Geeky DNA T-Shirt: 99% Chimp

by Dr. Hsien-Hsien Lei
Posted December 20, 2007 in Geeky DNA T-shirts

You’re probably sick of shopping by now but in case you’re still in the mood, this 99% Chimp t-shirt from Teefly would be the perfect gift for that special someone in your DNA-filled life.

How much DNA do you share with the zoo’s favourite attraction?

Tags: genetics, genes, dna, tee, t-shirt, chimp

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Singapore Biotech Sector Loses Stem Cell Researcher Alan Colman

by Dr. Hsien-Hsien Lei
Posted December 18, 2007 in Business of DNA, DNA in General

Singapore, with its well-educated, English-speaking population, has long been thought of as a potential Asian hub of biotech research and business. Up till now, many of the top tier scientists leading the biotech effort in the country have been recruited from overseas, including British scientist Alan Colman who was a member of the team that cloned Dolly the sheep.

Now Alan Colman is leaving Singapore for King’s College London following the departure of molecular and cell biologists David and Birgitte Lane for Scotland’s University of Dundee. Dr. Colman was executive director of the Singapore Stem Cell Consortium. Last year, the World Bank gave Singapore a 50-50 chance of success in the biomedical arena because of an overreliance on “footloose” star researchers rather than local scientists.

According to Reuters, Singapore has invested more than 2 billion US dollars in the biomedical sector. They’ve encouraged start-up companies, new labs, and welcomed controversial projects, such as stem cell research. Although Colman and the Lanes claim they will continue to spend a significant amount of time in Singapore, there are doubts that they will be able to accomplish much for the local sector in such limited amounts of time.

Despite this set of bad news, I’m not convinced the situation is so dire. I personally know of companies in Singapore who are on the cutting edge of genomic technology and research. In addition, a number of my classmates at Stanford and Johns Hopkins were from Singapore (including my husband!) and returned to the country to work for locally-owned, international companies or to conduct research. My family and I will be living in Singapore in the future and I look forward to finding out for myself all the many opportunities available there.

If you’re involved in the Singapore biotech sector, I’d love to learn more about the situation there. Please email me!

via Tomorrow

Tags: singapore, biotech, biotechnology, biomedical, alan colman, genetics, genes, dna

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Opaldia to Offer Diagenic Breast Cancer Genetic Test

by Dr. Hsien-Hsien Lei
Posted December 18, 2007 in DNA Testing, DNA and Disease

UK genetic testing company Opaldia will be offering the Diagenic breast cancer blood test starting in 2008. The test detects gene expression patterns in peripheral (circulating) blood and is touted as being able to diagnose asymptomatic breast cancer before it can be detected by manual breast exam or mammograms. In 2005, Diagenic company researchers published an article in Breast Cancer Research detailing 37 predictive genes for breast cancer (pdf).

Dr. James Mackay, Opaldia Medical Director:

I think it is really important to investigate better ways of detecting early breast cancer in young women.

All health professionals who work with breast cancer are concerned that mammograms may be sub optimal in young women under 47. Therefore a new test used alongside mammography would provide the optimal chance of detecting the cancer as early as possible.

Analyzing gene expression signatures from peripheral blood is based on the following principles (adapted from the Diagenic website):

• The body responds to disease in a way that can be detected by measuring the amount of mRNA transcribed from a specific set of genes associated with disease
• These gene expression patterns can be analyzed using whole genome microarrays
• Gene expression signatures can be used to diagnose disease

Diagenic also offers a similar test for Alzheimer’s Disease.

