2008 February

DNA Excerpt: Carly Fiorina

by Dr. Hsien-Hsien Lei
Posted February 29, 2008 in DNA Quotes and Excerpts

tough choices carly fiorinaFrom Tough Choices: A Memoir by Carly Fiorina:

The goal was not for Hewlett-Packard to take over Compaq, as Compaq had done with DEC and Tandem. The goal was to use the best of both companies to build something stronger and better. We would use the best of both product lines, both management teams, and both cultures. We needed the DNA of both companies to form a new company that could compete and win in the twenty-first century. We needed two strands of DNA to adapt to the changing industry landscape.

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Eye on DNA Headlines for 28 February 2008

by Dr. Hsien-Hsien Lei
Posted February 28, 2008 in Eye on DNA Headlines

  • Thanks to Berci at ScienceRoll for hosting Grand Rounds 4.22: The Future of Medicine.
  • Congratulations to Dr. Jonathan Eisen at The Tree of Life! He’s the new Academic Editor in Chief of PLoS Biology.
  • Congratulations also to my employer, DNA Direct . The company has closed $7 million in Series B financing. More from DNA Direct’s official blog. (Press release below the fold.)
  • The Johns Hopkins Genetics and Public Policy Center (GPPC) is holding a series of public town hall meetings to gather opinions on biobanks for the effects of studying genetic and environmental factors on health. Register to attend at http://www.dnapolicy.org.

    *March 8 – Kansas City, MO
    *April 5 – Phoenix, AZ
    *April 19 – Jackson, MS
    *April 24 – Portland, OR
    *May 13 – Philadelphia, PA

  • Kevin Kelly at The Quantified Self has some interesting insights into studying our own genomes in Wiki Your Genes.

    If a third-party vendor were to start selling the naked chip’s data for a small fee above its costs, it would be possible to do a large personal sequence using one of these tests and managing your data using open-source wiki technology like SNPedia. Hard-core recreational genomist could probably do a better job than either 23andMe or Decode are doing right now.

    Could you be a hardcore recreational genomist?

dna strands

Continue reading…

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Fetal Gender DNA Tests Answer Common Pregnancy Question…Or Not

by Dr. Hsien-Hsien Lei
Posted February 27, 2008 in DNA Podcasts and Videos, DNA Testing

I am now 26 weeks pregnant with my second baby and the second most popular question people ask me is: “Do you know if it’s a boy or girl?”* And, yes, we do know based on an ultrasound at week 22. Of course, the technician would say nothing more confirmatory except: “It appears to be a girl. I saw the McDonald’s sign. Three lines together looking like a hamburger.” (The following is not my own ultrasound.)

girl ultrasound

Fetal gender prediction is big business. Some parents, like us, just want to know so as to prepare for the new arrival. While others have strong cultural and personal preferences. Unless parents have availed themselves of sperm sorting or preimplantation genetic diagnosis, people previously relied on the following methods to figure out if their baby is a boy or girl (from Pregnancy & Childbirth at About.com):

  • Ultrasound
  • Amniocentesis
  • Chorionic villus sampling (CVS)
  • Old wives tales
  • Chinese lunar calendars
  • Fetal heart rate
  • Belly size and shape

The latest and most controversial way of determining a baby’s sex is by analyzing the mother’s blood for fetal DNA. Two such tests are the Early Baby Gender Mentor and Pink or Blue Early Gender Test. A mother who’s pregnant with a boy is expected to have circulating amounts of Y-chromosome DNA. If no Y-chromosome bits are detected, then the baby is presumed to be a girl. But, of course, it’s not so straightforward.

Last summer, Karen Kaplan of the LA Times began gathering personal stories for a piece on gender DNA tests that was published this past weekend: Accuracy of gender test kits in question. The focus of the article is on sex determination but there’s also mention of quality control issues in the genetic testing market.

Marketing directly to consumers, the new crop of companies has jumped into a realm of dubious science, mining DNA to offer information on ethnic heritage, long-lost relatives, personalized dieting plans — even the sports for which one is best suited.

The tests are loosely based on legitimate scientific research, much of which has been funded by the National Institutes of Health, among others. But often, the companies’ claims of accuracy have not been backed up by independent laboratory analysis.

Thousands of consumers have bought tests — and analysts say the number will only grow as entrepreneurs find more ways to market the mysteries of the human genome.

