by Dr. Hsien-Hsien Lei
Posted September 29, 2008 in DNA Testing, Personalities with DNA
Of all the direct-to-consumer genetic tests currently available to the public, early gender DNA tests are among the most controversial. The test allows pregnant women to submit finger prick blood samples which the lab screens for the presence of Y-chromosomal DNA from the fetus; Y-chromosomal DNA positive indicates a boy, negative indicates a girl.
Karen Kaplan of the LA Times looked into the accuracy of gender DNA test kits in February of this year. And a lively discussion among Eye on DNA readers follows my post: Is the Pink or Blue early baby gender DNA test accurate? One of the commenters is Terry Carmichael, VP of Marketing & Sales at Consumer Genetics, manufacturer of The Pink or Blue Early DNA Gender Test.
Terry is the founder of Gene Tree DNA Testing Center which was sold to Sorenson Genomics in 2001. He also helped launch at-home DNA paternity DNA tests in major U.S. drugstores in 2007 (see previous Eye on DNA post). I was impressed with Terry’s openness and invited him for an email interview.
Hsien: What is your company’s motivation for providing an early gender DNA test direct to consumers?
Terry: Trying to predict the sex of a baby has been a centuries old game within families. Families want to know the sex of a baby for many reasons. Most want to make an announcement at a family gathering, or surprise their husband with the anticipated gender, or preparing siblings for a new baby boy or girl. Others want to know so that they can prepare siblings that will have to share rooms, or to begin to decorate a room for the baby based on gender. The main motivation for Consumer Genetics is the gratification we get when helping families plan for the future by offering them the information they are seeking to know.
Hsien: Can you tell us more about the quality assurance protocol for the Pink or Blue DNA Gender Test?
Terry: The Pink or Blue test is based on several large scale studies that have scientifically proven the ability to determine gender by detecting Y-chromosomal DNA of fetal origin in a large sample of a mother’s blood (10 ml). The accuracy of this method in a clinical setting has been shown to be between 97.8 to 100% within a population of 1,837 pregnant women. The Pink or Blue test uses the same molecular technique as in the studies (Polymerase Chain Reaction) along with a proprietary method of purifying and amplifying the baby’s Y chromosomal DNA within a much smaller sample of the mother’s blood (usually 60-120 microliters). The company looks for data from the DNA test that shows the baby is a boy. If this data does not show this, then this suggests that the baby is a girl. There are times when the data is not clearly one or the other – imagine a few data points that are on either side of a line. In this case, we report the test as inconclusive. Due to this complex â€œsignal-to-noiseâ€ issue, we regularly run at least 2 tests for each sample to increase the probability of a conclusive result. If all tests are â€œinconclusive,â€ we then ask the customer for a new sample. Therefore, just like ultrasound, we have a portion of samples that we cannot determine gender from, and we have the customer send a new sample for re-testing. This second sample will nearly always give us a conclusive result.
Our laboratory has a documented quality assurance system in place to ensure the proper functioning of all equipment and reagents. All new reagents are thoroughly tested before entering the production line. We also purify a control sample along side a batch of real samples to ensure that there is no reagent failure or laboratory-caused contamination. About 33% of all the sample wells in a PCR reaction are controls, ensuring that all reagents are working properly. For each portion of a sample that is tested, the Pink or Blue DNA Gender Test laboratory procedure is run in triplicate. So, for a standard sample, where 2 portions are tested, there are actually 6 data points showing boy or girl, 10 data points with unique controls for that specific sample, and dozens of controls indicating that all reagents were working properly.
The lab documents all this activity and is working towards ISO and CLIA accreditation. Although accreditations are not currently needed for gender testing due to it is not used for medical or diagnostic purposes, the company recognizes that accreditation will add more creditability, and as more regulatory guidelines are expected in the future, it makes good business sense to have a strong, accredited quality system in place.
Hsien: What factors can contribute to inaccurate results? How can consumers ensure the most accurate results possible?
