Genome management? The rise of genome factories? A Personal “Omics” cloud? A for clinical trials?

Genome management? The rise of genome factories? A Personal “Omics” cloud? A for clinical trials?  Audacious and achievable goals discussed at PMWC2014.

(This blog was originally posted at, earlier this year)

In January of this year,  thought leaders from across multiple industries assembled at the Computer History Museum in Silicon Valley to discuss key themes in personalized medicine at the Personalized Medicine World Conference 2014 (PMWC).  Having been in the genomics space for over 17 years and as now part of team that leads Invitae’s marketing and commercial development efforts, I have been attending PMWC since its inception in 2010.   Over the past 4 years, it has been fascinating to see how rapidly the field is advancing.  Importantly, despite the numerous challenges we face in democratizing genomics, there are inspiring opportunities ahead. This year’s meeting was filled with incredible speakers and ideas, and as much as I wish I could capture them all – I can only scratch the surface by highlighting the few themes I believe will be most impactful on our industry in the coming years.

From $1000 Genome to Genome Factories

The meeting opened with Jay Flatley, CEO of Illumina and recipient of the PMWC luminary award. He revisited milestones in personalized medicine over the last 10 years and showcased how Illumina’s history is intimately intertwined with this story, from genomics research, to translational medicine, to personalized medicine in the fields of cancer, reproductive health, and NIPT.

Most notable was his statement that “demand for genome factories is about to explode,” referencing Illumina’s recent announcement of a new platform HiSeq X, which boasts the ability to sequence a $1000 genome. In order to get to this price point, you need to purchase 10 of these new instruments (approximately $10 million). Economies of scale get you to the $1000 genome and means that a lab with this set-up, can sequence 18,000 genomes a year.  This is a key landmark in advancing and democratizing personalized medicine and making it more widely available to the masses.

In addition, Flatley emphasized that to really use genomes in medicine, “Big Data” sets need to be generated and shared between researchers and clinicians.  He then announced Illumina’s goal “to get 1 million sequenced oncology patients into a database within the next 5 years.” Not an unachievable goal for the man whose company brought us the $1000 genome…

Entering A New Era of Genome Management

Flatley subsequently participated in an impressive panel titled, “10 Years into Personalized Medicine: What Have We Learned and What’s Next.” Other panelists included our founder and CEO Randy Scott, Kim Popovits of Genomic Health, Brooke Byers  of Kleiner Perkins Caufield & Byers, and Ralph Snyderman of Duke University.

Snyderman opened the panel with, “The ability to predict, track, and precisely define the nature of a disease was one of the revolutions of medicine. Although personalized medicine started over 10 years ago and is potentially a $450 billion industry, things haven’t actually changed in healthcare that much. It’s still not personal, prospective, proactive or planned.”

Popovits shared that upon joining Genomic Health 10 years ago, Randy taught her about The Innovator’s Dilemma and the concept of “disruption.” As a pioneer of genomic diagnostics, she reflected upon some of the challenges they faced with Oncotype Dx. “If we had tried to approach this as a traditional diagnostic, we would have failed…I hadn’t anticipated that payers and regulators weren’t ready for genomic medicine.”

Scott also reminisced of his early days at Genomic Health, “We were wonderfully naïve… no one in the pharma industry was prepared to incorporate genomic data into routine clinical trials….  We just had to bypass pharma and go straight to the physicians.”   “Genomic medicine is here to stay,” added Popovits.  “The value is just too high. We will overcome the barriers and there will be a shift to prevention and early diagnosis.” In looking ahead, Kim predicted, “The next decade will be a revolution as transformative as antibiotics.  Every cancer patient will be sequenced.”

Scott’s vision of the future was influenced by his own family experiences of inherited genetic disease – he tells the story of his nephew’s daughter who had galactosemia, a rare Mendelian metabolic disorder.   “5-10% of the population suffers from a Mendelian disease…. Our goal at Invitae is to aggregate all the worlds’ genetic tests into a single assay for less than $1000,” commented Randy.  “We are focusing on germline genetics and the future is family health and comprehensive genome management.“

Genome management.  What is genome management? At its simplest, over the coming years, as the price of sequencing drops further and further, more and more people will have their genome sequenced for a variety of reasons: medical applications, carrier screening, pharmacogenomics, eventually newborn testing at birth, or just because people are genetically curious about themselves and their families.  As our CMO Jill Hagenkord points out in a previous blog, “DNA information will just exist.”

