George Church: Standards & Open-Access Genome-Environment-Trait Data
Upcoming SlideShare
Loading in...5
×
 

George Church: Standards & Open-Access Genome-Environment-Trait Data

on

  • 3,415 views

 

Statistics

Views

Total Views
3,415
Views on SlideShare
3,386
Embed Views
29

Actions

Likes
0
Downloads
49
Comments
0

3 Embeds 29

http://www.dnalinklabs.com 21
http://twitter.com 4
https://twitter.com 4

Accessibility

Categories

Upload Details

Uploaded via as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

George Church: Standards & Open-Access Genome-Environment-Trait Data George Church: Standards & Open-Access Genome-Environment-Trait Data Presentation Transcript

  • Standards & Open-Access Genome-Environment-Trait DataNIST 10:15-10:45 AM 16-Aug-2012Thanks to:.gov|| NIGMS NHGRI||.edu|| LSRF ArmRev.org||.org Oppenheimer Foundation||||.com|| Azco|| Gen9 Read = = = = = = = = I/O = = = = = = = Write 1
  • Technology & Genome Standards(1) Reference Material : cell lines, primary cells, synthetic DNA spiking(2) Sequencing: Haplotype, nanopore, in situ other methods: Forensic, immune DNA(3) Bioinformatics, Data Integration, & Data Representation: methods to analyze & integrate the data(4) Performance Metrics & Figures of Merit 2
  • Individually Rare -- Collectively Common (10%)2443 diseases (~6000 genes) are highly predictive &medically actionable 1963 PKU 1991 BRCA 2010 HCMPGEd.org Genetests.org 3 View slide
  • Case studiesNic Volker: not intestinal surgery à cord bloodBeery twins: not cerebral palsy à Diet 5HTPDr. Lukas Wartman: Leukemia à SunitinibIvacaftor: treat CFTR G551D à 3 months in FDAPGEd.org View slide
  • Genomes = Traits Standards and improved QC: Cohorts approved for global & commercial sharingPERSONAL TRAITS GENOME (Phenome) 3M alleles 5
  • Genomes + Environments = Traits PersonalGenomes.org Standards and improved QC : Cohorts approved for global & commercial sharing Therapies Immunome Immunome Epigenome TRAITSPERSONAL RNA,mC GENOME (Phenome) Proteome 3M alleles Microbiome 4D-Imaging Stem-cells Metabolome/Tox Cancer Food 6
  • Genomes + Environments = Traits PersonalGenomes.org US, Korea, Israel, Germany, CanadaIndividuals willing to have their genomes, cells(saliva, blood, skin, iPS), extensive trait dataOpen-access : CC016K volunteers registered in 74 countriesHarvard IRB approval for 100K2,418 achieved 100% on entrance exam 7
  • Wireless environment, drug & physiology monitors PGP#1Kim et al Science 2011, GE Vscan ultrasound, Piix cardiac monitor 8
  • Rare Protective alleles e.g. MyostatinEnhanced muscle growth, decreased body fat &decreased atherosclerosis (2009 Endocrine Society, Bhasin, et al BU)Flex Wheeler MSTN -/- 9
  • Correlation → Cause → Cure/Prevention Rare Protective alleles• MSTN -/- Lean muscles <0.001%• LRP5 -/+ Extra-strong bones 0.001-8%• PCSK9 -/+ Lower coronary disease 3, 0.06%• CCR5 -/- HIV-resistant (Pox/Plague) ~0, 1%• FUT2 -/- Stomach flu resistant 20%Embrace the extremes: informative, easy, powerful blog.personalgenomes.org 10
