Eye on DNA — How will it change your life?

Video: Knome’s Ari Kiirikki Speaks with Medgadget

by Dr. Hsien-Hsien Lei
Posted October 30, 2009 in DNA Podcasts and Videos

via Medgadget

(>> Start a discussion!)


People Who’ve Had Their Genomes Sequenced

by Dr. Hsien-Hsien Lei
Posted September 21, 2009 in DNA in General

Trying to compile a list of people who’ve had their genome sequenced and announced it publicly:

  1. Craig Venter
  2. James Watson
  3. Stephen Quake
  4. George Church
  5. Marjolein Kriek
  6. Hermann Hauser
  7. Han Chinese
  8. Seong-Jin Kim
  9. Korean AK1
  10. Yoruban African NA18507
  11. 14 others sequenced by Complete Genomics
  12. Unknown number sequenced by Knome
  13. 6 genomes sequenced at high depth by the 1000 Genomes Project
  14. 180 genomes sequenced at low coverage by the 1000 Genomes Project
  15. Two acute myeloid leukemia patients

Know any I’ve missed?

Please see the comments for more links.

Sources: Technology Review, Nature 2009 Aug 20; 460(7258):1011-5

Last edited 22 September 2009



Consumer Genetics Show 2009 in Boston

by Dr. Hsien-Hsien Lei
Posted November 19, 2008 in Business of DNA, DNA Testing

dna string Here’s where most of my fellow DNA Network members would surely like to be next summer – the First Annual Consumer Genetics Show at the Hynes Convention Center from June 9-11, 2009.

Speakers include:

Show objectives include:

  • Regulatory issues
  • Intellectual property considerations
  • Interaction between biotechnology, molecular diagnostic, and pharmaceutical markets
  • Role of physicians in helping patients interpret results from direct-to-consumer (DTC) genetic tests
  • Effect of DTC market on molecular diagnostic laboratories
  • Patient and consumer security (Blaine at The Genetic Genealogist recently wrote about security at Navigenics and 23andMe)
  • Public relations and business strategies to optimize public perceptions of DTC genetic testing (given persistent negative opinions issued by various experts and professional societies)

Are you planning to attend?

Photo credit: Pieter Musterd



How To Make Money Selling Personal Genomic Services

by Dr. Hsien-Hsien Lei
Posted May 8, 2008 in Business of DNA

Given my limited knowledge of how to run a business (my sister’s the Harvard MBA of the family), I’d always thought having a bigger market is the key to success (as I alluded to in my previous post, Using Dispoable Income for Genetic Tests). macbook airThere is, of course, another way of increasing company profits as Steve Jobs demonstrated with Apple:

Apple’s stock has shot up more than 70% over the past year, thanks to Jobs’ strategy of focusing on his most profitable customers and coming up with new things to sell them—the ultra-thin MacBook Air most recently—rather than just chasing more market share. [emphasis added]

~The 2008 Time 100

So what does this mean for personal genomics companies? Perhaps Knome with its $350,000 genome sequencing service isn’t too far off the mark.

NB: If you’ve got an extra $2500 that you don’t know what to do with, check out my list of DNA services you can buy with $2500.



What $2500 Can Buy in DNA Services

by Dr. Hsien-Hsien Lei
Posted April 9, 2008 in DNA Products, DNA Testing

raining money 5Genetic testing continues to get cheaper but not to the extent where everyone can afford every DNA service they have their heart set on. But that’s life, isn’t it?

My mom used to equate everything with the cost of pizzas as in “this pair of shoes could get you three large pizzas!” In that vein, let’s see how much $2500 can get you in the personal genomics marketplace.

$2500 can buy you:

  • One Navigenics Health Compass membership – initiation and one year subscription
  • Ten years of Navigenics annual subscription fees at $250 each year after initial purchase
  • Two 23andMe accounts at $999 USD each with $502 to spare
  • Two deCODEme accounts at $985 USD each with $530 to spare
  • Twelve General Interest Panels of genetic tests from DNA Traits at $199 each with $112 to spare
  • Seven alpha-1 antitrypsin deficiency genetic tests at DNA Direct at $330 each with $190 to spare
  • 0.71% of a $350,000 whole genome sequence from Knome
  • Two Gene Essence genetic tests from BioMarker Pharmaceuticals at $1195 each with $110 to spare
  • Two 1-working day express service DNA paternity tests from DNA Diagnostics Center at $995 each with $510 to spare
  • Sixteen HairDX genetic tests at $149 each with $116 to spare
  • Eight Suracell “DNA Based Age Management” DNA tests (via Bitar Cosmetic Surgery Institute) at $300 each with $100 to spare
  • Twelve Advanced Paternal Lineage Test (Y-chromosome 46) from DNA.Ancestry.com at $199 each with $112 to spare
  • Four DNA11 DNA art portraits at $525 each with $400 to spare.

