Prenatal Primer: Interactive Guide to Prenatal DNA Testing Options

by Dr. Hsien-Hsien Lei
Posted January 30, 2008 in DNA Testing

Prenatal genetic testing has become so routine that almost all the women I know have gone through it even if they were pregnant before age 35. All of us, including me, experienced some degree of confusion and spent a significant amount of time researching various tests and potential outcomes. To help pregnant women and their families understand their options, DNA Direct* and Lenetix Medical Screening Laboratories have created the Prenatal Primer, which includes:

• An online questionnaire
• Information on prenatal risk assessment tests and diagnostics
• Flow-charts and visual representations of testing options

“It’s very important for patients to fully understand and weigh the screening and diagnostic options,” said Dr. Thomas Musci of San Francisco Perinatal Group. “A web-enabled tool that provides comprehensive education about prenatal screening options will help ensure that patients truly obtain informed consent.” Musci is working with DNA Direct to develop the beta version of the tool to be piloted at his practice. (Press Release )

On a related note, Sequenom is enrolling patients in a study to clinically assess their noninvasive cell free fetal nucleic acid SEQureDx Technology for detecting fetal aneuploidy, including Down syndrome. SEQureDx requires only a blood sample from the mother without the need for invasive amniocentesis or chorionic villus sampling.

And, the AP also has a story about increased prenatal testing leading to higher termination rates - Down syndrome groups anxious about increased prenatal testing.

*I work for DNA Direct.

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Eye on DNA Headlines for 29 January 2008

by Dr. Hsien-Hsien Lei
Posted January 29, 2008 in Eye on DNA Headlines

• Check out my Editor’s Note in the January 25 issue of KromoNews, a weekly human genetics newsletter!
• Looking for info on genetic genealogy? Kevin Duerinck’s Genetic Genealogy Pages is one place to go. He has information on Why DNA Testing for Genealogy and How to Manage It, DNA Storage Methods (DNA Direct’s DNA Archive is included), and Genetics and Privacy.
• I don’t know anything about coding but Bert Hubert obviously does. The computer programmer has written up some “ramblings” on DNA that may make sense to some of you g33ks:

  …as almost all cells carry around a full copy (’distribution’) of the genome, a system is needed to #ifdef out stuff not needed. And that is just how it works. The genetic code is full of #if/#endif statements.

• Congratulations to DNA Direct*, the first national provider to offer genetic testing services on Carol. Carol is the first healthcare marketplace that makes it possible for consumers to shop, compare, and purchase care services online. More from Crossover Healthcare.
• Here’s some fashion advice for those wishing to look as if you belong to the “it” crowd in personal genomics - navy blue trousers, matching jacket, and/or blue shirt as modeled by (L to R) Francis Collins, George Church, Linda Avey, and Craig Venter at the World Economic Forum 2008 (photo credit: Esther Dyson).

*I work for DNA Direct as a genetic information specialist.

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American Journal of Medical Genetics Special Issue on Children and Genetics

by Dr. Hsien-Hsien Lei
Posted January 28, 2008 in DNA Testing

The February 15, 2008 issue of the American Journal of Medical Genetics is devoted to ethics and policy regarding children and genetics. Some of the articles touch on topics I’ve covered here at Eye on DNA, including:

• Waiving informed consent in newborn screening research: Balancing social value and respect (Eye on DNA post 1, post 2)

  Waiving the informed consent requirement facilitates the development of flexible strategies for informing and educating parents about NBS research that reflect the logistics of population-based NBS screening. A strict interpretation of the regulatory requirement of informed consent may create significant logistical and financial barriers to adequate evaluation of NBS tests.

• Ethical implications of including children in a large biobank for genetic-epidemiologic research: A qualitative study of public opinion (One of the authors is a former Johns Hopkins classmate of mine - Dr. David Kaufman. Hi, Dave!)

  Many of the concerns expressed by participants [of focus groups] mirrored those addressed in pediatric research guidelines. These concerns included minimizing children’s fear, pain, and burdens; whether to include young children; and how to obtain children’s assent. …To successfully include children, proposed cohort study would need to address children’s changing capabilities and rights as they grow and reach the age of consent.

• You’re one of us now: Young people describe their experiences of predictive genetic testing for Huntington disease (HD) and familial adenomatous polyposis (FAP) (See Eye on DNA interview of Kathy Flake whose mother had HD.)

  Harms described included knowledge of future illness, witnessing distress in parents, negative effects on family relationships and friendships, effects upon employment and school, experiencing regret, feeling guilty and having to confront difficult issues. Benefits included knowledge of gene-negative status, relief from uncertainty, witnessing relief in parents, feeling able to plan for the future, positive effects on family relationships and friendships, feeling empowered and experiencing a sense of clarity about what is important in life.