  • Precise Genome Therapy:prevent/cure HIV"Long-Term Control of HIV byCCR5 Δ32/Δ32 Stem-CellTransplantation" 2009 New England J MedicineSangamo Phase 2 clinical trialU.S. District Court rules that stem cells are drugs 11
  • Microbiome & Immunome Impact MetabolomeMicrobe tests: Detect Drug resistance spectrumEarlier warning (e.g. meningitis)Immune tests: Focus on response to exposureLonger times to detect exposure (e.g. HIV, TB) 12
  • PGP Immunome time seriesHarvard/MIT: Vigneault, Laserson, Lieberman-Aiden, Church 13Roche: Egholm, Simen
  • Rare (therapeutic) antibodiesBroadly reactive antibody … potentneutralization of HIV-1 … unusuallylong, 28-amino acids (84 bp),CDR3… towers above the antibodysurface. Pejchala et al. PNAS 2010Antibody-based protection againstHIV infection by vectored immunoprophylaxisBalazs, Baltimore et al. Nature 2012RNAi & Drug alternative #2 14
  • PGP CDR3 size distribution 84 bp 15Laserson, Vigneault
  • PGP Vaccination 3 year time series. -8 -2 -0.04 1 3 7 14 21 28 days 16
  • Proteome Antigen Libraries Human, bacterial, viral, food, allergensLarman et alNatureBiotech 2011 17
  • $1000 bp/$ Genome When? 2040 2004-6: $400M ------Moore’s law 2000-4: $3 billion 1.5x/yr for 0.1 electronics 0.01 2015 2020… 2025 2030 2035 2040 18
  • Factors of bp/$ 2012 $0.8K 10/yr 2011 $4K $1000 2007: $2M When? 2012 2004-6: $400M ------Moore’s law 2000-4: $3 billion 1.5x/yr for 0.1 electronics 0.01 19
  • How? Next-generation technologies1. Polonator MA 33. Nanophotonics Biosci CA 18. GnuBio MA2. Roche-454 CT 34. Network Biosystems MA 19. Bionanomatrix PA3. AB-SOLiD MA 35. SeiraD NM 20. Halcyon CA4. Illumina UK,CA 36. Affymetrix CA 21. ZS Genetics NH5. CGI CA 37. Population Gen Tech UK 22. Electron Optica CA6. Helicos MA 38. AQI Sciences AZ 23. Genizon BioSci QC7. Pacific Bio CA 39. Base4innovation UK 24. LaserGen TX8. IntelligentBioSys MA 40. Li-Cor NE 25. GE Global NY9. Ion Torrent CT 41. U.S. Genomics MA 26. Stratos Genomics WA17. LightSpeed CA 42. Mobious Genomics UK 27. Reveo NY10. Genapsys CA 43. Visigen TX 28. Firebird FL11. Electronic Biosci CA 44. Starlight CA 29. Zeiss MA12. Nabsys RI 30. Lucigen WI13. OxfordNanopore UK 31. Adv. Liquid Logic NC14. IBM-Roche NY 32. Caerus Molec Diag CA15. NobleGen MA16. Genia CA 20 http://arep.med.harvard.edu/gmc/nexgen.html
  • Nanopore : Polymer vs Monomer 1995: “use a polymerase …ONT & Genia while recording conductance changes” Church, Deamer, Branton, Baldarelli, Kasianowicz. 2009 Clarke, Bayley, et al 2010 Derrington, Gundlach, et al 2012 Cherf, Akeson, et al 21
  • 2012 Sequencing ONT/Genia Danaher/IBS $/device 0-30K 150K $/PG 100k-2K 1K Read length 100K 70 Speed (days) 0.1 30 Size (kg) 0.2 50 Sorting No Yes In situ No Yes June 2012 22http://arep.med.harvard.edu/gmc/nexgen.html
  • Clinical Importance of Haplotype vs WGS/Exome 2 mutations in cis vs trans! 386 kb fosmid Kitzman, et al Nat Biotech 2011 1429 kb LFR CGI Peters, et al. Nature July 2012 65pg =10 cells à 60-300 kb in 384 aliquots. 1 false positive SNV per 10 Mb. (Q70)
  • Why long haplotypes -- gaps in thereference genome 20Mb Multiple gap Sclerosis Reich et al. Nature Genetics 2005 24
  • Stretched DNA Fiber FISh/FISSEQ 3Mbp
