Next Generation Sequencing in Science and Medicine

1. Next Generation Sequencing in Science and Medicine The Presidential Commissionfor the Study of Bioethical Issues 28 February 2011 Washington D.C.

2. DNA Has Only Two Jobs It serves as a store of information Ensuring that information is passed on to each new cell upon division (and the next generation) It directs the synthesis of proteins Which are necessary to carry out the functions of a living organism It’s important before we launch into DNA sequencing to spend a moment reviewing why DNA is imporant and what sequencing it can tell usIt’s important before we launch into DNA sequencing to spend a moment reviewing why DNA is imporant and what sequencing it can tell us

3. DNA’s Structure Explains How it Accomplishes Both Jobs

4. DNA’s Structure Explains How it Accomplishes Both Jobs It is the order of the bases that provides the instructions for protein synthesis One stretch of DNA directs the synthesis of one type of protein, another stretch directs the synthesis of another type of protein Joke about my mutation causing color blindness and apoologize for the color sheme in my slides Joke about my mutation causing color blindness and apoologize for the color sheme in my slides

5. Collagen Collagen

6. DNA Sequencing You have 3 billion bases arrayed in a unique order, with ~20,000 genes that direct the synthesis of all the proteins that comprise you “Sequencing” DNA is simply the elucidation of the order of the bases in an organism’s DNA strand The unique order of your bases greatly influences your health, e.g. What disease you are more - or less - prone to How you will react to different medications A human “genome” is about 6 feet of DNA And each of your cells contains two copies of your genome

7. A Human DNA Sequence ~1/1,000,000th of the Human Genome Interspersed with genes And “polymorphisms” which differ between people Are sometimes important, influencing traits or medically important characteristics About 4000 nucleotides, about 1 / millionth of the human genome If I showed you one such slide each second it would take 11.5 days to show you all million slides of a single genomeAbout 4000 nucleotides, about 1 / millionth of the human genome If I showed you one such slide each second it would take 11.5 days to show you all million slides of a single genome

8. Sequencing DNA Early techniques were developed in the 1970’s A variety of approaches now exist The biggest limitation to sequencing is that the genome is big So carrying out these reactions for an entire genome is slow and expensive One easlity visualized approach, pyro sequencing, takes advantage of the fact that under the right circumstances, a flash of light is emitted each time a base is added to a DNA molecule being synthesized The newest technoloies are attempting to “read” directly the sequence of DNA from “inspecting” the double helix in a varitey of waysOne easlity visualized approach, pyro sequencing, takes advantage of the fact that under the right circumstances, a flash of light is emitted each time a base is added to a DNA molecule being synthesized The newest technoloies are attempting to “read” directly the sequence of DNA from “inspecting” the double helix in a varitey of ways

9. Next Generation Sequencing Takes advantage of miniaturization to engage in massively parallel analysis Essentially carrying out millions of sequencing reactions simultaneously in each of 10 million tiny wells Sophisticated computer analysis of huge amounts of information allows “assembly" of a given sequence 10 million tiny wells in a single machine, each of which 10 million tiny wells in a single machine, each of which