The Federal Trade Commission, which protects consumers from false and misleading advertising, has warned buyers to be skeptical of at-home genetic tests, which are now unregulated.

In most cases, customers have no way of judging if their test results are accurate. But if a prenatal gender test is wrong, parents will surely find out.

Some consumers of genetic testing services, like Dr. Ann Turner, will test their DNA with more than one company, but most people rely on only one test from a company that may or may not have standards that indicate good business practices. We cannot rely on regulation from government bodies like the FDA even though they have been discussing what to do.

eppendorf tubesHere are my tips for choosing a reputable genetic testing company (also see my tips for how to prepare yourself for a genetic test):

  1. The company should state specifically the genetic markers they are testing and the reasons for selecting those marker for the test.
  2. The company should have a clearly stated standards page that demonstrates their commitment to quality.
  3. The company should say which labs are processing your DNA sample and indicate certifications, such as CLIA.
  4. The company should have clearly stated contact info that includes mailing address, phone number, and emailing address.
  5. The company should respond quickly to any queries you may have.
  6. The company should have a good reputation which you can check online via search engines, such as Google.

While mistaken results from genetic genealogy testing may not affect life or death decisions, the same can’t be said for medical genetic testing or gender determination DNA testing. As William Saletan said in Slate:

Notice how the new transforms the old. What’s old is sex selection: choosing whether to abort your fetus based on whether it’s a boy or a girl. What’s new is the combination of ease, safety, and privacy with which you can now do this deed.

According to a UK Parliament publication (pdf), here are some of the reasons why a family may want to engage in sex selection.

  • There are several hundred known genetic diseases that affect only males – e.g. haemophilia and Duchenne’s muscular dystrophy.
  • Family balancing
  • Rebuild a family after the death of a child with another of the same sex
  • To fulfill a general preference for children of one sex over another because of economic, cultural or social reasons.

Whatever the reason for sex selection/preference, it seems that predictions are often inaccurate and babies are born every day who surprise their parents by being the opposite of what they’re “supposed to be.” I’m lucky enough to be happy with whatever our little one turns out to be. Sadly, that’s not the case for everyone.

Just for fun, here’s a music clip from Headless Hens, a song from Human Future that includes a stanza about genetic engineering babies (HT: Question Technology):

Perfect world, just in time
Perfect babies, by design
Purge the ones that can’t run
Judge the lives won’t be much fun
Labs getting patents, DNA owning
Remaking people, through human cloning

Used to love any kid that breathed
But now we don’t want ‘em unless they’re Ivy League

powered by ODEO

*The most popular is: “When are you due?”



Ann Turner on Personal Genomics Companies 23andMe vs deCODEme

by Dr. Hsien-Hsien Lei
Posted February 25, 2008 in DNA Testing, DNA and Genealogy

Dr. Ann Turner is the most knowledgeable personal genomics customer I know. She has purchased the services of both 23andMe and deCODEme and generously shares her viewpoint. Yesterday on the GENEALOGY-DNA list, she compared 23andMe vs deCODEme with respect to genetic genealogy and gave me permission to reprint her comments here.

Now that 23andMe and deCODEme both have demo records, you can explore the user interface aspects yourself. Both companies are introducing new features lickety split, though, so it’s a moving target.

I don’t think you should make a decision based on mtDNA or Y features, unless you’re only interested in “deep ancestry.” Neither company can provide the resolution of the genealogical HVR/STR tests. However, 23andMe does get down to much more detail in the haplogroup labels. 23andMe is using a smaller number of Y-SNPs (current reports make use of 284, vs 858), but these seem to be more targeted toward the currently defined phylogenetic tree. We don’t know yet how the additional Y-SNPs in the deCODEme set will pan out, and deCODEme is not reporting subclades as deeply as they could right now (i.e. just R1a and R1b). I suspect lots of the extra SNPs will end up being “phylogenetically equivalent” for the deepest splits in the tree, like the long lists of SNPs in that paper by Underhill and Kivisild, but we’ll only know that when we’ve seen actual results for many people in different haplogroups.

Both companies are making use of the HapMap samples for geographic ancestry in the 50-some population cell lines from the Human Genome Diversity Project, and in fact 23andMe partially funded the analysis which is the basis for the current flurry of technical articles. They must be using a slightly different algorithm in their presentations, though — deCODEme says it breaks the chromosomes down into segments for comparison purposes, and that seems to change the rank order slightly. Only deCODEme gives an admixture estimate, and that only for the three broadest categories of European, African, and Asian. You can, however, compare your results to a representative sample from any of the 50 populations at deCODEme on a segment by segment basis.

