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Human Reference Genome Browser Presentation at BIO-ITWorld 2008

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Saul Kravitz
Saul Kravitz

Presentation by Saul Kravitz on JCVI's Human Reference Genome Browser April 2008. See http://huref.jcvi.org.

Technology
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Towards Personal Genomics Tools for Navigating the Genome of an Individual Saul A. Kravitz J. Craig Venter Institute Rockville, MD Bio-IT World 2008
Personal Genomics: The future is now
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
Genome of a Single Individual: Goals ,[object Object],[object Object],[object Object],[object Object],[object Object]
How does HuRef Differ? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The HuRef Genome PLoS Biology 2007 5:e254 September 4, 2007
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],The HuRef Genome
Variants: NCBI-36 vs HuRef ,[object Object],SNP MNP Insertion Deletion NCBI HuRef variant: G/A variant: TA/AT variant: variant:
Computing Allelic Contributions ,[object Object],Reads ACCTTT GT AATTCCC ACCTTT GT AATTCCC ACCTTT GT AATTCCC ACCTTT AC AATTCCC ACCTTT AC AATTCCC ACCTTT AC AATTCCC Haploid Consensus ACCTTT GC AATTCCC
Computing Allelic Contributions ,[object Object],[object Object],[object Object]
Computing Allelic Contributions ,[object Object],[object Object],MNP Variant Reads ACCTTT GT AATTCCC ACCTTT GT AATTCCC ACCTTT GT AATTCCC ACCTTT AC AATTCCC ACCTTT AC AATTCCC ACCTTT AC AATTCCC True Diploid Alleles ACCTTT GT AATTCCC ACCTTT AC AATTCCC Haploid Consensus ACCTTT GC AATTCCC AC / GT
HuRef Variations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
HuRef Browser ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
http://huref.jcvi.org Search by Feature ID or coordinates Navigate by Chromosome Band
Zinc Finger Protein Chr19:57564487-57581356 Assembly Structure Variations Transcript Gene Haplotype Blocks NCBI-36 HuRef Assembly-Assembly Mapping
chr19:57578700-57581000 Protein Truncated by 476 bp Insertion Homozygous SNP Heterozygous SNP
Assembly Structure
Drill Down to Multi-sequence Alignment Validation of Phased A / C Heterozygous SNPs in HuRef
14kbp Inversion Spanning TNFRSF14 chr1:2469149-2496613
Browser for Multiple Genomes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Future Challenges ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Conclusion ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Acknowledgements HuRef Browser : Nelson Axelrod, Yuan Lin, and Jonathan Crabtree Scientific Leadership : Sam Levy, Craig Venter, Robert Strausberg, Marvin Frazier Sequence Data Generation and Indel Validation : Yu-Hui Rogers, John Gill, Jon Borman, JTC Production, Tina McIntosh, Karen Beeson, Dana Busam, Alexia Tsiamouri, Celera Genomics. Data Analysis : Sam Levy, Granger Sutton, Pauline Ng, Aaron Halpern, Brian Walenz, Nelson Axelrod, Yuan Lin, Jiaqi Huang, Ewen Kirkness, Gennady Denisov, Tim Stockwell, Vikas Basal, Vineet Bafna, Karin Remington, and Josep Abril CNV, Genotyping, FISH mapping : Steve Scherer, Lars Feuk, Andy Wing Chun Pang, Jeff MacDonald Funding : J. Craig Venter Foundation DNA : J. Craig Venter

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Human Reference Genome Browser Presentation at BIO-ITWorld 2008

  • 1. Towards Personal Genomics Tools for Navigating the Genome of an Individual Saul A. Kravitz J. Craig Venter Institute Rockville, MD Bio-IT World 2008
  • 2. Personal Genomics: The future is now
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  • 6. The HuRef Genome PLoS Biology 2007 5:e254 September 4, 2007
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  • 14. http://huref.jcvi.org Search by Feature ID or coordinates Navigate by Chromosome Band
  • 15. Zinc Finger Protein Chr19:57564487-57581356 Assembly Structure Variations Transcript Gene Haplotype Blocks NCBI-36 HuRef Assembly-Assembly Mapping
  • 16. chr19:57578700-57581000 Protein Truncated by 476 bp Insertion Homozygous SNP Heterozygous SNP
  • 18. Drill Down to Multi-sequence Alignment Validation of Phased A / C Heterozygous SNPs in HuRef
  • 19. 14kbp Inversion Spanning TNFRSF14 chr1:2469149-2496613
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  • 23. Acknowledgements HuRef Browser : Nelson Axelrod, Yuan Lin, and Jonathan Crabtree Scientific Leadership : Sam Levy, Craig Venter, Robert Strausberg, Marvin Frazier Sequence Data Generation and Indel Validation : Yu-Hui Rogers, John Gill, Jon Borman, JTC Production, Tina McIntosh, Karen Beeson, Dana Busam, Alexia Tsiamouri, Celera Genomics. Data Analysis : Sam Levy, Granger Sutton, Pauline Ng, Aaron Halpern, Brian Walenz, Nelson Axelrod, Yuan Lin, Jiaqi Huang, Ewen Kirkness, Gennady Denisov, Tim Stockwell, Vikas Basal, Vineet Bafna, Karin Remington, and Josep Abril CNV, Genotyping, FISH mapping : Steve Scherer, Lars Feuk, Andy Wing Chun Pang, Jeff MacDonald Funding : J. Craig Venter Foundation DNA : J. Craig Venter

Editor's Notes

  1. Introduce yourself Relate our experience with individual genomics and building tools for individual genomics