Genome sequencingprojects

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Coursework 100 Bioinformatics CSIR - IICB

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Genome sequencingprojects

  1. 1. Sucheta Tripathy, 27th September 2012https://sites.google.com/site/suchetalab/
  2. 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. 3.  Gene + Chromosome -> Genome A/T/G/C A/U/G/C
  4. 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. 5. Organism Year Institute Genome SizeBacteriophage 1976 Walter Fiers at 3569 bpMS2 the University of GhentPhage Φ-X174 1977 Fred Sanger 5386 bp CambridgeHaemophilus 1995 TIGR 1,830,138 bpinfluenzaeSaccharomyces 1996 European 12,495,682cerevisiae Effort (16 chromosomes)Human 2000 Multiple 3.3 x 109Genome Organizations (3 billionProject letters)
  6. 6.  Eukaryotes [2231] ◦ Animal ◦ Fungi ◦ Plants ◦ Protists ◦ Others Prokaryotes [14268] Viruses [3219]Ref: http://www.ncbi.nlm.nih.gov/genome/brows e/
  7. 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. 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 technologyhttp://www.ncbi.nlm.nih.gov/books/NBK20261/
  9. 9. http://www.springerimages.com/Images/Biomedicine/1-10.1007_s12575-009-9004-1-1http://en.wikipedia.org/wiki/Sequence_assembly
  10. 10.  Gene Prediction Comparative Genomics Orthologs search Blast Analysis Functional Categories
  11. 11. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  12. 12. http://www.insdc.or http://www.ebi.ac.uk/eg/ mbl/Contact/collaborati on.html
  13. 13.  JGI – IMG [http://img.jgi.doe.gov/] Broad TIGR WashU VBI at Virginia Tech
  14. 14. 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
  15. 15. http://www.youtube.com/watch?v=N4i6lYfYQzY
  16. 16. 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.
  17. 17. Encyclopedia Of DNA Elements
  18. 18. Some of the useful 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/
  19. 19. http://www.gencodegenes.org/data.html
  20. 20. http://www.nature.com/nature/journal/v489/n7414/full/489049a.html
  21. 21. 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.
  22. 22. Key Findings:• Genes and 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)
  23. 23. Copy Number Variation SNPs Indels http://en.wikipedia.org/wiki/1000_Genomes_ProjectYoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utahresidents with ancestry from northern and western Europe; Luhya inWebuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Peruvians inPerú; Gujarati Indians in Houston; Chinese in metropolitan Denver; people
  24. 24.  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.

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