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2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
2010StanfordE25 Michele dragoescu e25 project
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2010StanfordE25 Michele dragoescu e25 project

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  • http://www.chicagotribune.com/business/ct-biz-0512-genetic-tests-20100511,0,7466502.story for more
  • Transcript

    • 1. By Michele Dragoescu E25, 2010
    • 2. Overview <ul><li>Genetic sequencing technique </li></ul><ul><li>Direct to Consumer (DTC) Genetic Testing </li></ul><ul><ul><li>Purposes and benefits </li></ul></ul><ul><ul><li>Financial impact </li></ul></ul><ul><ul><li>Current examples </li></ul></ul><ul><ul><li>Privacy concerns </li></ul></ul><ul><ul><li>Tips for the future </li></ul></ul>
    • 3. What’s a genome, anyway? <ul><li>Review from class </li></ul>
    • 4. Sequencing Technology <ul><li>Quick review of Solexa technique from class </li></ul><ul><li>Break down double stranded genomic DNA into fragments </li></ul><ul><li>Add single 3’ A overhangs, then ligate adapters that have 3’ T overhangs </li></ul><ul><li>Get 4 possible results </li></ul>
    • 5. Continue E25 review <ul><li>Amplify fragments with two different adapters using PCR. Heat them, make single stranded </li></ul><ul><li>Attach 5’ end to a solid surface that contains attached primers complementary to the adapters </li></ul><ul><li>Perform bridge amplification by solid phase PCR </li></ul><ul><li>Solid surface coated with primers </li></ul>
    • 6. Still Review <ul><li>Use helicase to separate the strands. Now have single stranded clusters </li></ul><ul><li>Cleave all of one type of the two adapter types </li></ul><ul><li>Left with image: </li></ul><ul><li>Add fluorescently labeled terminating dNTP, DNA polymerase, and sequencing primer complementary to the adapter. </li></ul>
    • 7. Final Steps to Sequencing <ul><li>DNA polymerase adds only one nucleotide because of the terminating group </li></ul><ul><li>A laser excites the fluorescent terminating group </li></ul><ul><li>The color indicates which base is present </li></ul><ul><li>Terminator removed, next base is read </li></ul><ul><li>Sequence many fragments with repeated sections, piece them together for full sequence </li></ul>
    • 8. More Seq. Technologies <ul><li>454 Life Sciences </li></ul><ul><li>Illumina, Inc. </li></ul><ul><li>Pacific Biosciences http://www.dnatube.com/video/3003/SMRT-DNA-Sequencing or PB homepage for demo video </li></ul><ul><li>Helicos BioSciences Corporation </li></ul><ul><li>Applied Biosystems’ SoLiD system </li></ul>
    • 9. Human Genome Project <ul><li>Completed in 2003 and coordinated by the U.S. Dept. of Energy and the NIH </li></ul><ul><li>Identified the 20,000-25,000 genes in human DNA </li></ul><ul><li>Determined the sequences of the 3 billion chemical base pairs </li></ul><ul><li>Then, cost about $1 billion. Goal: $1,000 </li></ul><ul><li>Stanford prof (Steve Quake) who sequenced his entire genome, says he could use Helicos for $12,000 now and the $1,000 goal can be met within three years </li></ul>
    • 10. Genotyping <ul><li>Not the same as full sequencing </li></ul><ul><li>Genotyping - determining which genetic variants an individual possesses. At 23andMe, they look at Single Nucleotide Polymorphisms (SNPs) </li></ul><ul><li>Sequencing - determining the exact sequence of a certain length of DNA. A given stretch may include some SNPs, in addition to regions that are constant </li></ul>
    • 11. Direct to Consumer (DTC) Genetics <ul><li>At home genetic testing! Predict phenotype based on genotype </li></ul><ul><li>It’s controversial – because no doctor advice involved </li></ul><ul><li>Often test for (1) genetic novelties (fun things like wet or dry earwax), (2) ancestry, and (3) health risks </li></ul>