23andMe has a nice Genome Browser in place, where you can use the web interface to look up individual genes or rs numbers you encounter in the technical literature (or their own Spittoon blog, which has frequent posts about items that crop up in news releases). DeCODEme doesn’t have a genome browser yet, but promises it will be “soon.” In the meantime, you can of course check your own alleles in the big download set and use dbSNP to learn more about the gene.

dna graffiti

As for the medical aspects, I think you should thoroughly explore the sample reports and understand what’s really being offered. They are association studies using “common” SNPs, not diagnostic tests for single mutation / single gene disorders, like the ones DNATraits is now offering (with a special emphasis on mutations more commonly found in people with an Ashkenazi Jewish background).

23andMe’s Gene Profiles strike me as chattier, with historical background and interviews with specialists, but both companies cover the fundamentals. Both companies also do an admirable job of providing citations to the literature, with data about the frequency of the genotype in cases and controls, and how that contributes to relative risk. Many pundits are complaining that people might get freaked out by learning that their risk is doubled (the way newspapers often report new findings), but I have to wonder if they’ve examined the actual reports, which provide more details about the absolute frequency etc. Most people will learn that there are multiple genes “associated” with each condition, with some alleles adding to the calculated risk and others subtracting from it, and a doubling of risk might take you from 2% to 4%.

It’s very important to realize that these are population studies, and the statistical associations don’t necessarily apply to an individual case. If you have a “high” relative risk for colon cancer, the odds may still be low in absolute terms that you will contract it. If you have a low relative risk, that does not absolve you from the need for regular examinations, since not all causes of colon cancer are known yet (and may be idiosyncratic for a particular family line, like the George Frye pedigree we discussed recently). That kind of mutation might never be picked up on a chip using common SNPs.

The SNPs aren’t necessarily causal, either, even the small percentage found in actual coding regions. In fact, most of them are probably SNPs in the vicinity of the mutation responsible for the actual effect, and they’re just along for the ride as that segment of the chromosome is passed down through the generations. They are tagging/mapping SNPs that provide guidance for which genes to study in more detail. That’s the main business of deCODE, and they are folding their discoveries into the deCODEme reports as soon as they are published. Of course, 23andMe has access to those articles, too.

The feature I found most intriguing at deCODEme was the graphic display, comparing any two gene profiles on a segment by segment basis (about a million bases). You can do a similar thing at 23andMe, but in practice, it only highlights connections for first degree relatives, who share broader regions of their chromosomes. But now that both companies give access to raw data, anyone can create a novel approach to visualizing data (sort of like open source software) — if people are willing to share their profiles. You don’t need to share data about individual SNPs for the deCODEme display, like the ones I’ve uploaded (zip file).

One remaining difference between the companies is the number of SNPs, and deCODEme has a head start there. That may prove to be the deciding factor for me, as I have a scheme in the back of my mind for locating the mutation responsible for the hereditary hearing loss that runs in my family. We’ve already participated in several genetic studies, but the mutation has not been found. I could test various relatives (for instance the two sons of my first cousin) to see what segments I share with the just one who has the hearing loss. The sticky points are deriving haplotypes from genotypes and downplaying segments that we share because of our generic European ancestry. I’ll need to do some pretty heavy-duty cost-benefit analysis here!

On the other hand, 23andMe has added some custom SNPs to their suite. There are autosomal SNPs, in addition to the ones for mtDNA and Y, but I haven’t seen a comprehensive list of why they were selected. One example is a test for the CCR5-delta32 mutation (HIV resistance), which some of you have ordered as a stand-alone test.

Neither company is really promoting the genealogical possibilities for the autosomal SNPs. They may be (justifiably) pessimistic about that application, since there’s only a 50% chance of passing on a particular DNA segment to the next generation. Nonetheless, all of our DNA came from somewhere, and we now have unprecedented access to huge amounts of data. We ought to be able to mine a few little nuggets out of it, and I’m lobbying the companies to pay attention to this segment of the market.

