2007 November

Eye on DNA Interview with Knome CEO Jorge Conde

by Dr. Hsien-Hsien Lei
Posted November 30, 2007 in DNA Testing, Personalities with DNA

jorge condeAs promised, here’s my exclusive interview with Jorge Conde, President and CEO of Knome – the latest company to offer personal genome services. Jorge is a graduate of Harvard Business School and also holds an MS from the Harvard-MIT Division of Health Sciences and Technology (HST) and a Bachelor’s degree in Biology from The Johns Hopkins University. He previously worked in business development at Helicos Biosciences as well as other life sciences companies. Jorge is clearly motivated and energized by the promise of personal genomics. He’s an up-and-coming player in the field who’s one to watch!

Hsien: Knome claims to be the first company to offer whole-genome sequencing and analysis to private clients but it certainly won’t be the last. How will Knome distinguish itself from competitors like Navigenics, 23andMe, and (to an extent) The Personal Genome Project?

Jorge: We’re focusing on whole-genome sequencing now because we believe that this is the approach that will drive personal genomics forward. An advantage for us to being first is that, from inception, we’ve built our platform and services specifically around whole-genome applications. And because we’re initially focusing on a limited number of clients, we can provide first-in-class service – customized and personalized to each individual client.

We’ve also spent a considerable amount of time thinking about our responsibilities as a personal genomics company. At Knome, we’ve taken a novel approach to ensuring that our clients’ genomic information remains private and secure. We’ve built our platform to completely avoid centralized storage of databases containing sensitive genomic information. As you can imagine, these databases could prove to be very tempting targets.

Security is further strengthened by keeping control in the hands of those that value it most. Using our platform, our clients control how their information is accessed and shared, and they retain full ownership over their own genomic information – after all, they’re paying us to help them understand their genome and not to take possession of their DNA.

Hsien: At this point in time, it’s far easier to sequence the genome than to understand it. How does Knome plan to organize genomic information and make it directly relevant to the average consumer?

Jorge: We’ll be talking much more about this in the near future, but clearly this is central to the service we will be providing to our clients. Broadly speaking, there are two key challenges to relating whole genome information to the average consumer.

The first, of course, is making sense of all the research that is currently out there and staying current on new information as it becomes available. Of course, we want to be sure that our analyses accurately and responsibly represent the best and most current scientific knowledge, and we’re working with teams of leading bioinformaticians, geneticists and clinicians to tackle this challenge.

The second challenge will be to communicate inherently complex, and often inconclusive, information in a way that the average consumer can understand. As you know, our genomes provide a wealth of information about us but there are very few yes/no answers, so it will be critical that our clients understand what this information may tell us – and what it cannot tell us. Our focus on individualized interpretation and consultation services will enable us to establish a direct line of communication with them to help guide them.

And because a client’s whole-genome will have already been sequenced, we will be able to update our analyses as our understanding improves.

Hsien: In the Knome FAQ, it seems that the company is positioning itself as a comprehensive genome services company, including both medical genetic information along with ancestry and genealogy. How are these two sides of genetic testing compatible?

Jorge: We want our clients to understand that our genomes can tell us more about ourselves than just our risk for developing disease. Our ancestry and genealogy make up a very important part of who we are, and this is an application that the average consumer can appreciate and enjoy. That said, our initial focus will be on medical genetic information analysis and interpretation services. In the future, we hope to develop ancestry, genealogy and other novel applications.

Hsien: What kind of person do you think will be a first generation Knome customer? What kind of person do you think will benefit most from whole genome sequencing?

Jorge: Pricing for our service starts at $350,000, so our first generation clients will of course need to have the financial means to use our services. That said, these early adopters will also be pioneers in the personal genome revolution and will be amongst the first people in history to be fully sequenced. These participants will be on the cutting edge of science and medicine. They will have access to the latest information as it becomes available and those that are willing to learn as we learn (and can appreciate risk prediction and the changing nature of our scientific understanding) will be best positioned to benefit.

We also hope to attract people who have a personal desire to contribute to expanding the scientific frontier, which is why we also offer each client the option of allowing researchers to have access to their anonymous sequenced genome. But, as I mentioned previously, while we hope that a significant percentage of our customers choose to participate, it is certainly not required.

Hsien: What do you think are the biggest obstacles to overcome in the personal genome revolution?