• Should genetic testing for BRCA1/2 be permitted for minors? Opinions of BRCA mutation carriers and their adult offspring (Eye on DNA, press release)

  Combining the responses of parents and offspring, 40 percent supported genetic testing of minors with half in favor only in certain circumstances. A majority of sons and daughters — potential consumers of genetic testing, supported testing minors.

NB: The ultrasound above is of my own to-be newborn due June 2008.

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Football-Related Puppy Genetics

by Dr. Hsien-Hsien Lei
Posted January 27, 2008 in DNA Fun

It’s football as in soccer not as in American football that looks like rugby….

From NewsBiscuit:

The marketing department of Premier league giants Manchester Utd have announced they are to have puppies breed in their team colours in an attempt to attract supporters at a younger age. ‘We considered many options but our market research confirmed that everyone loves puppies,’ said Mark Stanion senior marketing manager at the club. ‘With advances in genetics we can apparently have them in any colour and size we like.’

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DNA Video: 23andMe Genetics 101 Part 2

by Dr. Hsien-Hsien Lei
Posted January 26, 2008 in DNA Podcasts and Videos

New personal genomics company, 23andMe, created a series of videos introducing basic genetics concepts. Have a look at part 2 - What are SNPs? (Watch part 1.)

Tags: genetics, genes, dna, 23andme, personal genomics, genomics, science, video

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Genetic Genealogist Ann Turner’s Opinion on deCODEme, 23andMe, and Whole Genome Testing

by Dr. Hsien-Hsien Lei
Posted January 25, 2008 in DNA Testing

While David Hamilton of VentureBeat Life Sciences has been scrutinizing deCODEme’s sample reports for “demo user,” Dr. Ann Turner has been on the inside. Not only is she a customer of both deCODEme and 23andMe, Dr. Turner is the co-author (with Megan Smolenyak) of Trace Your Roots with DNA: Using Genetic Tests to Explore Your Family Tree. Trained as physician at Stanford University, she now develops software for neuropsychological testing as well as those for use in genetic genealogy. She is also the founder of the very active GENEALOGY-DNA mailing list at RootsWeb and is on the editorial board of the Journal of Genetic Genealogy.

