George Church Thu 15-Jun-2006 at noon. BIDMC Kirstein Living Room Thanks to: New projects at the interfaces of genomics & societies

New interfaces of Genomics & Societies Issues - Proactions Synthetic Pathogens - Surveillance of DNA resources Global Warming - DOE BioEnergy/Ecology Project Research Privacy - Personal Genome Project Consent June 2006

Old interfaces of Technology & Societies Issues - Reactions Manhattan Project Animal testing Genetically Modified Organisms (GMOs) Robots & Nanotech

Increasing cost of therapeutics Ref: PhRMA $ billion

3 Exponential technologies Shendure J, Mitra R, Varma C, Church GM, 2004 Nature Reviews of Genetics. Carlson 2003 ; Kurzweil 2002; Moore 1965 urea E.coli B12 tRNA operons telegraph Computation & Communication (bits/sec~m$) Synthesis (amu/project~M$) Analysis (kamu~base/$) tRNA

Options in the midst of exponential change “Do no harm” Hippocrates 400 BCE Epidemics BkI:2:5. (Precautionary principle 1988) Do nothing (AIDS pre-1990; New Orleans pre-Katerina) Moratorium (Recombinant DNA Feb-75 to Jun-76) Hide the science (A & H bombs & USSR biowarfare) Get advice (Genome Project ELSI)

Is Bioterror a real threat? 1995 cult Aum Shinrikyo, aerosolize anthrax & botulinum in Tokyo on 8 occasions. 1977

Bio-risks, Biosecurity Unexpected Arising Bio-Risks "Recently immunized genetically resistant mice with the virus expressing IL-4 also resulted in significant mortality due to fulminant mousepox." Jackson et al. (2001) J Virol. 75: Purposeful Bio-Risks "Anthrax after another accident..disinfected the sewer but..one of the rodents captured in the Kirov sewers.. more virulent than the original. The army immediately ordered him to cultivate the new strains.“ --Ken Alibek in "Biohazard" Resurrecting Bio-risks Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus" Tumpey, et al. Science (2005) 310: 77–80.Science A smallpox victim in Gloucester, 1923

Smart therapeutics example: Environmentally controlled invasion of cancer cells by engineered bacteria. Anderson et al. J Mol Biol Optical imaging: bacteria, viruses, and mammalian cells encoding light- emitting proteins reveal the locations of primary tumors & metastases in animals. Yu, et al. Anal. Bioanal. Chem accumulate in tumors at ratios in excess of 1000:1 compared with normal tissues. Regulated Capsule TonB, DapD for safety

Defensive options Global monitoring bio-weather-map (airborne & medical fluids). International bio-supply-chain licensing (min research impact, max surveillance) Rapid vaccine development & deployment. Cells resistant to most existing viruses via codon changes For more info see: arep.med.harvard.edu difficulty

Safer Constructive Biology (CB) Church, G.M. (2004) A synthetic biohazard non-proliferation proposal. /SBPhttp://arep.med.harvard.edu /SBP Monitor oligo synthesis via expansion of Controlled substances, Select Agents, Recombinant DNA Computational tools are available; small number of reagent, instrument & synthetic DNA suppliers at present. Educational & news emphasis on positive uses International Genetically Engineered Machines Competition (IGEM)

CB & PGP ELSI Advisors (Personal Genome Project, Ethical Legal Social Issues) Jeantine Lunshof (EMGO Institute, Amsterdam) Daniel Vorhaus (Harvard Law) Ting Wu (Harvard Medical School) Eric Juengst (CWRU Center for Biomedical Ethics) Andrea Kalfoglou (NIH) Mildred Cho (Stanford) Laurie Zoloth (Director, Bioethics, Center for Genetic Medicine, Northwestern Univ) Paul Rabinow (UC Berkeley) Lisa Geller (WilmerHale IP Dept). Dan Brock (Harvard Program in Ethics & Health) Ruth Chadwick (CESAGen, Cardiff Univ.) HMS, Partners, Caregroup IRBs >200 Volunteers

Change “The number of personal facts considered stigmatizing has been dropping since the 1960s when cancer, depression, sexual dysfunction, & STDs were taboo topics, while today discussion of personal decisions on Iressa, Viagra, Prozac, & AZT are common.” Molecular Systems Biology 2005

What if no treatment exists? Huntington's Chorea Nancy Wexler, Hereditary Disease Foundation Adrenoleukodystrophy Augusto Odone Doug Melton, & son, Sam, who has diabetes Some families inspire expert activists. Mike Milken: Prostate Cancer Foundation.