In the meantime, I think the tests are most suitable for those willing to explore the next frontier, with all its unknowns and with the possibility of less expensive tests coming online within the next few years. The cost-benefit analysis will be tricky for everyone, not just for my own little niche. But if you decide to proceed, I don’t think you can go wrong with either company. There’s a third company, SeqWright, which is flying under the radar right now, due to their “late” entry into the field.

Ann Turner

NB: You may also find Jay Cross’s experience with 23andMe interesting.

Update: David Hamilton at VentureBeat has written his own comparison of the online interface for both 23andMe and deCODEme.



Genetic Testing and Health Insurance in the New York Times

by Dr. Hsien-Hsien Lei
Posted February 24, 2008 in DNA Testing, DNA and the Law

Genetic information should by rights be our own to share when we think it’s appropriate. The reality, however, is not so straightforward. In today’s New York Times article, Fear of Insurance Trouble Leads Many to Shun or Hide DNA Tests, Amy Harmon writes of people who have a very real fear of having to pay jacked up insurance premiums or being denied insurance altogether. The problem may be especially bad in the US where health insurance is not a citizen’s right.

The culture of secrecy around genetic information is stronger in the United States, some experts say, than in countries where people are guaranteed health care.

life insurance

In the UK (where I currently live), medical genetic testing is available through the National Health Service (NHS). While there does not appear to be any issues regarding insurance coverage should a person test positive for a disease-causing mutation, greater issues are availability and timeliness of testing and results. Also, many UK citizens have private insurance through their employers in addition to their free NHS insurance.

Two years ago, Cancerbackup found in a survey of regional genetics centers that waiting time for appointments to receive a BRCA genetic test can be as long as nine months with a further wait of 1 to 2 years for results. In some ways, this could be construed as discrimination in that other forms of testing are probably taken more seriously and performed more speedily.

From CancerBackup regarding the Concordat and Moratorium between the Department of Health and the Association of British Insurers (lasting until November 1, 2011):

In the agreement, amongst other things, insurers give ten commitments on the information that they will ask of customers. For example, customers will not be asked to:

  • have a predictive genetic test in order to obtain insurance
  • tell them about a family member’s test results
  • tell them about any predictive or diagnostic genetic test results acquired as part of clinical research
  • tell them about any predictive test results that are made available after their policy has started, for as long as that policy is in force.

There are caveats to the Moratorium including one in which insurers can ask about Genetics and Insurance Committee approved predictive tests for policies over £500,000 of life insurance, or £300,000 of critical illness insurance.

Last June, BMJ debated the use of genetic information to determine insurance eligibility. I, along with other readers, sided with those who believe that insurance companies do not have an automatic right to our DNA data while HG Stern at InsureBlog disagreed .

…to the extent that such information is helpful to an underwriter, it’s in the realm of pricing (or whether or not to offer coverage at all). It’s really no different than knowing whether or not the applicant is a smoker, or a diabetic, or recently had knee surgery. All of this goes into the mix, and genetic information may (or may not) play some role.

Of course, the results of genetic testing may be moot if you have a strong family history of a certain disease. If so, a negative genetic test could work in your favor.

For other comments on the NY Times story:

Photo credit: “The life insurance office,” Wellcome Collection under Creative Commons

(1 comment)


DNA Video: Dr. Kari Stefansson of deCODE genetics

by Dr. Hsien-Hsien Lei
Posted February 23, 2008 in DNA Podcasts and Videos

Kari Stefansson M.D., Ph.D, CEO of deCODE genetics talks about deCODEme.

Tags: , , , , , , , ,

(1 comment)


Eye on DNA Headlines for 22 February 2008

by Dr. Hsien-Hsien Lei
Posted February 22, 2008 in DNA Testing, Eye on DNA Headlines

  • dna moleculeThe genetic testing market is getting so crowded I’ll have to start elbowing people aside. Genetic genealogy company Family Tree DNA has launched DNATraits which “specializes in DNA testing to identify genetic disorders and susceptibility to inherited diseases and characteristics.” Blaine at The Genetic Genealogist and Daniel at Genetic Future have more on this new launch. (NB: I work for competitor DNA Direct.)
  • Welcome to the 47th member of The DNA Network – Dr. Simon Lin of Retail Genomics.
  • Three interesting genetics websites to check out: Check Your Genes, Responsible Genetic Testing, and YourGenome.org. Check Your Genes focuses on BRCA1 and BRCA2 genetic testing for people with a significant family history of breast and/or ovarian cancer. (HT: Derek) Responsible Genetic Testing focuses on direct-to-consumer advertising for genetic testing. YourGenome.org is from the Wellcome Trust Sanger Institute and is a genetics 101 website good for basic info. (HT: Thomas)
  • While NBC Nightly News ran their series on DNA, ABC’s Nightline did their own piece on 23andMeCracking the Genetic Code.
  • Webcasts are now available from the Health and Human Services Secretary’s Advisory Committee on Genetics, Health and Society met in Washington on February 12-13, 2008 to discuss genetic testing. Excerpt from Pharmacogenomics Reporter (does anyone have access and can email me their article?):