Jorge: Clearly there are many challenges today to fully realizing the potential of personal genomics. The most immediate obstacle is the cost of sequencing. Fortunately, some very smart people are out there working to solve this problem. The next challenge will be to enhance our understanding of human genetic variation, and we believe Knome is well-positioned to make a significant contribution here. And, of course, the overarching obstacle will be how we as a society deal with the legal, privacy and ethical issues surrounding the use, and potential misuse, of personal genomic information.

Thanks for taking the time to answer these questions, Jorge! I cannot believe that it is now possible to get our genomes sequenced without signing up to be a research subject.

For anyone interested in learning more about Knome and perhaps exploring career opportunities, email careers@knome.com. More info on their contact page.

Update: David Hamilton of Venture Beat has more on Knome.

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DNA Quote: Digging to America by Anne Tyler

by Dr. Hsien-Hsien Lei
Posted November 30, 2007 in DNA Quotes and Excerpts

digging america anne tyler

She said, “When I was a girl, how I hated it all! At any of the family parties, I’d be sitting where you are this minute.”

She wondered if there was a gene for that – for holding oneself back, resisting the communal merriment. It had never before occurred to her that she had passed this trait on to Sami.

~From Digging to America by Anne Tyler

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Genome Paranoia At Its Craziest

by Dr. Hsien-Hsien Lei
Posted November 29, 2007 in DNA Testing

genome babyAnnalee Newitz of the San Francisco Bay Guardian needs to read Eye on DNA and the rest of The DNA Network. She’s the author of Are you my genome friend? Home genomics: just another self-help scam? in which misinformation and exaggerations abound.

For instance:

A company called 23andme.com launched last week and got wads of media attention for being the first user-friendly Web site devoted to home genomics tests and analysis.

Nuh uh. Plenty of companies, like DNA Direct*, have been offering direct-to-consumer genetic testing for years!

For just $1,000, the company will take a swab of your cheek, sequence your genome, and tell you a bunch of things about how you fit into the Family of Humanity.

Check your facts, missy. 23andMe requests a sample of saliva and they don’t sequence customers’ genomes (Knome does that). 23andMe analyzes single nucleotide polymorphisms (SNPs) in a person’s genome.

And 23andme is just the beginning. Another company called DeCode offers a similar service called DeCodeMe, and more are sure to follow.

Now here I’m just going to be nitpicky. It should be deCODE and deCODEme with “code” in ALL CAPS. And, yes, more personal genomics companies have followed already.

People are desperate to understand themselves, and so they turn to genetics as if it were a self-help manual instead of a still poorly understood science. While there are many theories about how genetic expression works on our personalities and health, there are few solid facts.

Poorly understood science as opposed to what? String theory? Neurophysiology? Paleontology? And did she say “few solid facts”? Clearly, Annalee needs to read my list of 100 Facts About DNA.

What I see when I look at a site like 23andme is nothing less than the future of eugenics. I don’t mean the scary capital-E eugenics of the 1930s that involved killing Jews and sterilizing “loose women.” I mean wild-type eugenics, the kind of genetic engineering that happens in nature without any dictatorial intervention. It’s the sort of eugenics that results when people of the same races and classes tend to marry each other. It’s the genetic engineering that results when men can choose their mates but women can’t.

If I weren’t so tired, I think I’d bash my laptop screen in. What is “wild-type eugenics”?! Is she talking about evolution? Annalee needs to look up the meaning of “eugenics” in the dictionary.

…they [23andme] do offer users the chance to compare their genomes with those of the general population.

They do? I had no idea that so many people in the “general population” had already had their genomes analyzed! And they were even so thoughtful to have entered their genomes into a database for comparisons. To think I’ve been tracking genetics and the genome revolution for over 15 years and had no idea everyone except me had their genomes sequenced already.

After they sell it to insurance companies — who will use the information to charge higher rates to people with “bad” genes — they’ll sell it back to users in the form of social networks.

Talk about paranoia. The Genetic Information Nondiscrimination Act (GINA) aims to prevent all this!

Annalee Newitz is a surly media nerd who thinks your genome isn’t worthy of hers.

Niiiice. No wonder she keeps harping on eugenics.

*Yes, I work for DNA Direct!

Photo: Jelly Baby by Mauro Perucchetti representing a cloned human on exhibit at the Wellcome Collection in London, UK.