Visible traits, genealogy, forensics Trait Genes Chromosome location Ocular albinismOA1X p22.3X p22.3 Ocular albinismOA2X p11.4-p11.23X p11.4-p11.23 Green/blue irisEYCL1 19 p13.1-q p13.1-q13.11 Brown/blue irisEYCL315 q11-q1515 q11-q15 Brown/blond hairHCL1 19 p13.1-q p13.1-q13.11 Brown/blond hairHCL3 15 q11-q1515 q11-q15 Brown/red hairHCL2 4 q28-q314 q28-q31 Skin&hair colorMC1R16 q q24.3 Occulocutaneous -AlbinismOCA215 q11.2-q1215 q11.2-q12 Height (Marfan)MFS 15 q q21.1 Height GH117 q22-q2417 q22-q24 Height (Laron)GHR 5 p13-p125 p13-p12 Short StatureSSX&Y pX&Y p Surname 12 Y loci CODIS Combined DNA Index System 13 autosomal loci

Consent & de-identification “Because the database will be public, people who do identity testing, such as for paternity testing or law enforcement, may also use the samples, the database, and the HapMap, to do general research. However, it will be very hard for anyone to learn anything about you personally from any of this research because none of the samples, the database, or the HapMap will include your name or any other information that could identify you or your family.” Ibadan, Nigeria; Tokyo, Japan; Beijing, China; Utah, USA.

Is anonymity in genomics realistic? 1) Re-identification after “de-identification” using other public data. Group Insurance Commission list of birth date, gender, and zip code was sufficient to re- identify medical records of Governor Weld & family via voter-registration records (1998) (2) Hacking. “Drug Records, Confidential Data vulnerable via Harvard ID number & PharmaCare loophole” (2005). A hacker gained access to confidential medical info at the U. Washington Medical Center files (names, conditions, etc, 2000) (3) Combination of surnames from genotype with geographical info An anonymous sperm donor was traced on the internet 2005 by his 15 year old son who used his own Y chromosome genealogy to access surname relations. (4) Inferring phenotype from genotype Markers for eye, skin, and hair color, height, weight, racial features, dysmorphologies, etc. are known & the list is growing. (5) Unexpected self-identification. An example of this at Celera undermined confidence in the investigators. Kennedy D. Science :1237. Not wicked, perhaps, but tacky. (6) A tiny amount of DNA data in the public domain with a name leverages the rest. This would allow the vast amount of DNA data in the HapMap (or other study) to be identified. This can happen for example in court cases even if the suspect is acquitted. (7) Identification by phenotype. If CT or MR imaging data is part of a study, one could reconstruct a person’s appearance. Even blood chemistry can be identifying in some cases. (8) 26 million Veterans’ medical records including SSN and disabilities stolen Jun 2006.

"Open-source" Personal Genome Project (PGP) Harvard Medical School IRB Human Subjects protocol submitted Sep-2004, approved Aug-2005 renewed Feb Start with 3 highly-informed individuals consenting to non- anonymous genomes & extensive phenotypes (medical records, imaging, omics). Cell lines in Coriell NIGMS Repository (B-cells, keratinocytes, fibroblasts) G M Church GM (2005) The Personal Genome Project Nature Molecular Systems Biology doi: /msb Kohane IS, Altman RB. (2005) Health-information altruists--a potentially critical resource. N Engl J Med. 10;353(19):

Genotype % chances if a subject has one copy of a (co)dominant allele "Aa" & most people are "aa". Aa 13 Great-grand-parents grand-parents parents Aa Aa 50 aa Aa 6 Aa 13 uncle sibling aa Great-grand-child grand-child child Aa 25 Aa 13 Aa 25 Aa 6 cousin aa Aa 3 1c+1r Aa 3 aa Aa 2 2c 2c-2r 2c-1r Aa 13 2c2r = 2nd cousin twice removed aa Aa 1 2c+1r half sibling aa Aa 25 Aa 50 Family Risks Genotype % chances if a subject has one copy of a (co)dominant allele "Aa" & most people are "aa".