    The HHS Secretary’s Advisory Committee for Genetics, Health, and Society said that a “mandatory, publicly available, web-based registry … would offer the best approach to address the information gaps” regarding lab-developed genetic tests. But it stressed that “unresolved issues, including practical and legal questions,” must be answered before the government can decide “how and where to implement the registry.”

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DNA Excerpt: Diana Gabaldon’s A Breath of Snow and Ashes

by Dr. Hsien-Hsien Lei
Posted February 22, 2008 in DNA Quotes and Excerpts


…Before he could explain his errand, Mrs. Bug had sat him down with a bowl of his own, a jug of honey, a plate of savory fried bacon, hot toast dripping butter, and a fresh cup of something dark and fragrant that looked like coffee. Jem was next to him, already smeared with honey and buttered to the ears. For a traitorous instant, he wondered whether Brianna was perhaps a bit of a sluggard, though certainly never a slattern.

Then he glanced across the table at Claire [Brianna's mother], uncombed hair standing on end as she blinked sleepily at him over the toast, and generously concluded that it probably wasn’t a conscious choice on Bree’s part, but rather the influence of genetics.

~A Breath of Snow and Ashes by Diana Gabaldon

This book is part of the Outlander series featuring Claire who is a time traveler flitting between the 1940’s and 1770’s. The books are set in Western Europe and Colonial America. I can imagine many amateur genealogists would love to be able to time travel and sneak a peek at their ancestors while gathering some DNA samples. Just be careful not to be mistaken for a witch!

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Storing Your DNA In Outer Space

by Dr. Hsien-Hsien Lei
Posted February 21, 2008 in DNA Fun

bionic man spaceAre you worried about your precious DNA being lost in space and time once you die? If so, BeInSpace will help you send it into space for safekeeping.

BeInSpace will be collecting 1TB of digital data and DNA, putting it on a rocket and launching it out into orbit, to our solar system, far, far way.

From their FAQ:

Who knows where you will be 2 billion years from now?

No one!

Dude. I can tell everybody on this planet today where they will be 2 billion years from now. NOWHERE! We’re all going to be dead, dead, dead, and DEAD.

BeInSpace reminds me of the Alliance to Rescue Civilzation (ARC). They want to create a back-up on the moon of all recordable aspects of human civilization, including DNA samples.

ARC’s mission:

The mission of the Alliance to Rescue Civilization (ARC) is to protect the human species and its civilization from destruction that could result from a global catastrophic event, including nuclear war, acts of terrorism, plague and asteroid collisions. To fulfill its mission, ARC is dedicated to creating continuously staffed facilities on the Moon and other locations away from Earth. These facilities will preserve backups of scientific and cultural achievements, and of the species important to our civilization. In the event of a global catastrophe, the ARC facilities will be prepared to reintroduce lost technology, art, history, crops, livestock and, if necessary, even human beings to the Earth.

Unlike BeInSpace, however, ARC is not publicly soliciting submissions. Whatever and whoever they decide to include will hopefully NOT be a representative sample of what we have on earth today but an improved version. On the other hand, what would I do for entertainment without Britney Spears to ogle?

Photo credit: Wellcome Images under Creative Commons.



Geeky DNA T-shirt: AAAS Gene Sequence Tee

by Dr. Hsien-Hsien Lei
Posted February 21, 2008 in Geeky DNA T-shirts

aaas gene tee

Now here’s a DNA t-shirt that almost looks like something you’d find at Missoni (one of my favorite designers). The American Association for the Advancement of Science is selling this tee featuring the annotated gene sequencing map of human chromosome 1 in celebration of Science’s Breakthrough of the Year for 2007. The shirt is available for $22.50.

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