NB: Opaldia CEO Elaine Warburton blogs about their partnership with Diagenic at Genetics and Health.

via Medgadget

Tags: genetics, genes, dna, breast cancer, opaldia, diagenic

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Eye on DNA Headlines for 17 December 2007

by Dr. Hsien-Hsien Lei
Posted December 17, 2007 in DNA and Disease, DNA and the Law, Eye on DNA Headlines

• Illumina, provider of SNP genotyping BeadChips to companies like 23andMe and deCODEme, is in the spotlight at the San Diego Business Journal. Over the past five years, Illumina has grown 250 percent and now has operations in five countries.
• So far, it’s pretty obvious that 23andMe is winning the PR campaign with celebrities and other noted technorati signing up for their services. Andrew Meyers of Buzzyeah wants to join them and is asking for donations. Frankly, I’m astounded that he’s already raised $300. Andrew promises to blog all if he is able to get his genome scanned.
• The SciAm 50 Awards have been announced. I’m a little embarrassed to say that I don’t know most of the names on the list but I do recognize the X Prize Foundation at #3.
• Topping the genetics headlines today is the discovery of genetic variants at the CRAC1 (HMPS) locus on chromosome 15q13.3 that are associated with an increased risk of colorectal (colon) cancer. The CRAC1 aka HMPS gene was previously associated with colon cancer in the Ashkenazi population. This study has found that it also moderately increases cancer risk in the general population from an average 5% lifetime risk in the UK to 7% for people with both “bad” copies of the genetic variant. (via The Guardian)
• Dayton Daily News has created a Frequently Asked Questions (FAQ) about DNA in forensic investigations. I found this Q&A particularly interesting:

  Q How do forensic scientists determine if there is DNA evidence and how do they examine it in the lab?

  A Generally, we’re looking for a body fluid, mainly blood, semen and saliva. There are tests to identify these body fluids. We can also take samples on evidence that might contain skin cells. Usually, we are looking for evidence discarded at the scene which might contain DNA from the perpetrator. Next we take these samples through the DNA process to see if we obtain a DNA profile.

Tags: genetics, genes, dna, forensics, colon cancer

(2 comments)

Just In Time for Christmas – More DNA Art

by Dr. Hsien-Hsien Lei
Posted December 17, 2007 in DNA Products

One of the most unique gifts you can give this Christmas is DNA art. One new option in this growing market is Cell Portraits founded by molecular biologist Dr. Phil Fisette. His multicolor DNA prints are created from a 1000X magnification of chromosomes contained in white cells. Customers give two to three drops of their blood which is then incubated in cell-growth medium for about five days.

Dr. Fisette stains the white blood cells and uses a microscope to look for a display of chromosomes suitable for immortalizing on canvas or paper. Customers can choose the colors they prefer and a sample proof is emailed for approval before final printing. Prices range from $250 to $500.

If I were running a consumer genomics company, I would offer Cell Portraits or other complementary services to my customers. DNA holds so much meaning and promise that any early adopter of personal genomics would appreciate having a gorgeous and tangible representation of their genetic past, present, and future.

via Wisconsin State Journal

Tags: genetics, genes, dna, cell portraits, philip fisette, dna art, art

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What’s in your DNA? #22

by Dr. Hsien-Hsien Lei
Posted December 16, 2007 in In Your DNA

Keith Robison at Omics! Omics! beat me to the punch this week when he probed corporate DNA.

The question posed is this: what do companies asking this really mean, or more specifically what might it mean that they don’t intend (very Dilbert-esque). Presumably they are trying to make a statement about deeply embedded values, but what does it really mean to have something in your DNA?

Speaking of corporate DNA, VortexDNA provides “core infrastructure technology” that protects your privacy during Web searches and helps to create a more personalized Web experience (whatever that means). Interestingly, their blogger, Kaila, even uses 23andMe vs. Epigenetics as examples.

This science has profound implications for the offerings of 23andMe and similar companies, and it takes the question of human empowerment and freedom to another level altogether. The people doing gene-sequencing say that you are empowered to run around trying to prevent diseases you may never have gotten. VortexDNA and epigenetics say you are empowered to live exactly the life you want, with no limitations.

Layla at Beneath Skin Deep has got a bunch of stuff in her DNA:

It’s in my DNA that I worry. It’s in my DNA that I have thunder thighs. It’s in my DNA that I love to whine.

Truth be told there ain’t no truth in the first 3 sentences of this blog entry. Don’t give me that look but it’s probably in my DNA to be so melodramatic as well and random and all the weird things that I do.