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Personal Genome Sequencing Company Knome Launches

by Dr. Hsien-Hsien Lei
Posted November 29, 2007 in DNA Testing

knomeHope you’ve been saving your pennies because starting today, you can order your entire genomic sequence from Knome. Please see Eye on DNA’s interview with Knome CEO Jorge Conde is due to be published this week (he promised!) but until then. Here you can feast your eyes on the press release!

HUMAN WHOLE-GENOME SEQUENCING HITS COMMERCIAL MARKET
20 individuals to be among first in history to be fully sequenced

CAMBRIDGE, Massachusetts – Nov. 27, 2007 – Knome, a personal genomics company, today announced the launch of the first commercial whole-genome sequencing and analysis service for individuals.

“In 2003, the Human Genome Project completed a 12-year effort to sequence the first human genome at a cost of $3 billion. Only very recently have costs come down to a level where it is now feasible for private individuals to be sequenced and analyzed. We expect this evolution to quickly usher in a new era in personalized medicine,” said Dr. George Church, PhD, a cofounder of the firm and Professor of Genetics at Harvard Medical School.

First to know, first to benefit
Knome today opens enrollment for its first sequencing flight. Because the sequencing and analysis process is both labor and computationally intensive, initial capacity is expected to be limited to approximately 20 clients.

“To date, Craig Venter and James Watson are the only named individuals to have their genome sequenced. Our first 20 clients will have a historic opportunity to help pioneer the emerging field of personal genomics. They will be among the first to know and the first to benefit from the latest advances in our rapidly developing understanding of the human genome,” said Jorge Conde, the firm’s CEO.

Building the gold standard
Whole-genome sequencing decodes the 6 billion bits of information that make up an individual’s genome. Unlike existing genome scanning or “SNP chip” technologies that provide useful but limited information on approximately 20 conditions, whole-genome sequencing allows for the analysis of up to 2,000 common and rare conditions, and over 20,000 genes – numbers that are rapidly growing.

“Whole-genome sequencing is the endgame,” according to Mr. Conde. “It will enable us to look at nearly 100% of your genetic code compared to the less than 0.02% currently available on SNP chips. This is the approach that most fully reveals what our genomes can tell us about ourselves.”

Pricing for Knome’s service will start at $350,000, including whole-genome sequencing and a comprehensive analysis from a team of leading geneticists, clinicians and bioinformaticians. This team will also provide continued support and counseling.

“Knome’s goal is to establish the gold standard in personal genomic services for individuals. We are bringing our clients the latest sequencing technology, Knome’s proprietary analytic engine and security solutions, and access to top genomic scientists and medical professionals,” said Conde. “Analytics, privacy and on-going client service are as important to us as the actual sequencing.”

Core to the fundamental principles of the company, clients will retain full ownership of their personal genome and have the ability to anonymously share all or portions of their genome with researchers and other medical professionals.

Continue reading…

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DNA Video: deCODEme Buccal Swab DNA Collection Instructions

by Dr. Hsien-Hsien Lei
Posted November 28, 2007 in DNA Podcasts and Videos

How can she keep smiling after scraping her cheeks with that high tech popsicle stick aka buccal swab? I think it might make me gag.

Check out pictures of other types of buccal swabs and DNA collection procedures at Google Images.

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Proof of Graduation

by Dr. Hsien-Hsien Lei
Posted November 28, 2007 in DNA in General

This isn’t exactly my diploma but here I am with my parents and sister in May 1998 on the day I graduated with my PhD in epidemiology from the Johns Hopkins Bloomberg School of Public Health. The title of my dissertation was “Case-control studies in genetic epidemiology: candidate gene associations with type 2 diabetes mellitus and familial clustering of renal disease.”

hopkins sph graduation

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Eye on DNA Headlines for 27 November 2007

by Dr. Hsien-Hsien Lei
Posted November 27, 2007 in DNA Testing, DNA and the Law, Eye on DNA Headlines

  • Serial killer Allan Legere, who committed his crimes in 1989, was the first to be convicted in Canada using DNA typing. Now Science East wants to convert his jail cell into an exhibit on DNA, science, and law. Heck if you can drag me into jail just see this despite my devotion to DNA arcana.
  • Despite the brouhaha over new next-gen personal genomics services, it bears repeating that we are more than our DNA. The Toronto Star gets into epigenetics today.