10. Accelerating Technology & Plummeting Cost 1977, the Commodore PET 2001, including either 4 KB (the 2001-4) for $795 or, later, 8 KB (2001-8) of 8-bit RAM. an iPhone has 8 million times more memory $795 in 1977 is $2800 in 2010 dollars So, 3 times as expensive and 8 million times less capacity. After receiving your sample, lab professionals extract DNA from cells in your saliva. Your DNA is then chopped up into shorter strands and copied many times via a process called amplification. Next, your DNA is washed over a small microchip-like device that contains short strands of synthetic DNA. The synthetic DNA fragments latch onto the pieces of your DNA that are a complementary match. Then a laser-scanning step reveals which strands of synthetic DNA are stuck to your DNA to determine your genotype. The chip used in our process is the Illumina HumanHap550+ BeadChip, which reads more than 550,000 SNPs (single nucleotide polymorphisms) plus a 23andMe custom-designed set that analyzes more than 30,000 additional SNPs. What this means is that the laboratory process reads nearly 600,000 data points on your genome. Find out more about our genotyping process. 1977, the Commodore PET 2001, including either 4 KB (the 2001-4) for $795 or, later, 8 KB (2001-8) of 8-bit RAM. an iPhone has 8 million times more memory $795 in 1977 is $2800 in 2010 dollars So, 3 times as expensive and 8 million times less capacity. After receiving your sample, lab professionals extract DNA from cells in your saliva. Your DNA is then chopped up into shorter strands and copied many times via a process called amplification. Next, your DNA is washed over a small microchip-like device that contains short strands of synthetic DNA. The synthetic DNA fragments latch onto the pieces of your DNA that are a complementary match. Then a laser-scanning step reveals which strands of synthetic DNA are stuck to your DNA to determine your genotype. The chip used in our process is the Illumina HumanHap550+ BeadChip, which reads more than 550,000 SNPs (single nucleotide polymorphisms) plus a 23andMe custom-designed set that analyzes more than 30,000 additional SNPs. What this means is that the laboratory process reads nearly 600,000 data points on your genome. Find out more about our genotyping process.

11. Genomics’ Long Term Promise An avalanche of Genome Wide Association Studies (GWAS) in common diseases WGS is now a practical reality Will shed light on the genetic underpinnings of every disease imaginable The long-term promise of genomics is readily evident…But this fundamental difference between medical science and medical practice lies at the root of the challenges we face as we try to implement the fruits of the HGP to realize better health for our patients and the public Published Genome-Wide Associations through 9/2009, 536 published GWA at p < 5 x 10-8 The HuGE navigator does that http://www.hugenavigator.net/HuGENavigator/startPagePubLit.do click on GWAS Also, it connects with the GWAS catalog from NHGRi  http://www.genome.gov/gwastudies/ The long-term promise of genomics is readily evident…But this fundamental difference between medical science and medical practice lies at the root of the challenges we face as we try to implement the fruits of the HGP to realize better health for our patients and the public Published Genome-Wide Associations through 9/2009, 536 published GWA at p < 5 x 10-8 The HuGE navigator does that http://www.hugenavigator.net/HuGENavigator/startPagePubLit.do click on GWAS Also, it connects with the GWAS catalog from NHGRi  http://www.genome.gov/gwastudies/

12. Medical Science = Medical Practice Medical Science is the indispensible foundation of Medical Practice But medical practice is far more complex More variables Individual values matter – and they differ Theory alone is insufficient to guide practice Time-line for translation is long Successful translation into practice is not guaranteed by scientific understanding See sickle cell disease It’s far more expensive The stakes are much higher in Medical Practice Because the power to harm is real and potent

13. Where Does the Clinical Promise of Genomics Lie?Probably not in risk assessment for common disease Common diseases have many factors, of which genetics is only one The bulk of any individual’s genetic risk for common disease is modest Thus assessing genetic risk only “nudges” that risk slightly Few data to suggest that knowledge of one’s genomic status for common disease is useful or is effective in changing behavior

14. What’s The Right Nail For Sequencing Technology? As a diagnostic tool in enigmatic patients As a public health tool to identify those apparently well individuals with dramatically increased risk of preventable disease What I’ve been discussing is how the research agenda, enabled by technologies such as WGS, might impact patient care in the realm of improved diagnostics and treatment. But what about the actual implementation of WGS in the clinic? New technologies are often metaphorically derided as hammers with the adage that when you have a hammer everything looks like a nail. But the flip side to this is that hammers are powerful. And if applied to the right targets (i.e. actual nails) they can be very useful. So with the hammer of WGS soon at hand, we need to ask what the promising targets really are… and how we might contemplate its introduction into the clinical arena. What I’ve been discussing is how the research agenda, enabled by technologies such as WGS, might impact patient care in the realm of improved diagnostics and treatment. But what about the actual implementation of WGS in the clinic? New technologies are often metaphorically derided as hammers with the adage that when you have a hammer everything looks like a nail. But the flip side to this is that hammers are powerful. And if applied to the right targets (i.e. actual nails) they can be very useful. So with the hammer of WGS soon at hand, we need to ask what the promising targets really are… and how we might contemplate its introduction into the clinical arena.