*bolded emphasis added

Tags: genetics, genes, dna, in my dna

(1 comment)

DNA Video: Archon X PRIZE for Genomics

by Dr. Hsien-Hsien Lei
Posted December 15, 2007 in DNA Podcasts and Videos

To stimulate breakthrough innovation in the field of genomic sequencing, the X PRIZE Foundation has launched a global competition with a $10 million prize to the first privately funded team that can sequence 100 human genomes in 10 days. For more information about the X PRIZE Foundation and our other prizes, please visit www.xprize.org.

via ScienceRoll

Tags: Archon X Prize, genetics, genes, dna, science, genomics

(2 comments)

Crazy Genetic Marketing Ideas

by Dr. Hsien-Hsien Lei
Posted December 14, 2007 in DNA Fun, DNA Products, DNA Testing

Less than three weeks until the start of 2008 and everyone’s making their final marketing push. Genetic services companies are not exempt.

Boston-based dating service, ScientificMatch.com , uses a “patent-pending technology” that analyzes DNA having to do with the immune system to find a match who:

• Smells good to you (but probably not to me)
• Has complementary genetic material to yours so you can produce healthier children (unless you feed them McDonald’s every day and smoke around them)
• Is so good in bed that you’ll wonder if a good sex life is in your DNA

Not to be topped by DNA-induced, euphoric love, the much maligned Genebase DNA Ancestry Project claims that Rudolph the Red Nose Reindeer has joined their online networking community where you can email, post photos and messages, and join his network. You can even send an electronic postcard that shows that human HVR-1 mtDNA is 65% similar to Reindeer mtDNA. I guess Genebase thinks going goofy will somehow boost their credibility.

deCODE Genetics thought stirring the pot would keep the spotlight on them too. This past week, they put out the word that Dr. James Watson has 16 times the number of African-origin gene than the average white European (see this post for background about Dr. James Watson’s comments about race and intelligence). John Hawks said it best :

I mean, what is the purpose really of spreading a news story that Watson may be 1/16 African, without adding the context of how common this degree of genetic mixture has been in American history in particular, and between populations generally? Why would a geneticist working with humans not realize the ethical problem?

Personally, I’m pretty worn out after the excitement of the past few weeks and months. Great advances have been made in the field of personal genomics but we’re still taking things step-by-step. What may seem to have happened overnight is actually the culmination of years of hard work. And as 2007 draws to a close, we have more years of hard work ahead of us.

Tags: genetics, genes, dna, personal genomics, genomics, genebase, dna ancestry project, decode genetics, scientific match, dating

(7 comments)

DNA Quote: May Contain Nuts by John O’Farrell

by Dr. Hsien-Hsien Lei
Posted December 14, 2007 in DNA Quotes and Excerpts

It was the first really hot weekend of the summer, when millions of Londoners are spontaneously drawn by some genetic migration instinct that sees us all jump into the Land Rover and seek out the lush greenery of the natural world that lies beside the garden centre car park.

~May Contain Nuts by John O’Farrell

I can attest to this observation. At the first tiny jump in the thermometer each Spring, Londoners put on their spaghetti strap dresses, tube tops, shorts, flip flops, or even worse, go TOPLESS and swarm the city sidewalks. Letting it all hangout on parade at 20 degrees C.

Tags: genetics, genes, dna, quotes, excerpts, books, john o’farrell, london, summer

(2 comments)

Author Jon Entine on Genetic Genealogy

by Dr. Hsien-Hsien Lei
Posted December 12, 2007 in DNA and Genealogy

Recently, there have been a slew of articles decrying genealogy DNA tests as scams. Blaine at The Genetic Genealogist has covered the controversy in depth. And today, I’ve invited author Jon Entine back to Eye on DNA to share his thoughts on genetic genealogy. As you can see, it is possible to recognize the power of genetic genealogy as well as its limitations without writing the whole thing off.

