Eye on DNA Headlines for 22 April 2008

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

• Rick at My Biotech Life hosts Gene Genie : the better late than never personal genomics special edition.
• Please welcome Pamela Ronald at Tomorrow’s Table to The DNA Network. She’s our 53rd member!
• Congratulations to Trisha on the relaunch of the Ideas for Women blog.
• Molecular biologists are in the movies. Peggy at Biology in Science Fiction looks at Splice starring Adrien Brody and Sarah Polley scheduled for release in 2009.
• Auckland University professor Andrew Shelling says personal genomics companies are offering “health horoscopes.” On the other hand, he admits that access to genetic testing in New Zealand is very limited.

  “New Zealand is doing an appalling job of providing adequate genetic testing. We’re well behind Australia and the rest of the world.”
  
  So what’s an info-seeking person to do?

• Here’s a genetic genealogy quagmire. DNA testing of children from the polygamist religious group in West Texas to sort our* out family relationships has commenced. Problem is, many of the children are closely related and have parents who are genetically related as well.

  Because of the group’s isolation, Dr. Einum said he thought it was likely that the parents of any given child were related by a common ancestor, and that any man examined as a possible father could share genetic traits with many other men in the group.

*No, I’m not affiliated with the FLDS.

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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

Here’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.

Hey, whatever gets the job done, right?

(>> Start a discussion!)

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

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).

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China Now Exporting Genomic Biotechnology

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

Early 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

Tags: knome, genomics, genome, sequencing, genetics, genes, dna, china, bgi, beijing genomics institute

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How the UK uses DNA from the National Database

by Dr. Hsien-Hsien Lei
Posted January 13, 2008 in DNA Around the World, DNA Fun

Seen on Queensway, London

Crime Prevention Advice

Your Safer
Neighbourhood Team

Protecting your street
with
DNA property marking

So that’s what they do with DNA in the UK National DNA Database They use it to mark property!

Tags: uk national dna database, dna, genetics, genes, crime, uk, great britain, london

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Beijing Genomics Institute Sequences Fourth Human Genome in the World

by Dr. Hsien-Hsien Lei
Posted January 7, 2008 in DNA Around the World

Chinese scientists at the Beijing Genomics Institute (BGI) have completed the fourth human genome to be sequenced worldwide. The first two were James Watson and J. Craig Venter, the third was a researcher of Han Chinese descent in October 2007, and this fourth genome was a Chinese volunteer.

The Chinese-British collaborative BGI genome project, called The Yanhuang Project, aims to map the 100 Chinese genomes. It’s not clear whether all of them will be expected to be as generous as the Chinese volunteer who donated approximately 1.3 million US dollars to the project. (Note: Harvard’s Personal Genome Project will not be expecting their volunteers to donate anything except their DNA, tissue samples, and medical data.)

The Yanhuang Project has three phases:

1. To sequence a Chinese individual’s genome that serves as the reference.
2. To sequence at least 99 more individuals’ genomes to construct a Chinese genetic polymorphism map.
3. To study the results of the first two phases and apply the findings to medical science.

Researchers plan to use the Chinese genome database to “solve problems related to Chinese-specific genetic diseases*” as well as improve diagnosis, prediction, and therapy.

*What Chinese-specific genetic diseases might they be referring to? Unlike the Ashkenazi Jewish community, I was unaware of any hereditary diseases that disproportionately affected the Chinese population. Maybe I just don’t know because most of the studies conducted in China stay in China and aren’t even indexed in PubMed.

Tags: genetics, genes, dna, chinese, genome, genomics, diseases, illness, health

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“Jacket Children” and DNA Testing in Jamaica

by Dr. Hsien-Hsien Lei
Posted October 23, 2007 in DNA Around the World, DNA Testing

A reader of the Jamaica Cleaner is proposing that everyone looking to be married in Jamaica undergo DNA testing first.

The Editor, Sir:

Based on the ‘jacket’ situation in Jamaica, DNA testing may become a way of life. If we do not know who our fathers are we may end up marrying our cousins, brothers, sisters, aunts, uncles, nieces, nephews and even our fathers.

Under these circumstances I would not recommend anyone get married without both partners doing DNA tests to see if they are blood-related. This is one situation where the women can’t blame the men for. Ladies if you have only one sex partner every nine months then you won’t have to worry about who the daddy is.

I am, etc.,

DAN VASSE

According to Out-of-Wedlock Births by Mark Abrahamson,

When people suspect that a Jamaican child’s social and biological fathers are not the same, but the child is publicly presented as the offspring of the social father, the child is called a “jacket” [emphasis added] in local gossip. The imagery implied is that a jacket child is something a husband “wears” to protect his honor.