    • 12. Expanding Market <ul><li>23andMe </li></ul><ul><li>Navigenics </li></ul><ul><li>Pathway Genomics </li></ul><ul><li>The March 2010 version of this chart is 14 pages long! </li></ul>
    • 13. What is Pharmacogenomics? <ul><li>Predicting efficiency and safety of a drug on an individual based on their genes and SNPs (regions of variability among humans) </li></ul><ul><li>PharmacoKinetics – how the body absorbs and metabolizes drugs </li></ul><ul><li>PharmacoDynamics - how the drug acts on the body: target region and mechanism of action </li></ul><ul><li>Even having the same SNP can lead to different phenotypes, depending on how many copies you have </li></ul>
    • 14. Pharmacogenomic Database
    • 15. Warfarin <ul><li>Used to thin blood, prevent clots/strokes/heart attacks </li></ul><ul><li>Very difficult to dose--can’t predict based on size of patient </li></ul><ul><ul><li>Overdose & underdose both dangerous </li></ul></ul><ul><li>SNPs on two genes explain much of variability in dose needed (CYP2C9 and VKORC1) </li></ul><ul><li>Research set the dose using demographics + genetics </li></ul><ul><li>Stanford Prof. Russ Altman’s (creator of PharmGKB) dosing algorithm now on FDA labels for warfarin </li></ul>
    • 16. <ul><li>Health spending $4.3 trillion or 19.5% of GDP by 2017 </li></ul><ul><li>The global market for personalized medicine is expected to grow to $452 billion in 2015 (Pricewaterhouse Coopers) </li></ul><ul><li>The core diagnostic and targeted therapeutic segment of the market is presently estimated at $24 billion </li></ul><ul><ul><li>expected to grow by 10 percent annually, reaching $42 billion by 2015 </li></ul></ul>Personalized medicine - a good investment
    • 17. Current Events <ul><li>Walgreens is awaiting FDA approval to sell genetic testing kits </li></ul><ul><li>The kit would be $20, with a vial and envelope to ship off to Pathway Genomics </li></ul><ul><li>The report would cost $79 to $179, depending on the type of test </li></ul><ul><li>Signals trend of ease of access of genetic testing </li></ul><ul><li>No doctor intervention is required, and scientists worry that consumers will misinterpret the tests, which don’t give definite diagnoses </li></ul>
    • 18. Genetic Testing In the News <ul><li>UC Berkeley is asking the Class of 2014 to voluntarily submit sample for genetic testing for susceptibility to too much alcohol, dairy, and not enough vegetables </li></ul><ul><li>Freshmen get two bar code labels, one to put on the sample and one to keep. </li></ul><ul><li>After genotyping, results will be posted online using only the bar code identification to protect privacy </li></ul>
    • 19. Privacy Concerns <ul><li>Too many SNPs revealed lead to the ability to figure out the identity of the individual in question </li></ul>
    • 20. Privacy Concerns <ul><li>Increasing number of genetic databases exist to support research, and they have long stretches of DNA. </li></ul><ul><li>Of 1,000,000 locations in genome where people may differ, only 60-100 need to be measured to give a unique fingerprint of a person </li></ul><ul><li>If this information is associated with phenotype data, it can be a risk to the study subjects </li></ul>
    • 21. Past Issues of Re-Identifiability <ul><li>Sperm donor in UK </li></ul><ul><ul><li>A teenager used some genetic information, general region of country to look up the identity of his father (a sperm donor) </li></ul></ul><ul><ul><li>Is the father now responsible for playing a role in his son’s life? </li></ul></ul><ul><li>Governor of Massachusetts used public records (public health, voter, DMV) to prove she could trace identities </li></ul><ul><li>Patients with rare diseases are easily identified (public health records, Medicaid billing, voter, DMV) </li></ul>