15. Next Generation Sequencing as a Clinical Diagnostic Tool 47 yo female with sudden cardiac arrest Resuscitated successfully EKG reveals “Long QT Syndrome” High risk for sudden death Dozens of genes implicated Application of NGS to detect mutation Thereby guiding patient’s treatment and prevention of death in family members

16. Next Generation Sequencing as a Public Health Tool ~0.25% of US women (375,000) carry a mutation in BRCA1/2 At very high risk of breast and ovarian cancer 85% lifetime breast cancer risk 25-50% lifetime ovarian cancer cancer Knowledge of risk allows prevention Currently we only can identify such women once several family members have developed cancer NGS allows population screening for high risk preventable disorders Cancer predisposition, cardiac disease, etc. ~1-2% of population carry such mutations 3-6 million individuals in the US with preventable disorders if identified

17. Challenges to Harnessing NGS in Clinical Medicine & Public Health Accuracy 99.99% accuracy x 3 billion nucleotides = 300,000 errors per patient Interpretation of the variants we find Storage and access in the medical record Education of patients and public Issues of consent and reporting Education of providers

18. Incidental Information Upon WGS we discover many things we weren't looking for, which we can do nothing about Some are trivial or indeed beneficial But some are problematic And we will occasionally discover lethal, untreatable late onset conditions Some wish to know such information; others do not We must grapple with how to inform patients about such information protect patients from harm but also allow individual autonomy and choice

19. In the Clinical Arena, Genetic Information Presents Few Qualitatively New Challenges Genetic tests affect others Infectious Disease Provide probabilistic information to the asymptomatic Cholesterol Our genome cannot be changed Nor can much of what we discover medically Insurance discrimination Actually better for genetics than the rest of medicine Unexpected results, FPs/FNs Are a routine part of all clinical care DNA is “uniquely identifiable” Zip code + DOB + spouse’s first name I want to leave on a note of optimism. Dealing with genomic technology in medicine presents tremendous challenges. But for the most part they are quantitative in nature, not qualitative. We can surmount them. And many of the answers in doing so lie in understanding that we’ve dealt with many of these questions before. Try getting health insurance if you’ve had a stroke The identifiability of DNA has much more profound implications for research than for clinical medicine, where we’re used to dealing with uniquely identifiable information as a matter of routine.I want to leave on a note of optimism. Dealing with genomic technology in medicine presents tremendous challenges. But for the most part they are quantitative in nature, not qualitative. We can surmount them. And many of the answers in doing so lie in understanding that we’ve dealt with many of these questions before. Try getting health insurance if you’ve had a stroke The identifiability of DNA has much more profound implications for research than for clinical medicine, where we’re used to dealing with uniquely identifiable information as a matter of routine.

20. Challenges to Realizing Genomic Medicine Creation of a centralized, evidence-based, iterative process to define clinically significant genomic findings Thorough health-oriented phenotypic annotation of variants Enabling realistic shared decision making among a range of providers, technology interfaces and patients Understanding the ethical dimensions, patient preferences & values regarding returning incidental results Maintaining a sober focus on evidence

24. A Human DNA Sequence ~1/1,000,000th of the Human Genome Interspersed with genes And “polymorphisms” which differ between people Are sometimes important, influencing traits or medically important characteristics About 4000 nucleotides, about 1 / millionth of the human genome If I showed you one such slide each second it would take 11.5 days to show you all million slides of a single genomeAbout 4000 nucleotides, about 1 / millionth of the human genome If I showed you one such slide each second it would take 11.5 days to show you all million slides of a single genome

27. “We have discovered the secret of life” The mystery of heredity was converted into a tractable problem on a February afternoon in Cambridge England in 1953….Naom Chomsky’s quoteThe mystery of heredity was converted into a tractable problem on a February afternoon in Cambridge England in 1953….Naom Chomsky’s quote