Bacteriophage 1976 Walter Fiers at 3569 bp MS2 the University of Ghent Phage Φ-X174 1977 Fred Sanger 5386 bp Cambridge Haemophilus 1995 TIGR 1,830,138 bp influenzae Saccharomyces 1996 European 12,495,682 cerevisiae Effort (16 chromosomes) Human 2000 Multiple 3.3 x 109 Genome Organizations (3 billion Project letters)
- 6. Eukaryotes [2231] ◦ Animal ◦ Fungi ◦ Plants ◦ Protists ◦ Others Prokaryotes [14268] Viruses [3219] Ref: http://www.ncbi.nlm.nih.gov/genome/brows e/
- 7. Sanger Dideoxy Sequencing methods(1977) Maxam Gilberts Chemical degradation methods(1977) Two Labs that owned automated sequencers: 1. Leroy Hood at Caltech, 1986(commercialized by AB) 2. Wilhelm Ansorge at EMBL, 1986(commercialized by Pharmacia-Amersham and GE healthcare) 3.Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)Alu sequences 4. Hitachi Laboratory developed High throughput capillary array sequencer, 1996.1991, A patent filed by EMBL on media less, solid support based sequencing.
- 8. 454 sequencing methods(2006) ◦ Principles of pyrophosphate detection(1985, 1988) Illumina(Solexa) Genome sequencing methods(2007) Applied Biosystems ABI SOLiD System(2007) Helicos single molecule sequencing(Helioscope, 2007) Pacific Biosciences single-molecule real-time(SMRT) technology, 2010 Sequenom for Nanotechnology based sequencing. BioNanomatrixnanofluidiscs RNAP technology http://www.ncbi.nlm.nih.gov/books/NBK20261/
- 10.
- 11. Gene Prediction Comparative Genomics Orthologs search Blast Analysis Functional Categories
- 12.
- 13. http://www.insdc.or http://www.ebi.ac.uk/e g/ mbl/Contact/collaborati on.html
- 14. JGI – IMG [http://img.jgi.doe.gov/] Broad TIGR WashU VBI at Virginia Tech
- 15. NHGRI Solicited RFAs were First pilot sought for Publicat proposal full ion in for ENCODE ENCODE 2000 In October GWAS - 1990 Human Finished 90% lies First Report ENCODE Genome paper in outside on Encode published project 2003 coding Published 2005 2012 started in 2007
- 16.
- 17. What we knew •95% of the genome is “junk”. – 2.94% of the genome is coding • cis regulatory elements occur within a limited genome distance. • Most of the genome is transposable elements that are of obscure origin are dying. • Transcribed elements are most often translated than not.
- 18. Encyclopedia Of DNA Elements
- 19. Some of theuseful links: • http://www.nature.com/encode/ • http://www.encodeproject.org/ENCOD E/ • http://www.factorbook.org/ • http://encodeproject.org/ENCODE/dat aStandards.html • http://1000genomes.org • http://genome.ucsc.edu/ENCODE/
- 20.
- 21.
- 22. Key Findings: • 80%of the human genome is active!! – 70,000 promoters and 400,000 enhancers • 75% of the genome transcribed in some tissue or other during life time. • Environment plays great role in switching on or off of a lot many genes. [Epigenetics] • Most of the diseases don’t lie with the genes but the switches!! • Dark matters controlling the genes are physically close to the genes they control.
- 23. Key Findings: • Genesand the switches don’t hold one to one relationship! • 4 million switches controlling 21,000 genes!! • Identical twins are NOT identical – greatly influenced by environments. • Astronomy and genetic Biology looks similar(95% of the Universe is called as dark matter – we don’t understand)
- 24. Copy Number Variation SNPs Indels http://en.wikipedia.org/wiki/1000_Genomes_Project Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Peruvians in Perú; Gujarati Indians in Houston; Chinese in metropolitan Denver; people
- 25. To study the effect of environment and their effects on diseases. 99.5% DNA are similar. 269 individuals genotype. One million SNPs genotyped ◦ Rose to 10 million including polymorphic sites.