What can DNA genealogy tests really tell us?
23notME

by Jon Entine

I was bemused by the headlined stories over the past month touting new genetic genealogy services, including the start-up, 23andME, launched by the wife of the founder of Google, and AfricanDNA, the brainchild of Harvard scholar Henry Louis Gates, Jr. in cooperation with FamilyTreeDNA. According to 23andME, its service will “shed new light on your distant ancestors, your close family and most of all, yourself.”

But what do these services really offer? I have more than a passing interest in this question because my recently published book, Abraham’s Children: Race, Identity and the DNA of the Chosen People, is the first of a new genre: using DNA to help us connect with our common ancestors—our ethnic identities. DNA can do that. The more responsible genetic genealogy testing firms, like FTDNA, are very clear about what current technology can do. What DNA testing services can’t do, however, at least not yet, is provide the average identity seeker with anything but a vague snapshot of our personal genetic profile and ancestry.

Remember a few years ago when Adrian Targett, an English schoolteacher, was linked by DNA to a 9,000-year-old skeleton found in a cave near where he lived in Cheddar, a tourist town famed for the distinctive cheese made there. “Cheddar Man Found Alive in South of England,” touted one headline. Well, not really. The genetic test—identical to some of the tests sold to the public today by commercial firms–indicated only that the two were linked to the same female ancestor. In kinship terms, they were cousins approximately 450 times removed. But they share only a few bases out of more than 3 billion nucleotide pairs in the human genome. Applying exponential math, Targett has inherited the DNA from many trillions of other relatives as well (though because of intermarriage among cousins and community members, the actual number of his ancestors is far less). His relationship to Cheddar Man is certainly fascinating and important for researchers, but it’s genealogically tenuous, to say the least.

Going back ten generations we each have about 1,000 ancestors, which means we share about one millionth of a random neighbor’s DNA by direct descent. Twenty-five generations ago, about the time when Columbus happened on the shores of the Americas, the number of our potential ancestral cousins swells to an astronomical 30 million, almost all of the world’s population at that time. Yet, we have only one continuous male and female lineage. The male and female lines have become popular markers of identity because of the historical importance of surnames and the fact that these two DNA lineages are so easy to track. Yet, they are only two of millions of ancestral lines that we each carry. Many millions and perhaps billions of people living today are genetically linked to Cheddar Man, although that extremely distant connection might not show up in the few sections of the DNA that current technology can track.

This vast majority of the human genome, which amounts to more than 99 percent of our DNA, remains beyond the reach of current commercial DNA tests. Services such 23andME do provide glimpses of this genetic bounty but the information is virtually meaningless. Yes, its reports may indicate that we have a gene that is linked to weight gain, ear wax build up, or IQ, but even these seemingly simple traits are rarely the result of individual genes. There are more than 10 million tiny differences, known as single nucleotide polymorphisms, or SNPs scattered across the 23 pairs of human chromosomes and potentially interrelated in a myriad of ways. They are activated—“expressed” is the term used by geneticists—by gene-gene and gene-environmental interactions.

Make no mistake about it. Genetic genealogy is fascinating and it provides scientists with greater insight into our distant ancestors. We are also learning more and more about diseases, which is particularly of interest to Jews, who are subject to more than 40 disorders as a consequence of their separatist history. In fact, Bennett Greenspan’s FTDNA is launching an Ashkenazi Genetic disease panel this week that will test for 25 common Ashkenazi diseases for only $500, an example of the responsible use of genetic genealogy.

But for the vast majority of us, DNA genealogy is little more than expensive entertainment, and potentially misleading. Those in search of certifying their identity or evaulating behavioral quirks using DNA tests may find disappointment as much as illumination. For example, in my book, I mention the case of Lisa Black, a systems administrator in Oakland who is African American. She was shocked to find that the DNA lineage that current technology can track, her female ancestors, was a blend of Native Americans, Chinese, and Sardinians. It came as a major blow to a veteran of the Black Power movement of the 1960s. “For me to have a whole half of my identity to come back and say, ‘Sorry, no African here.’ It just negates it all. … What does this mean? Who am I then?”

Tags: genetics, genes, dna, genetic genealogy, genealogy, dna testing, genetic testing, 23andme, family tree dna, ftdna, african dna

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