At Invitae, we require a physician to order and interpret our medical tests. However, we believe that every individual has the right to access their own genetic information and that each individual should own their genetic information.   When it becomes common that a plethora of genomic information just exists, the questions will become: Where will you store your genomic information safely and securely? How will you be able to access it?  Who will you choose to share it with and how?  How can you benefit from it?

That’s one of our goals at Invitae: to make genetic testing accessible to a billion people on the planet and then to safely and securely manage it for them.  Enter an era of genome management.

Personal “Omics Cloud” and the Rise of the Wellness Industry

Dr. Leroy Hood, the scientist who discovered how to automate DNA sequencing that revolutionized biomedicine and forensic science, added another dimension to the concept of genome management.  He proposed that, in the future of this space, every individual would have his or her own personal  “Omics Cloud.”

Hood started off talking about the need to unite the stakeholders in personalized medicine through education.  He also echoed Flatley’s sentiment regarding building “big data” databases that can be shared by various stakeholders.

He proposed that a step in getting there is conducting a “longitudinal Framingham type study of 100,000 patients.” His plan is to collect data three times a year from every patient, including “genomic and proteomic data, clinical chemistry, microbiome, and biomarkers from the heart, liver, brain, and blood.” Further, he also suggests layering in “quantified self “ phenotypic data.  This “Big Data” set can then be mined for actionable variants to reveal the early origins of disease.

This mammoth project will create a data cloud for each individual that can track his or her transition from wellness to disease. Eventually, we will be able to optimize factors for wellness. Hood predicts that this initiative will reduce costs, improve outcomes, and result in the creation of a “wellness industry that dwarfs the healthcare industry.”

A for Clinical Trials

Many companies claim that they put patients at the center of their approach, but by virtue of the questions from the audience and the panel discussion, clearly we as an industry are not succeeding at this goal.

Brave Neil Schiffman, stage IV lung cancer fighter, was an inspirational part of a panel entitled, “Personalized Medicine in Oncology Today”.  He is a classic example of a growing movement of patients who take matters into their own hands to self-educate and self-advocate, “I have my patient advocacy gene turned on” he says.

He shared his experience of searching for and extensively researching clinical trials, which he eventually participated in for a year before going back to his Tarceva treatment. Clinical trials give cancer patients hope, Neil continues, “The old model was that entering a clinical trial was the end. Today, it’s actually the beginning of treatment.”

With less than 10% of patients participating in clinical trials, it’s obvious that we have a problem and need to rethink our strategies around clinical trial recruitment.  One of the most poignant moments of the meeting was the emotional plea to the panel from a woman in the audience who moved us all to tears. She had sadly lost her husband to glioblastoma just last week and she shared their story of how once her husband was diagnosed, it was very hard for them to find any clinical trials, they didn’t know who to talk to or what resources were available to them.

“It’s terrible that there are still questions of what do I do next?  How do I find a clinical trial?” lamented Edgar Staren (CTCA Medicine and Science)to which George Demitri (Dana Faber/Harvard) responded,  “We need a so that patients with metastatic cancer can find clinical trials.”

Marty Tenenbaum @martyenenbaum (Cancer commons) supported this further. “We can cut a decade out of the clinical trial process if we can connect patients and  researchers who need each other,” he said. “Your zipcode is not the area to find the right clinical trial for you, it is your molecular zipcode.”

The inclusion of a patient on this panel made it one of the most impactful sessions of the whole conference.  We should emulate this approach. Edgar Staren suggests, “All industry leaders should include patients in their board meetings…it’s always helpful.” Neil supported this, saying, “Ask the patients to participate in the processes, in real time and you will get a better outcome…. don’t wait for patients to come to you. They’re often very sick.”

The participation and opinions of patients and patient advocates in the audience and panels, provokes a sense of urgency that we as an industry need to act swiftly to help make their voices heard and include them in our processes. We REALLY need put the patients at the heart of everything we do. “Every patient is a clinical trial of one,” said Tenenbaum. Disease is personal to every individual, but medicine is not personalized enough… at least not yet.