Today at Eye on DNA, Dr. Turner shares her thoughts on deCODEme, 23andMe, and whole genome testing.

~~~~~
David Hamilton at VentureBeat finds the deCODEme demo to be “underwhelming.” Consumer access to whole genome testing is totally unprecedented, and we have no foundation for knowing what to expect, but I’m considerably more intrigued by the potential myself.

First of all, I expect deCODEme and 23andMe felt under intense competitive pressure to get a product out the door, since rumors had been circulating widely for months. I don’t regard either website as being mature, but they are each expandable as science learns more from whole genome association studies. The raw data will be constant, and I find myself scanning news releases about research studies to see if they mention any rs (Reference SNP) numbers. For instance, a recent article by Gina Kolata in the New York Times mentioned a commercial prostate cancer test to be marketed for $300, which will include five SNPs that seem to elevate the risk several-fold if many of them are present. The deCODEme and 23andMe download of raw data includes four of those SNPs. I expect both websites will be incorporating findings like these into their interpretive reports, too.

I agree that the website does not make for easy pickings — it takes some thought to grasp the principles behind the reports and graphics. The whole notion of relative risk is not something many people have even thought about. But, as Kevin Kelly said in a WIRED article reviewing the Genographic Project and my book Trace Your Roots with DNA, “a basic level of genetic literacy will be essential… ” and learning about our own DNA is a great motivator. When David Hamilton complained that clicking on the Relationship Check for “nephew” revealed a “rat’s nest of possible family ties” that’s exactly what he could have expected. All those relationships share about 25% of their DNA on the average, as the chart in the WIRED article illustrates.

Since I’m interested in genetic genealogy, I am more attuned to the ancestry components of the deCODEme results. The admixture results are interesting to anyone who suspects they may have ancestors from different geographical areas. The detailed chromosome graphs also show the potential for tracing segments of DNA shared with even more distant relatives. For instace, it was recently found that a block carrying a colon cancer gene could be traced back to a couple who arrived in the US in the early 1600’s. This sort of thing might very well show up in the “Compare Me” feature.

Early adopters do take some risks — I’m sure that prices will drop and features will increase as time goes on. But I’m in the game, as I want to start on the learning curve right away.

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Books About DNA: Elizabeth Blackburn and the Story of the Telomeres

by Dr. Hsien-Hsien Lei
Posted January 25, 2008 in Books About DNA, DNA Quotes and Excerpts

…her [Elizabeth Blackburn's] delight in books exceeded the bounds of obedient studiousness - in particular, she was thrilled by her recent discovery of a biology text complete with detailed illustrations of amino acids, strung together in long chains and then folded up into complex three-dimensional shapes to form enzymes and other proteins. For Liz, these elegant structures had a teasing beauty, promising tantalizing clues to the processes of life and yet also enfolding that mystery. Even the names of the amino acids–phenylanine, leucine–struck her as poetic. Though she confessed her fascination to no one, she traced drawings of amino acids on large, thin sheets of white paper and then tacked them up on her bedroom wall.

From Elizabeth Blackburn and the Story of Telomeres: Deciphering the Ends of DNA by Catherine Brady

Tags: telomeres, elizabeth blackburn, genetics, genes, dna, science, books, scientists

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Eye on DNA Headlines for 24 January 2008

by Dr. Hsien-Hsien Lei
Posted January 24, 2008 in DNA and Disease, Eye on DNA Headlines, Genetically Modified Foods and Organisms, Personalities with DNA

• Gene Genie Issue #24 is up at Biomarker-Driven Mental Health 2.0.
• Sue Trinidad at Women’s Bioethics Blog wants to know how far genetic researchers can take your DNA beyond your initial informed consent.
• Sam Karlin of Stanford University who created BLAST with Stephen Altshul died in December of a massive heart attack.

  “Because of the common descent of all living things, it is often possible to learn a lot about a new DNA sequence by finding out what is known about other sequences that are similar,” (Russ) Altman said. BLAST compares the new sequence to an enormous database of sequences. “It estimates the significance of the match between the input sequence and the ‘hits’ that are pulled out. This is where Sam’s contribution was—he worked out the statistical theory for how to judge which matches really meant something. So BLAST is basically the Google of biological research.”

• The newest (42nd) member of The DNA Network is Genetic Future by Australian researcher Daniel MacArthur. His latest post looks at the ethical challenges of whole-genome sequencing. Welcome, Daniel! We’re glad to have you.
• Four reasons why genetically modified food is inevitable. (HT: Mark Evans)
• Hypertensive patients with a copy or more of the T2238C variant of the atrial natruiretic precursor A (NPPA) gene may have a decreased risk of coronary heart disease (CHD), stroke, all-cause death, combined CHD, and combined CVD if treated with the diuretic chlorthalidone (also known as Clorpres, Tenoretic, and Thalitone). Those with the most common TT genotype appear to do better when treated with a calcium channel blocker (amlodipine aka Norvasc). (Medical News Today)

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DNA Auction: UK DNA Double Helix Coin

by Dr. Hsien-Hsien Lei
Posted January 24, 2008 in DNA on Auction

The £2 coin from the UK you see on the left was minted in 2003 to celebrate the 50th anniversary of James Watson and Francis Crick’s discovery of DNA’s double helix . It was designed by sculptor John Mills. This DNA coin is now available on e-Bay UK for a starting bid of £0.99. Auction ends on January 27, 2008 at 21:26 GMT.

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Applied DNA Sciences - Technology for Anti-Counterfeit and Security

by Dr. Hsien-Hsien Lei
Posted January 23, 2008 in DNA Products, DNA and the Law

Earlier this month, I had some fun with a sign that I saw on Queensway in London, UK. It claimed that the neighborhood was safer because they were marking property with DNA. Perhaps they were referring to the SigNature Program from Applied DNA Sciences.

Applied DNA Sciences uses DNA markers from botanical sources. They rearrange the markers into unique encrypted sequences then embed the DNA onto consumer products that need to be protected, including drug tablets and capsules, banknote threads, holograms, artwork, and collectibles. The company claims that the markers embedded in indelible SigNature DNA ink is safe to consume.

There are varying levels of product verification:

• A SigNature DNA Encryption Pen can be used to detect the presence of their proprietary overt ink.
• An instant reader can be used to detect DNA.
• Portable PCR machines can produce “absolute authentication” in less than 30 minutes.
• Forensic-level, authenticated PCR.

PCR DNA amplification is performed using specific primers that can only be synthesized if the unique encrypted DNA sequence is known.

Applied DNA Sciences states that false positives occur in less than 1 in 1 trillion cases and can authenticate at levels acceptable for forensic use. The SigNature Program is effective against counterfeiting, product diversion, piracy, fraud and identity theft.

NB: More about DNA marking of property in the UK at UK Crime Prevention.

HT: Trish

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