Lecture 3,4
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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

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  • 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