Free the Data, Unite the Data, and Share the Data

A theme that ran throughout the meeting was the need for patients,  clinicians and researchers to share data in order to accelerate our understanding of disease and develop better diagnostic, detection, prevention, and therapeutic strategies.

Flatley emphasized that Illumina builds and supports strategies for genomic data sharing.  Randy Scott echoed this sentiment when he mentioned the “Free the Data” movement” a grass roots effort to create a database of BRCA variants that can be shared by the scientific and medical communities. “Genes should be free and not patented,” according to Scott.

Marty Tenenbaum, himself a cancer survivor, summed it up nicely “Cancer is a great equalizer, most of us will confront it at close range at some point in our lives and when you do, you will want access to collective knowledge.”

What Can Genomics Do For Your Health and Wellness Today?

Disclaimer: This article is written for non scientist consumers who are interested in learning about how genomics can impact them today.

What’s in a Genome?

The sum total of the entire DNA in an organism is called a genome.  Genomes are composed of a series of 4 chemicals known as bases, A, C, T and G which are considered to be the building blocks or the code of life – – We can make some headway into understanding  our genomes by determining the exact order of the bases in a strand of DNA – Put simply, genomics is the decoding of all your DNA and this is done by a technique called DNA Sequencing.

Ok, so what?  If we can decode and understand our genomes, what does this mean for us – how will this impact our lives today or in the future?  In a series of posts, I wanted to share with you some ways in which genomics can impact us, on both an individual level and on a global population level.  Granted, there is a long way to go in genomic research and for sure, we don’t know everything yet but with what we do know today there some real examples of the impact genomics is having.

One of the most important aspects of knowing our genomes is the potential impact it can have on our health and wellbeing by arming us with information to make medical decisions and lifestyle choices.

Predicting Susceptibility to Cancer

Lets take cancer as an example. Cancer will affect 1 in 2 men and 1 in 3 women in our lifetime.  How can the application of genomics help?   Can we predict who is likely to be susceptible to Cancer?  In some cases yes, BRCA1 and BRCA2 are two genes, which substantially increase a woman’s risk of developing breast and/or ovarian cancer if she inherits a harmful mutation in those genes.  This type of breast/ovarian cancer often occurs at a young age, usually before menopause and the patient often has a family history. Luckily advances in genomics have enabled us to develop a predictive test for mutations in these genes.    The test was developed by a company called Myriad Genetics

Breast Cancer Screening

Currently this test is not used for routine screening of the population but only for those women with a strong family history of the disease.   Many of you may be thinking – why would I want to know this information?  Won’t this destroy my quality of life as I will be living in fear?  The reality is, that the best chances of surviving many cancers, is when they are detected early.    Knowing that you carry the harmful versions of these genes, can enable you and your clinician to make better medical decisions – like starting regular mammograms at 25 (10 years earlier than usual) and having cancer screening tests more frequently and taking preventative therapies. In some cases, tests like these can really save the lives of the women afflicted with these mutations.


Which Drugs Should I Take?

Another example where genomics has made a significant contribution in healthcare is in being able to select the right drugs or therapies for an individual.  Whenever I am prescribed a drug, I want to know, how effective will the drug be?  What is the correct dose for me? Will I suffer from side effects?  Cancer drugs for example are known to have some of the worst side effects and they only actually work in a small proportion of patients.  One report states that cancer drugs only actually work in about 25% of the patients that take them and yet the majority suffer from severe side effects.  Before you took a cancer drug and had to suffer the side effects, wouldn’t you want to know if it would even work on you?  The field of study, which defines how your genetic information can predict your response to a drug, is known as Pharmacogenomics.

warfarin flower

warfarin flower (Photo credit: hessiebell)


I recently learned about my genome from a company called 23andme ( .  One of the many fascinating things I found out was that I was sensitive to a drug called Warfarin.

Warfarin is a blood thinner often prescribed to people who are at high risk of blood clots.  It’s really important to get the dose of this drug right for the patient, too much and the patient can bleed to death, too little and the patient will be at risk of clotting, heart attack or stroke.  I share this information with my physician because people like me, with an increased sensitivity must be prescribed a lower dose to prevent bleeding.  It’s amazing that I can have knowledge of this information and these risks before ever needing to take the drug.  In this case, I can actually avoid trial and error medicine all together.