Of course, looking at price alone isn’t a fair comparison since each company above provides vastly different services and genetic information to their customers from genetic genealogy to art to single disease testing to whole genome sequencing. Cost is a factor, however, in most consumers’ purchasing decisions so it’s interesting to see how prices stack up.

What would you do with $2500?



Affymetrix and Illumina Moving Gene Chip Manufacturing to Singapore

by Dr. Hsien-Hsien Lei
Posted March 19, 2008 in Business of DNA, DNA Around the World

beltsHere’s one more sign that companies involved with personal genomics may be tightening their belts. Gene chip makers Affymetrix and Illumina are both outsourcing manufacturing from the U.S. to Singapore.

Affymetrix president Kevin King:

Affymetrix is consolidating its manufacturing operations to further increase operational efficiencies, enabling us to remain more competitive in the marketplace. Our recent manufacturing advances have enabled us to produce more (GeneChip) array volumes with a smaller manufacturing footprint.

One of the Affymetrix products to be manufactured in Singapore is the new Genome-Wide Human SNP Array 6.0, which can analyze more than 1.8 million DNA markers.

Affymetrix has already begun laying off workers in their West Sacramento, California manufacturing plant and will be making the move to Singapore by the end of 2008 where they opened a 150,000-square-foot manufacturing plant in 2006. Possible reasons for outsourcing genetic test manufacturing to Singapore include:

  • Cheaper labor costs – production workers in Singapore averaged $8.55/hour in 2006 compared to $23.82 per hour in the U.S.
  • Lower tax rates
  • Faster-growing demand for arrays in China and India make manufacturing in Singapore more cost effective

China’s genomic biotechnology is definitely on the rise. At the beginning of this year, the Beijing Genomics Institute (BGI) announced the complete sequencing of the fourth human genome in the world. BGI also formed a partnership with whole genome sequencing company, Knome. In terms of the local personal genomics markets in China and India, there may be great potential but not for the vast majority of people. For the time being, only the rich and famous in developing countries will have access and the chance to be “exploited” like the rest of the elite, according to Jesse Reynolds at The Cutting Edge News.

In the end, it’s all about the bottom line. Affymetrix chief financial officer John Batty:

I think from an economics standpoint, we have an incentive to get it to at least 50 percent [of Singapore plant capacity] because we can shield half of our revenue from the U.S. tax rate by manufacturing arrays in Singapore and shipping those to non-U.S. customers.

I have no doubts about Singapore producing high quality products for use in genetics/genomics. On the other hand, when outsourcing extends to China and other countries with a less educated workforce, it would be worth remembering that standards of quality control vary between countries. For proof, check out what writer James Fallows observed with airplane refueling techniques in Japan vs. China.

plane refueling japanplane refueling china

Hey, whatever gets the job done, right?

(>> Start a discussion!)


deCODE CEO Predicts Downswing in Personal Genomics Market

by Dr. Hsien-Hsien Lei
Posted March 5, 2008 in Business of DNA, DNA Testing

pink slip cakeWith the many genomics and genetics companies launching left, right, and center in recent months, you’d think the market is pretty robust. Not so, says deCODE CEO Kari Stefansson whose company is laying off 60 employees out of a total of 390 or about 15% of its workforce.

It is natural for us to operate the company in such a way that we can make the money that we have last longer than what we had expected to begin with. These are very simple and clear operational standpoints and it would even be wise for other companies in our community to follow our example. [emphasis added]

If what Stefansson says is true, then others like 23andMe, Navigenics, and DNATraits might be looking to tighten operations as well. Although it appears that most personal genomics companies operate with small staffs of less then 50-100, downturns in the market could mean that work is outsourced to independent contractors rather than being performed by full-time employees. (So if you’re looking for a job in the genomics industry, you know how to approach it.) However, not all companies suffer from as much pessimism as deCODE. bizjournals reported last week that Family Tree DNA led by Bennett Greenspan and Max Blankfeld saw a profit gross revenue of around $12.2 million in 2006.

deCODE is behind several genetics products available direct to consumers including:

  • deCODEme – A whole genome scan using Affymetrix DNA chips to analyzing over one million single nucleotide polymorphisms (SNPs) per customer.
  • deCODE T2 – A genetic test for type 2 diabetes that detects a variation in the TCF7L2 gene.
  • deCODE MI – A genetic test for myocardial infarction (aka heart attack, coronary artery thrombosis, or coronary artery occlusion).
  • deCODE Glaucoma – A genetic test for exfoliation glaucoma that detects SNPs located in the LOXL1 gene on chromosome 15. (For more, see this Eye on DNA post.)
  • deCODE ProCa (previously named deCODE PrCa) – A genetic test for prostate cancer.

Given their wide range of products, it’s surprising that deCODE is suffering from cash flow problems in which earnings, balance sheet, and profits from markets are not enough for them to continue growing. Perhaps this is an indication that the market is starting to experience saturation in the number of companies and services being offered yet has not seen a concomitant rise in the number of consumers willing to pay for personal genomic services.

What’s more interesting is that the price of technology continues to drop. BusinessWeek surveyed the DNA sequencing market and found that new technologies are faster and cheaper. Soon we will even have the coveted $1,000 genome. This means that companies should have to spend less to earn more. For example, Illumina’s margins are declining and their revenues are expected to rise 35% in 2008. And production costs will continue drop as labs open up in countries with lower overhead, e.g., China. So shouldn’t it be easier to make a profit now off of personal genomics than ever before?

In any case, while 23andMe and Knome focus on the rich, famous, and elite, there is a great need to show the general public how genetic testing of all types is relevant to their everyday lives. There aren’t enough millionaires like Dan Stoicescu to fund the entire personal genomics market. Until genetic testing is widely adopted for a variety of commercial uses by a greater segment of the consumer population, the pot of profits will not be big enough to share. In 2008, we will surely see companies drop out and others consolidate.

HT: The Genetic Genealogist, GENEALOGY-DNA



Whole Genome Sequencing Costs Continue to Drop

by Dr. Hsien-Hsien Lei
Posted February 11, 2008 in DNA Inventions and Gadgets, DNA Testing, DNA in General

money ben franklinsOne of the cheapest going prices for whole human genome sequencing has been set by Illumina at $100,000 with completion time of less than four weeks. Last year, 454 Life Sciences claimed a complete sequence in two months at around $1 million.

While Illumina and 454 Life Sciences (Roche) are considered by some to be leaders of the pack, Dr. Jonathan Eisen of The Tree of Life says competitors are emerging, including ABI and Helicos. Helicos BioSciences has received its first order for the Helicos Genetic Analysis System that includes HeliScope Single Molecule Sequencer, the HeliScope Analysis Engine, and the HeliScope Sample Loader.

Even as sequencing becomes cheaper and more efficient, Dr. Eisen reminds us of two considerations: data management and analysis as well as linking gene sequence to function. Writing from the Advances in Genome Biology and Technology conference in Marco Island, FL, Dr. Eisen:

Function and process have been replaced by terms like “systems biology” and “SNPs” and “networks” and “massively parallel.” We have in a way regressed in terms of treating organisms (or communities) as a black box. Fine scale detail has been lost in a sea of data.

Regardless, the big race now is towards the $1,000 genome and the Archon X PRIZE for Genomics. The first team to sequence 100 human genomes in 10 days for $10,000 or less per genome will win $10 million.

To aid in the sequencing of genomes, Pacific Biosciences aka PacBio is developing a “transformative DNA sequencing platform.” Their machines can read more bases at one go than others.

  • PacBio – 1,000+ bases
  • Human Genome Project – 800+ bases
  • Illumina – 30-50 bases
  • 454 Life Sciences – 200 to 450 bases

PacBio expects to begin selling machines in 2010 with second-generation machines that can perform $1,000 whole genome sequencing available in 2013. The New York Times has a profile of the company and their technology (Dr. Eisen has more). Other companies mentioned were Intelligent Bio-Systems, NABsys, VisiGen Biotechnologies, and Complete Genomics.

holy grailVentureBeat’s David Hamilton :

Although the “$1,000 genome” is a purely arbitrary goal, it’s become a Holy Grail of sorts for the genomics field. (The startup Knome, which we covered here, currently offers full-genome sequencing for $350,000.) Cheap, fast sequencing of all six billion DNA “letters,” or bases, in humans could make it possible, for instance, for doctors to better tailor treatments to a patient’s own genetic quirks or to identify the specific weaknesses of tumor cells. More broadly, it would also vastly increase our understanding of the genome, which has turned out to be a much more mysterious realm than just about anyone expected only a decade ago, and illuminate the ways DNA varies between individuals, groups and even among cells and tissues within a single individual.