    Epigenetic processes are a normal and necessary part of life. Much like a software program that tells a computer how to work, epigenetic processes tell our DNA when, where and how to express each of the body’s 25,000 genes. But if they go wrong or work ineffectively, there can be major health consequences. And scientists now believe that epigenetic changes are the root cause of many complex, chronic diseases, including cancer, neurological disorders and type 2 diabetes.

  • genetics cribsheetCramming for a test or just want a quickie genetics reference? Seed Magazine has a genetics cribsheet that may help.
  • As Steve Mount and Blaine Bettinger have pointed out, this week’s genetics flavor is DNA testing for ancestry and ethnicity. Edward Ball’s new book, The Genetic Strand, makes it all even more fascinating. See Susan Okie’s Washington Post review.
  • Yesterday, the Sorenson Identigene DNA paternity test hit the shelves of Rite Aid and other pharmacies. If you’re interested in family relationship testing, check out this Home Maternity DNA Testing Kit from Amazon.com. There’s “1 used & new available from $199.00.” Why not be the first customer to review it?

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Geeky DNA T-Shirt: Christmas Star DNA

by Dr. Hsien-Hsien Lei
Posted November 27, 2007 in Geeky DNA T-shirts

christmas star dna shirt

Less than four weeks to Christmas! (I don’t care if you don’t care because I don’t really care either.) Here’s the perfect thing to wear to all your holiday parties – the Christmas Star DNA t-shirt from Zazzle.

Don’t be such a Scrooge. Do you have the Christmas spirit so much it is in your DNA? Or do you just want a subtle, not gaudy shirt for the holidays? Big star with DNA made of small, holiday-colored stars in front of it.

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DNA Paternity Tests Available At Local Pharmacies

by Dr. Hsien-Hsien Lei
Posted November 26, 2007 in DNA Testing

dna paternity kit identigeneFeeling adventurous today? If you’re in California, Oregon, or Washington, head on down to Rite Aid and grab a Sorenson Identigene paternity test kit off the shelf for as little as $20 plus $119 for DNA analysis. Offer good while supplies last. (Ok, I added the last bit because I thought it sounded appropriate.)

Here’s what you get:

  1. Three sets of cotton swabs to collect cheek samples from the child, the alleged father, and the mother (optional)
  2. Envelopes to return the samples to the Soreson lab in Salt Lake City
  3. You receive your results within five days of the lab receiving the sample

Keep in mind that these paternity test results are for personal use only and would not be legally admissible. For paternity test results that you can use in child custody or immigration situations, you’d need to undergo chain-of-custody DNA testing which would document each step of the process to ensure that the samples are linked to the right person.*

Identigene was acquired by Sorenson Genomics in June 2007. Previously, Sorenson’s paternity testing was handled by GeneTree, which has since chosen to focus on genetic genealogy. According to the Identigene website, their DNA paternity test collection kits are also available at Meijer and other unspecified pharmacies.

The Sorenson Identigene test is not the only genetic test currently available on the shelf. Sciona’s Mycellf nutrigenomic test is also available through Pharmaca Integrative Pharmacy as well as online. In 2002, the Mycellf genetic tests were also available at some Body Shop stores in the UK until lobbying from GeneWatch UK and others forced the Body Shop to stop selling the tests. At the same time, 13 UK retailers, including Boots, John Lewis, and Marks and Spencer, also decided not to stock genetic tests.

via The New York Times

*The company I work for, DNA Direct, also offers both home and legal paternity testing.

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What’s In Your DNA? #19

by Dr. Hsien-Hsien Lei
Posted November 25, 2007 in In Your DNA

iguanaLazy Iguana on Man DNA:

…somewhere, buried deep in my DNA, is a gene that creates a protein that compels me to break things, then try to fix them again.

Neptune Baby on shopping:

What the heck is wrong with me? It’s my mom’s fault. She’s a shop-o-holic too so I always blame her. I swear it’s in my DNA.

Social network site eSnips introduced “Social DNA” this month (via TechCrunch):

The fun way to discover who you are, how you compare to others and who’s just like you

How? By matching your ‘Social genes’ for lifestyle, music, movies and more… with others

Almost feels like everyone is in cahoots with the next gen personal genomics companies!

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