Dodging The Disease Bullet

How about the ability to avoid diseases all together?  Many complex diseases like certain types of cancer, cardiovascular disease, obesity and diabetes may have genetic components to them, but your lifestyle and environment can have very strong influences on the outcome and maybe even delaying the onset or avoiding the disease all together.

Melanoma is a prime example of this.  Melanoma is a skin tumor that is responsible for the most skin cancer deaths.   Research has shown that exposure to UV light from the sun or tanning lamps hugely increases the risk of developing melanoma.  If you were aware that you carry an increased genetic risk of developing this disease, wouldn’t you want to take measures to control or limit the environmental or lifestyle factors that can increase your risk?  For Melanoma, there are some simple measures to take to avoid this like using high SPF creams every day on all the exposed areas of your body or avoiding being outside in strong sunlight, or wearing protective clothing.

Eliminating Disease From a Population

Another example of using genomic information to avoid disease, is in carrier screening for recessive disorders.  There are a class of diseases that an individual can be a carrier of genetically, although not actually suffer from the disease themselves.  Examples of these diseases are Cystic Fibrosis, Duchenne Muscular Dystrophy and Tay Sachs disease.  If two people who are both carriers of the same mutation have children, there is a very high chance that one or more of their children could be afflicted.  This is particularly prevalent, although not exclusive to, communities or cultures where Consanguineous or blood relation marriages occur (often first or second cousins).

A simple genetic test can tell you if you and/or your partner were carriers of mutations for these genes.  Knowing this information in advance would enable you to make informed reproductive decisions.  In the case of a couple where both are carriers of mutations for a specific disease; options such as assisted reproduction or IVF exist.  During the IVF process, the embryos can be screened for physical or genetic abnormalities before being implanted.  This is known as PGS – Pre Implantation Genetic Screening.  The Ashkenazi Jewish community, are known to have been afflicted with many of these recessive diseases in their populations.  However, through diligent screening programs, genetic counseling and assisted reproduction programs they have managed to reduce the incidence of a neurodegenerative disease known as Tay Sachs by 90%

Knowledge is Power

These are just a few examples of what genomics can do for you today. We are of course, a long way from understanding everything about the genome and the factors that influence it and we are learning more and more every day.  However some things that we do know today, really can impact your health and wellness.  When it comes to your genome, knowledge really is power.

In future posts I will share how Genomics is impacting us today in areas other than health and give you a view into the next frontiers for genomics …. stay tuned!

Biotechnology 101 Slides for Singularity University

Biotechnology 101 for Singularity University

As many of you are aware, I recently gave a talk at the very prestigious Singularity University.  This is a program co-funded by NASA and Google to study how exponential technologies can solve the global challenges that afflict 1 billion people or more.

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Biotechnology 101 for Singularity University SLIDES

The 2011 Graduate Studies Program or GSP11 as it is known among the Singularitans, is a 12 week program where 80 of the brightest and most accomplished individuals from over 35 countries have assembled at NASA AMES to learn the exponential technologies in the following areas

Technology Tracks AI & Robotics
Networks & Computing Systems
Biotechnology & Bioinformatics
Medicine & Neuroscience
Resource Tracks Futures Studies & Forecasting
Policy, Law & Ethics
Finance & Entrepreneurship
Application Tracks Energy & Ecological Systems
Space & Physical Sciences

I was lucky enough to be invited to give them the basics of Biotechnology and Genomics and for those of you that are interested, my slides are posted above.

Ruby Gadelrab’s answer to Has anybody shared their 23andme results with their physician?

I have tried to this several times and got the following reactions

  • Completely blank stare as if i suddenly started speaking to them in Arabic
  • Disapproving head shake as if i was crazy to have even taken such a test.
  • Denial that the test holds any value whatsoever.

On the occasions that I tried to share with the physicians, i tried to show them the most clinically useful information which is pharmacogenomics data.  None of them even knew that there was a test that could help predict Warfarin (Coumadin) dosing…..

Lack of physician education on genomics will hold us back significantly from utilizing the genomic information with clinical utility as standard of care.