  • In Situ Sequencing: metaphase haplotypes Zhang et al Nature Gen 2006 Mitra & Church NAR 1999 (FISSEQ) 26
  • Rare cells: Resistance in Leukemia ABL Tyr-KinaseNardi, Raz, Chao, Wu, Stone, Cortes, Deininger, Church, Zhu, Daley. Oncogene M244V T315I E255K
  • Personal Genome Project &Biobanks: iPS (with Coriell) iPS-derived teratoma Endoderm Ectoderm Mesoderm
  • Personalized organs-on-chip + neural, blood-brain- barrier, skin, testis Huh, Ingber et al. Science. 2010 29 Trends in Cell Biol 2011
  • Read: Fluorescent in situ Sequencing (FISSEQ) 60 cycles x 4 colorsSingle basedifferences 30Lee, Yang, Terry, Nilsson, Church et al.
  • 1. Fix cellsEpigenom, 2. Reverse transcribeTranscriptome in situ 3. Cross-linking cDNA 4. RNA digestion 5. Enzymatic circularization
  • Fluorescent In situ Sequencing (FISSEQ)3-D reconstruction of in situ RNA-seq in In situ sequence bar-coded FISH probehuman iPS cells showing DMNT3b, sequencing using confocal microscopy inGAPDH, EEF1alpha and GAL human fibroblasts
  • Signal to noise ratio remains stable over 60 cyclesReference Cycle 1 iPS FISSEQ (Manual cycling) Probe hyb Probe strip (average of 10 spots; 3 pixel x 3 pixel area per spot from 20x epifluorescence imaging)Cycle 25 Cycle 50 (Richard Terry and Chao Li)
  • Overcoming the imaging resolution barrier #1
  • Super-resolution #2: Polonies beads & Rolony grid 35 Synthetic Aperture Optics
  • Challenge of QC of (epi) genetic programming72/101 Non-silent changes in 20 hiPS cell linesNot random mutations during reprogramming (p < 8E-50)Gore, Zhang, et al. Nature.ABCA3, AKR1C4, ANKRD12, ANKRD12, ARHGEF5, ASB3,ATM, C14orf174, C1orf100, CABC1, CACNG3, CALN1,CARM1, CCKBR, CELSR1, DLG3, DNAH3, DSC3, DYNC1H1,FAT2, GDF3, GOLGA4, GSG1, GTF3C1, HK1, HK1, IFNGR1,IFT122, INTS4, IQGAP3, ITCH, KLRG2, LINGO2, LRP4,MARCKSL1, MMP26, MYRIP, MYRIP, NEK11, NEK5, NTRK3,NTRK3, OR6Q1, OSBPL3, PBLD, POLE, POLR1C, PPP1R2,PRICKLE1, PTPRM, RANBP3L, RASEF, RFX6, RGS8, RP4,SAL1, SCN1A, SCN1A, SDR16C5, SEMA6C, SH3PX3, SLC1A3,SLC1A3, SORCS3, SPATA21, SPEN, TM9SF4, TMEM40, TNR,UBA2, VAC14, VMO1, ZER1, ZNF16, ZNF471, ZZZ3 36
  • Technology & Genome Standards(1) Reference Material : cell lines, primary cells, synthetic DNA spiking(2) Sequencing: Haplotype, nanopore, in situ other methods & validation:(3) Bioinformatics, Data Integration, & Data Representation: methods to analyze and integrate the data(4) Performance Metrics & Figures of Merit 37
  • .
  • .
  • 1977 cm Q20 2012 600 nm Q70 55 bp 1000 genomes /month 50X 6Gbp CGI Drmanac et al. Science 2009nobelprize.org/nobel_prizes/chemistry/ 40laureates/1980/gilbert-lecture.pdf
  • Sequencing Technology: Next In Situ - Clinical - Portable Lauerman, Bloomberg In situ Sequencing Lauerman, Bloomberg Intelligent BioSystems Oxford Nanopore GeniaHairy =red, Kruppel=green,Giant=blue. Kozlov et al 41In Silico Bio 2002
  • John Lauerman (PGP#16) JAK2 polycythemia vera, essential thrombocythemia, myelofibrosisSteve Pinker (PGP#6) HCM
  • DIY Bio DNA Explorer (Ages 10 and up) PGP#14 John West Factor V LeidenOCTOBER 1, 2010Obsessed With Genes (Not Jeans),This Teen Analyzes Family DNA