Lecture 3,4
Upcoming SlideShare
Loading in...5
×

Like this? Share it with your network

Share

Lecture 3,4

  • 751 views
Uploaded on

Genome projects, Secondgen and Thirdgen genome sequencing, application of genome sequencing in predicting disease genes

Genome projects, Secondgen and Thirdgen genome sequencing, application of genome sequencing in predicting disease genes

More in: Education
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Be the first to comment
    Be the first to like this
No Downloads

Views

Total Views
751
On Slideshare
751
From Embeds
0
Number of Embeds
0

Actions

Shares
Downloads
7
Comments
0
Likes
0

Embeds 0

No embeds

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
    No notes for slide

Transcript

  • 1. Genome Sequencing Projects, GenomeSize, Application of sequence information for identification of disease genes
  • 2. Complete Genome Sequencing Whole genome shotgun sequencing BAC end sequencing Chromosome walking End sealing
  • 3. Reference: http://en.wikipedia.org/wiki/File:Genome_Sizes.png
  • 4. Cost of Genome Sequencing
  • 5. Nextgen sequencing methods 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/
  • 6. Sequencing methods http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTDV026689.htm Ref: http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTX056046.htm http://www.wellcome.ac.uk/Education-resources/Teaching-and- education/Animations/DNA/WTX056051.htm
  • 7. Ion Torrent
  • 8. SOLiD Sequencing
  • 9. http://www.genomesonline.org/cgi-bin/GOLD/index.cgi
  • 10. http://www.insdc.org/ http://www.ebi.ac.uk/embl /Contact/collaboration.ht ml
  • 11. Microbial Genome Sequencing• JGI – IMG [http://img.jgi.doe.gov/]• Broad [http://www.broadinstitute.org/]• TIGR [http://www.jcvi.org/]• WashU [http://genome.wustl.edu/]• VBI at Virginia Tech [www.vbi.vt.edu]
  • 12. Human Genome Project NHGRI Solicited RFAs were First pilot sought for Publicati proposal for full on in ENCODE ENCODE 2000 In October GWAS - Finished 90% lies First Report 1990 Human ENCODE paper in outside on Encode Genome coding published 2003 Published inproject started 2005 2012 2007
  • 13. What happens next? You have 10 million characters – what to do with them?  Locate genes  Determine the function of the gene  By similarity search  By domain search  By Predicting signal peptide  By locating transmembrane regionRef: http://www.nature.com/nature/journal/v406/n6797/pdf/406799a0.pdf
  • 14. Genome Annotation Run 6 frame Run Blastp ATGAAGATAGACAG translation with nr CATACTAGCAGCAT AGAATAGATAAGAG ATAGAAATAGAATA Matc h AATATAAGAGAGA found N o Repeat Finding, miRN Product found A Make an finding, tRNAs hmmsearch can etc. N O Pathway analysis Matc Other analysis h found Unknown Genes Hypothesis
  • 15. Genome Sizes  Gametic Nuclear DNA content  Represented as mass in pg(pico grams) or length in mega bases 1 pg = 10^-12 gms 1mb = 10^6 bases 1 pg = 978 MbRef: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669731/
  • 16. Genome Sizes Database of Genome Sizes  http://www.cbs.dtu.dk/databases/DOGS/ Plant Genome database  http://www.kew.org/genomesize/homepage.html Mamalian genome size database  http://www.unipv.it/webbio/dbagsdb.htm Animal Genome size database  www.genomesize.com Fungal Genome size database.  www.zbi.ee/fungal-genomesize
  • 17. Ref: http://www.kew.org/genomesize/homepage.html
  • 18. Ref: http://www.genomesize.com/
  • 19. Ref: http://www-3.unipv.it/webbio/dbagsh.htm
  • 20. Ref: http://www.zbi.ee/fungal-genomesize/
  • 21. Identifying Human Disease genesref: http://www.ncbi.nlm.nih.gov/books/NBK7561/  Before 1980, very few genes were recognized  Reverse Genetics: Know gene product and go back to gene and do a positional cloning  Genetic Redundancy: Multiple genes have the same function
  • 22. Identification of genes throughprotein product
  • 23. 1000 genomes project  1092 genomes of different individuals sequenced.  14 populations  Low coverage exome sequencing 38 million SNPs 1.4 million short insertions 14,000 large deletionsRef: http://www.nature.com/nature/journal/v491/n7422/full/nature11632.html