Transcript "aa". - Church Lab

New projects at the interfaces
of genomics & societies
George Church Thu 15-Jun-2006 at noon.
BIDMC Kirstein Living Room
Thanks to:
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
$ billion
Ref: PhRMA
3 Exponential technologies
Computation &
Communication
(bits/sec~m$)
1E+13
1E+11
1E+9
1E+7
1E+5
urea
1E+3
operons
Synthesis
(amu/project~M$)
tRNA
B12
1E+1
1E-1
E.coli
telegraph
1E-3
1830
1850
1870
Analysis
(kamu~base/$) tRNA
1890
1910
1930
1950
1970
1990
2010
Shendure J, Mitra R, Varma C, Church GM, 2004 Nature Reviews of Genetics. Carlson
2003 ; Kurzweil 2002; Moore 1965
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?
1977
1995
cult Aum Shinrikyo,
aerosolize anthrax &
botulinum in Tokyo on
8 occasions.
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. 75:1205-10.
Purposeful Bio-Risks
"Anthrax 836 .. 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.
A smallpox victim in
Gloucester, 1923
Smart therapeutics example: Environmentally
controlled invasion of cancer cells by engineered
bacteria. Anderson et al. J Mol Biol. 2006
Regulated Capsule
TonB, DapD
for safety
Optical imaging: bacteria, viruses, and mammalian cells encoding lightemitting proteins reveal the locations of primary tumors & metastases
in animals. Yu, et al. Anal. Bioanal. Chem. 2003.
accumulate in tumors at ratios in excess of 1000:1 compared with normal
tissues. http://www.vionpharm.com/tapet_virulence.html
Defensive options
• Global monitoring
bio-weather-map (airborne & medical fluids).
• International bio-supply-chain licensing
(min research impact, max surveillance)
• Cells resistant to most existing viruses
via codon changes
For more info see: arep.med.harvard.edu
difficulty
• Rapid vaccine development & deployment.
Safer Constructive Biology (CB)
Church, G.M. (2004) A synthetic biohazard non-proliferation proposal.
http://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?
Doug Melton, &
son, Sam, who
has diabetes
Adrenoleukodystrophy
Augusto Odone
Huntington's
Chorea
Nancy Wexler,
Hereditary
Disease
Foundation
Mike Milken:
Prostate Cancer Foundation.
Some families inspire expert activists.
Visible traits, genealogy, forensics
Trait
Genes
Ocular albinism OA1
Ocular albinism OA2
Green/blue iris EYCL1
Brown/blue iris EYCL3
Brown/blond hair HCL1
Brown/blond hair HCL3
Brown/red hair HCL2
Skin&hair color MC1R
Occulocutaneous
-Albinism
OCA2
Height (Marfan) MFS
Height
GH1
Height (Laron) GHR
Short Stature
SS
Surname
CODIS Combined DNA Index System
Chromosome location
X p22.3
X p11.4-p11.23
19 p13.1-q13.11
15 q11-q15
19 p13.1-q13.11
15 q11-q15
4 q28-q31
16 q24.3
15 q11.2-q12
15 q21.1
17 q22-q24
5 p13-p12
X&Y p
12 Y loci
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 reidentify 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 -- 4000 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. 2002 297:1237. 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-2006.
• Start with 3 highly-informed individuals consenting to nonanonymous 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:10.1038/msb4100040
Kohane IS, Altman RB. (2005) Health-information altruists--a potentially
critical resource. N Engl J Med. 10;353(19):2074-7.
Genotype % chances if a
subject has one copy of a
(co)dominant allele "Aa"
& most people are "aa".
Genotype % chances if a subject has one copy of a
(co)dominant allele "Aa" & most people are "aa".
Family Risks
Aa 13
aa
Great-grand-parents
Aa 13
Aa 6
Aa 25
Aa 25
grand-parents
2c-2r
aa
parents
aa
Aa 3
Aa 13
2c-1r
aa
Aa 2
Aa 50
Aa 50
aa
uncle
aa
Aa 6
2c
Aa 50
Aa
aa
half
sibling
Aa 25
cousin
sibling
Aa 1
2c+1r
Aa 3
child
aa
Aa 50
1c+1r
grand-child
aa
Aa 25
2c2r = 2nd cousin twice removed
Great-grand-child
Aa 13
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. 2002 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
Sequencing/genotyping with single
human chromosomes
153
Mbp
Zhang et al. Nature Genet. Mar 2006
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):635-41.
Copolymer effects on microglia and T cells in the central nervous system of
humanized mice. Eur J Immunol. 2005
Humanized liver in mice shows human-type metabolic responses to drugs.
Am J Pathol. 2004 Sep;165(3):901-12.
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