Photo: “A second grade boy at the Christiana Primary School [in Jamaica] waves and flashes a brilliant smile while our team builds a new shelter nearby.” ~ Jake Brewer

Tags: jacket child, jamaica, out of wedlock births, babies, genetics, genes, dna, dna testing, paternity

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Don’t Sell Our DNA Say Cook Islanders

by Dr. Hsien-Hsien Lei
Posted September 30, 2007 in DNA Around the World

The Karitiana Indians of the Amazon aren’t the only ones offended by the sale of their DNA. The Cook Islands has declared that it will no longer be “the guinea pig of the South Pacific.”

Foreign researchers wishing to conduct research on Cook Islanders, including the collection of their DNA, will have to abide by rules set by the Health Research Council of New Zealand and the office of the Cook Islands Secretary of Health Roro Daniel.

Sitaleki Finau from Massey University:

Some of us are fearing what happens to the specimen at the end of the analysis. Are they being used, are they being stored, are they being sold?

Pacific Islanders value body parts, body bits, body extracts, much more than say the average pakeha does.

The Cook Islands also want existing DNA samples being stored in the UK to be destroyed as well.

To learn more about research in the Cook Islands, see this presentation by Dr. Ngamau Wichman-Tou which is the last listed on this page for a workshop held during the 57th session of the WHO Regional Committee for the Western Pacific, 2006. And don’t miss the comments in response to my June post - Amerindian DNA Sells for 55 Dollars.

Tags: cook islands, genetics, genes, dna, science

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DNA Testing Too Expensive in Uganda

by Dr. Hsien-Hsien Lei
Posted August 8, 2007 in DNA Around the World, DNA Testing

Uganda may have gotten its first “DNA machine” but Josephine Nakato Matovu reminds us that costs are prohibitive for many people, including victims of sexual assault.

I know that the DNA machine could be utilised in solving crimes with the collection of DNA evidence to compare against suspects and/or offenders in sexual assault cases.

However, I am sure that few women and children are in a position to pay the large amounts of money for DNA testing that is required to prove their cases in court.

According to the UK Department for International Development , per capita income in Uganda is around $300 per year. With the average cost of paternity testing in Uganda set at $240*, it’s obvious that no average citizen could afford this. The question is, can the police?

DNA testing is not just too expensive for citizens of Uganda. The South Africa DNA Project was founded to address this issue and to support forensics DNA testing. Maybe charitable organizations, like the Bill & Melinda Gates Foundation, should consider tackling the availability of DNA tests not just for forensics, but for medical genetic testing as well. It’s certainly a more soluble problem than many other public health concerns.

*”At-home” paternity tests in the US where you collect your own DNA and send it in to the lab can be as little as $99.

Tags: uganda, south africa, dna testing, genetics, genes, dna, public health, forensics

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Eye on DNA Links for 26 July 2007

by Dr. Hsien-Hsien Lei
Posted July 26, 2007 in DNA Around the World, Eye on DNA Headlines

• Kromosoft names Eye on DNA their favorite genetics blog in this week’s issue of KromoNews! I’ve been a subscriber to this free weekly human genetics newsletter for a few months and particularly like their genetics “term of the week.” Kromosoft is a research services company with the motto: “Promoting Genetics Awareness for a Healthier Society.”
• Brandon Keim of Wired Science has been churning out genetics post after genetics post from Jackson Labs in Bar Harbor, Maine for Press Week during the second week of the 48th Annual Short Course on Medical and Experimental Mammalian Genetics. Can’t believe it’s been 10 years since I attended the Short Course myself. Two weeks of intensive genetics in a beautiful setting. It was heaven!
• Thank you to CourtTV’s Informer and Traces: Following the mtDNA Trail for adding Eye on DNA to their blogrolls.
• Whenever I make a trip to central London, I’m reminded of how bad the air quality is there. (Moscow air pollution is no better according to a friend who recently moved there.) UCLA researchers have found that microscopic particles in diesel exhaust interact with cholesterol to activate more than 1,500 genes involved in atherosclerosis, a risk factor for heart disease.
• Congratulations to Uganda! The Government Analytical Laboratories in Wandegeya has the first PCR machine in the country. One of the main uses for the machine is expected to be paternity testing for $240, which is less than the $400 charged in Kenya and $600 in South Africa.

Tags: genetics, genes, dna, uganda, kenya, south africa, kromosoft

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