    • 22. The Future <ul><li>The world is eagerly awaiting the future of pharmacogenomics and personalized medicine </li></ul><ul><li>Industry experts are making their predictions </li></ul><ul><li>And also offering some words of advice </li></ul>
    • 23. Key Findings <ul><li>Executive summary of Price Waterhouse Cooper </li></ul><ul><li>The blockbuster model currently pursued by the pharmaceutical industry won’t disappear any time soon </li></ul><ul><ul><li>Blockbuster means huge costs, but huge rewards </li></ul></ul><ul><li>Unexpectedly, stratifying prospective patients through pharmacogenomics can increase a product’s market </li></ul><ul><ul><li>Even though you’re making a smaller market, you’re can reduce advertising and dominate the niche </li></ul></ul>
    • 24. More findings on pharmacogenomics future <ul><li>Regulatory and reimbursement structures related to pharmacogenomics are in place </li></ul><ul><ul><li>Both the FDA and 3 rd party payers are drafting policies </li></ul></ul><ul><li>Pharm. will give life science companies greater options for leveraging their skills, expertise, and discoveries </li></ul><ul><li>Pharm. will likely be driven by a successful, compelling product </li></ul><ul><ul><li>The first high-profile pharmacogenomics product will probably be related to cancer </li></ul></ul>
    • 25. Suggestions for Future <ul><li>Nature paper compares two DTC genetics-testing companies </li></ul><ul><ul><li>Craig Venter one of the authors </li></ul></ul><ul><li>For seven diseases, 50% or less of the predictions of two companies agreed across five individuals </li></ul><ul><li>Paper advises: Companies should communicate high risks better and test for drug response markers </li></ul><ul><li>Community should study markers in all ethnicities and look at behavior after tests </li></ul>
    • 26. Bibliography <ul><li>&quot;- Genetics & Public Policy Center || News & Events || News Releases || Updated Chart of Direct-to-consumer Genetic Testing Companies Available.&quot; - Genetics & Public Policy Center - . The Genetics and Public Policy Center Johns Hopkins University Berman Institute of Bioethics, 9 Mar. 2010. Web. 24 May 2010. <http://www.dnapolicy.org/news.release.php?action=detail&pressrelease_id=137>. </li></ul><ul><li>Colliver, Victoria. &quot;Ethics of UC Berkeley's Gene Testing Questioned - SFGate.&quot; Featured Articles From The SFGate . Web. 24 May 2010. <http://articles.sfgate.com/2010-05-21/bay-area/20907654_1_genetic-testing-test-results-testing-kits>. </li></ul><ul><li>Justin. &quot;Healthcare Costs under the Microscope of Personalized Medicine « TheOTCInvestor.com.&quot; TheOTCInvestor.com . Web. 24 May 2010. <http://theotcinvestor.com/health-care-costs-under-the-microscope-of-personalized-medicine-715/>. </li></ul><ul><li>Ng, Pauline C., Craig J. Venter, Sarah S. Murray, and Samuel Levy. &quot;Access : An Agenda for Personalized Medicine : Nature.&quot; Nature Publishing Group : Science Journals, Jobs, and Information . J. Craig Venter Institute, Oct. 2009. Web. 24 May 2010. <http://www.nature.com/nature/journal/v461/n7265/pdf/461724a.pdf>. </li></ul><ul><li>Perton, Marc. &quot;FDA Investigating Walgreens Genetic-Testing Kits.&quot; The Consumerist . Web. 24 May 2010. <http://consumerist.com/2010/05/fda-investigating-walgreens-genetic-testing-kits.html>. </li></ul><ul><li>Wade, Nicholas. &quot;The New York Times Log In.&quot; The New York Times - Breaking News, World News & Multimedia . Web. 24 May 2010. <http://www.nytimes.com/2009/08/11/science/11gene.html?_r=3&hp>. </li></ul><ul><li>&quot;What Is the Difference between Genotyping and Sequencing? | PPH.&quot; The Mission of Palomar Pomerado Health Is to Heal, Comfort, and Promote Health in the Communities We Serve. Web. 24 May 2010. <http://www.pph.org/PPHContentPage.aspx?nd=44>. </li></ul><ul><li>Russ Altman’s talks on pharmacogenomics </li></ul><ul><li>Pharmgkb.org </li></ul>

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