What would you do with your genome sequence? Rank mutations/polymorphisms: affecting known disease genes (or related genes) affecting conserved genetic elements potential homozygous or semi-dominant alleles Generate hypotheses about related functions Tests: Association studies, animal models, human tissue culture, etc. Prioritize diagnostic tests, therapeutics, lifestyle, nutritional changes. Human non-synonymous SNPs Ramensky et al NAR 30: 3894; Amino-acid Mutational Spectrum of Human Genetic Disease. Vitkup, et al (2003) Genome Biol 4: R72

Non-anonymous phenotypes Einstein: EEG & brain anatomy Jernigan: Whole body MRI, CT, & serial sections Schwarzenegger : whole body cutaneous photography

PGP Risks The risks of public disclosure of your genotype and phenotype information could affect employment, insurance, and social interactions for you and your immediate family. For example, data such as facial images can be used to identify you which could result in higher than normal levels of contacts from the press and other members of the public motivated by positive or negative feelings about the study. This could mean a significant loss of privacy and personal time. You should also be aware of the ways in which knowledge of your genotype and phenotype might be used. For example, anyone with sufficient knowledge could take your genome and/or posted medical information and use them to (1) infer paternity or other features of your genealogy, (2) claim statistical evidence that could affect your employment or insurance, (3) claim your relatedness to infamous villains, (4) make synthetic DNA and plant it at a crime scene, (5) reveal the possibility of a disease or unknown propensity for a disease. The genetic and medical record information posted on the study website, while directly associated only with you, may also have relevance to your family members.

Environment/Genome/Phenome 1.Environment (genetic): maternal, allergens, microbes 2.Non-genetic: phys/chem, educational, health-care, etc. 3.Small mutations: whole genome vs targeted 4.DNA copy number & rearrangements (paired ends) 5.Haplotype: not mere linkage, but causative combinations in cis) 6.RNA Digital Analysis of Gene Expression (by counting) 7.RNA splicing (that arrays can’t handle) 8.Proteomics (serum, neutrophils, monocytes, CD4+, CD8+, B Cells) 9.Standard Clinical chemistry, Metabolomics 10.Questionaires, Surgeon General's Family History 11.Imaging: MRI, fMRI, CT, Pathology data 12.Response to drugs – personal toxicity & efficacy 13.Behavioral: compliance, happiness, anxiety, etc

Zhang et al. Nature Genet. Mar 2006 Sequencing/genotyping with single human chromosomes 153 Mbp

Single chromosome sequencing (single cell, RNA or particle) (1) When we only have one cell as in Preimplantation Genetic Diagnosis (PGD) or environmental samples (model organisms which don’t grow well in the lab) (2) Candidate chromosome region sequencing (3) Prioritizing or pooling (rare) species based on an initial DNA screen. (4) Multiple chromosomes in a cell or virus (5) RNA splicing (6) Cell-cell interactions in ecosystems (e.g. digestive) (predator-prey, symbionts, commensals, parasites)

Personal Genomics: from analysis to synthesis via stem cells 1.Access to many or all tissues for RNA & mC studies, cell therapies 2.Recombinational programming 3.Epigenetic programming (with mC sequence monitoring) Modeling for Lesch-Nyhan disease by gene targeting in human embryonic stem cells. Stem Cells. 2004;22(4): Copolymer effects on microglia and T cells in the central nervous system of humanized mice. Eur J Immunol Humanized liver in mice shows human-type metabolic responses to drugs. Am J Pathol Sep;165(3):

New interfaces of Genomics & Societies Issues - Proactions Synthetic Pathogens - Surveillance of DNA resources Global Warming - DOE BioEnergy/Ecology Project Research Privacy - Personal Genome Project Consent