Has anybody shared their 23andme results with their physician?

Know Thy Genome, Know Thyself – Coriell Personalized Medicine Collaborative

During the summer of 2009, I came across a fascinating Genetic Study that I decided to participate in Part 1 of this blog will describe the study and some of its features I particularly liked.  In Part 2, I will share some of my personal experiences in participating in the study.

The Coriell Personalized Medicine Collaborative (CPMC) is a research study with a goal of understanding if personalized genetic information can be used to improve health outcomes.

Participants are asked to contribute a Saliva Sample (by spitting a lot in a plastic tube) which is then screened for genetic variants, which can be attributable to common diseases and predict responses to certain medications.

The participants are also asked to complete an online profile of themselves in which they are asked a series of questions on their lifestyle, family history, current health and medications used.  This information in combination with the test is used to generate a personalized genetic report which is viewable by the participant online, once the results are available.  That’s it – it’s free and it’s really simple.

I wanted to highlight a few of the features of the study that I particularly liked

  • The complex diseases/that are reported on are certain types of cancers, diabetes, heart disease and other multi-factorial conditions.  The key thing that they have in common is that the risk of developing them can all be reduced by changes in behavior , lifestyle or medical management– only conditions which are potentially “actionable’ are reported.
  • Apart from multi-factorial conditions, samples are also screened for genetic variants which can influence how individuals metabolize certain prescription drugs, something that’s definitely useful to know when making treatment decisions.
  • One of my favorite things about the CPMC is the lengths they go to ensure that each participant has the opportunity for a great education in genetics, with up to date easily digestible information. The website gives the user a crash course in Genetics 101, the principles of heredity and a discussion on how genomics knowledge may be useful in making medical decisions.  The sections of the website dedicated to genetic education are excellent at dispelling a number of myths that the public believe about genetics and genomics.  One example is the distinctions made between sporadic cancers, familial cancers and hereditary ones.  When we say “cancer is genetic” many equate that only with hereditary genetics and may have fatalistic misconceptions when learning that they have inherited a ‘cancer gene.’ The explanations are simple, using accessible language and diagrams.
  • Once the results are made available on the website (approx 6 weeks after sample submission) participants are notified by email and then they have several choices.
    • To learn about the condition and what the risks actually mean.
    • To view  the results with a very easy to understand interpretation of what they mean
    • The choice NOT to view each or any of the individual results
    • To get genetic counseling, in person or over the phone before or after viewing the results.  This is a very key part of the study that I believe, differentiates it from some of the commercial ‘Direct to consumer’(DTC) genetic testing companies. It’s particularly important when you consider the ‘fear factor’ that the public currently have with respect to genetic information, particularly when we are talking about complex conditions and disease..
  • The study is ongoing over many years.  Genetic research is constant and every day new genes, are discovered and associated with different diseases.  As this happens this information will be made available to the participants provided they are ‘actionable’ and the participants continue to annually update their online medical and lifestyle profile.   I believe that this continuous engagement of the participants will also play a major role in improving the scientific literacy of the individuals with regards to personalized genomics.
  • Participants have the option to release their anonymous data to non profit or not for profit organizations to use as part of their studies into genetic disease.  Another  great feature of the study,  not only can participants gain more knowledge of their own genomes, but they can also make an active contribution to genetic and disease research which will ultimately benefit future generations.
  • The collaborative nature of this study is again a key differentiator from other commercial DTC entities.  This study brings together thought leading scientific researchers, genetic counselors, IT specialists, hospitals, clinicians, members of the public and many more groups who will all play a key role in advancing personalized genomics initiatives.
  • The ‘online ‘nature of the whole process is a view to the future of what Medicine 2.0 could look like.  A web based interface that enables patients to learn about medical conditions in general, get test results back electronically, learn specifics about their conditions and how to manage them, create and follow treatment plans, interact with their medical practitioners and schedule appointments for treatments without ever leaving their homes.

Once I heard about the CPMC and researched it a little, it didn’t take me long to decide that I wanted to participate. In Future posts I will share with you my 23andme experience as well as some of my results.

I would love to hear from others who decided to take a Personalized Genomics/Medicine test.

For further details on the study please visit