There’s obviously a lot of DNA sequencing going on and it’s not limited to the US. Medical Solutions has become the UK’s first commercial provider of Illumina’s DNA sequencing and genotyping platforms – Genome Analyzer and Infinium on the BeadStation platform, respectively.

For those preparing themselves to have their whole genome sequenced, I recommend following Misha Angrist’s lead – So You Want To Know Your Genome .

NB: Jonathan Eisen, David Hamilton, Misha Angrist, and I are all members of The DNA Network .



Latest Launches at 23andMe

by Dr. Hsien-Hsien Lei
Posted January 22, 2008 in DNA Around the World, DNA Testing

Starting today, 23andMe services are now available in Canada and Europe. (press release) The Guardian attempts to inject a few words of warning to potential customers by quoting Dr. Helen Wallace of GeneWatch:

“Our main concern is that the human genome is set to become a massive marketing scam,” she said, adding that special diet foods and pills had been promoted on the back of tests. “Genetic tests like these are not regulated and the science is still poorly understood – so there is a real danger people could be misled about their health.”

My question is: What isn’t a “scam” nowadays? Do I really need 10 different shades of eyeshadow? Does my five-year-old really need the whole collection of Ben 10 toys (which will never be amassed in our lifetime)? Should we be eating low fat cookies or high protein bread?

You want to know the truth? Everyone’s out to “scam” us. You have to make your own informed decisions about what you’re going to buy into. For some, it could be a genetic test for balding. For others, it could be a $350,000 personal genome sequence. Take some responsibility and initiative and figure out what’s right for you! /rant over

spittle bug spittoon

By the way, 23andMe has also launched their blog, the spittoon. Pop by and say “hi”! And maybe convince them to join The DNA Network (now numbering 41).



China Now Exporting Genomic Biotechnology

by Dr. Hsien-Hsien Lei
Posted January 14, 2008 in Business of DNA, DNA Around the World

beijing 2008Early last week, Beijing Genomics Institute (BGI) announced the complete sequencing of the fourth human genome in the world. Later the same week, whole genome sequencing company, Knome, announced a partnership with BGI where BGI will provide genome sequencing, assembly, and annotation capabilities. Knome will be responsible for analytic tools, security protocols, and genetic interpretation services. According the press release, BGI has over 120 sequencing machines, 10 supercomputers, and 500 terabytes of storage.

Given all the quality control issues surrounding Chinese-made products in Summer 2007, I wouldn’t blame anyone for doubting the quality of genomics in China as well. And although I’d already placed my bets on Singapore being the biotech hub of Asia because of my own positive experience with science in Singapore and scientists from the city state, it appears that I may be mistaken.

Nature Biotechnology reports that China is making great strides in health biotech and with a billion-patient market, who can resist? Shenzhen SiBiono GeneTech Co. developed Gendicine, the world’s first commercialized gene therapy for head and neck cancers. Shanghai United Cell Biotech is making the only tablet cholera vaccing available worldwide. Other Chinese biotech companies are working on vaccines for HIV, Japanese Encephalitis, SARS, and pandemic avian influenza (H5N1). And, of course, BGI has been sequencing genomes.

Development of health-related biotechnology in China is not without its obstacles. Some of the issues raised include:

  • China’s uncertain financial system
  • Rigid restrictions on exports
  • Quality control
  • Intellectual property rights
  • Lack of trust between China-based and international partners
  • Barriers created by language, travel, culture, and project management styles.

For biotechnology companies looking to expand their business in China, Stephen M. Sammut of Burril & Company has this advice:

…the country’s industry might be better served if Chinese residents in the West built transnational companies with a footprint in both China and the West.

While this practice is already common, regulations and taxation policies to encourage this approach would address many of the concerns of private and public capital, assure prospective alliance partners, and add depth to the pool of experienced managers. Such an approach would also promote China as a co-development partner rather than a purely low-cost venue to international companies to contract services.

So it appears that Knome is on the cutting edge of both genomics and international business. Because labor costs in China are much lower than in the US, partnering with BGI will surely improve the bottom line as well. Another smart move for a company that’s charging $350,000 and more for whole genome sequencing.

via Innovations Report

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