Terry: It is very important that our instructions are carefully followed. The DNA preservation cards must be completely filled with the appropriate amount of blood in all three specimen blotting areas of the card. The quantity of a baby’s DNA in the mother’s blood is very minute. Therefore, the more blood, the more fetal DNA; and the higher the chances are for a conclusive result. It is also important to collect the sample no earlier than 7 weeks, post-conception. Specimens collected earlier than this eligibility date may not have enough fetal DNA circulating in the blood for our DNA test to detect. Contamination of the sample with male DNA from outside the womb can also occur. We have a proprietary method that detects this kind of external contamination, but once contamination is confirmed we cannot provide accurate results and a new specimen is needs to be sent in. The best way to ensure the most accurate results is to follow our instructions, watch our instructional video, keep away from males while providing the sample, collect the proper amount of blood, and make sure that the area used for specimen collection is clean.
Hsien: Why do you think people are so eager to know the sex of their baby before delivery?
Terry: That is a complicated question and one that is highly specific to each individual. We do not survey our clientsâ€™ intentions, but many volunteer their reasons for DNA testing. Most commonly these are to make an announcement at a family gathering, surprise their husband with the anticipated gender, preparing siblings for a new baby boy or girl, and many women are simply excited and anxious about their pregnancy and want to know their babyâ€™s gender as early as possible. They just canâ€™t wait to find out.
Hsien: How would you respond to critics of early gender detection who say that the various methods, including DNA tests and ultrasound, are being used for sex selection?
Terry: There are several companies providing products to select gender, and gender selection is legal in the United States. Check out places like Amazon.com, where gender selection kits are for sale.
However, this is not what we are all about, here. We are about helping people who are excited and want to make an announcement at a family gathering, or surprise their husband with the anticipated gender, or preparing siblings for a new baby boy or girl, or just to help a mother-to-be who is thrilled about her pregnancy and wants to know her babyâ€™s gender as soon as she can.
Our DNA test are not be used for gender selection and our consent for states this. People using our gender testing service have consented not to use it for gender selection purposes. We are clear about this, and we will continue to refuse to provide our services for those means. To further assure this position we regularly turn people away trying to purchase from China and India, where gender selection procedures are of great demand.
by Dr. Hsien-Hsien Lei
Posted September 10, 2008 in DNA Podcasts and Videos, Personalities with DNA
Along with the DNA of other bright minds, musicians, and athletes, clever funnyman Stephen Colbert’s digitized DNA will also be included in Operation Immortality’s digital time capsule that’s being delivered to the International Space Station next month. See video above for his DNA sign-off from February 2006.
by Dr. Hsien-Hsien Lei
Posted September 5, 2008 in DNA Fun, Personalities with DNA
Three Silicon Valley celebrities are set to send their digitized DNA into space via NCsoft’s Operation Immortality project. Game designer Richard Garriott will deliver the DNA to the International Space Station on October 12. A digital time capsule is being created that includes “messages from people around the world along with the digitized DNA samples from some of Earth’s brightest minds, musicians, and athletes.”
The Silicon Valley celebrities participating are:
Draper’s desire for his DNA:
My hope is that aliens get a hold of my DNA so my clones can spread entrepreneurship to galaxies throughout the universe.
Some might wish for peace throughout the universe but I guess entrepreneurship ain’t too bad.
Photo credit: feastoffools
by Dr. Hsien-Hsien Lei
Posted May 28, 2008 in Personalities with DNA
About an hour ago, I received an email from the man himself announcing his plans to resign from the NHGRI starting August 1, 2008. (For a second I thought I was on some personal mailing list of his until I realized it was distributed via the Genetic Alliance Announcements List. D’oh. Delusions of grandeur….) He is leaving to devote time to “writing, reflection and exploration of other professional opportunities in the public or private sectors.” Alan E. Guttmacher, M.D., will become acting director.
Here’s an excerpt from his email:
Looking back, Iâ€™m tremendously proud of our collective work in leading the Human Genome Project (HGP) to its successful conclusion in 2003, and of our wide range of large-scale projects that built upon the foundation laid by the HGP. Collectively, these projects and the priceless data they generated have transformed biomedical research and empowered researchers all around the world. Iâ€™m also proud of these projectsâ€™ commitments to protecting the privacy of genetic information and addressing the ethical, legal and social implications of genome research.
In addition to his work on the human genome, Dr. Collins has also been known for his controversial religious beliefs. In a 2006 interview I conducted with Dr. PZ Myers of Pharyngula, he said the following of Francis Collins’ book – The Language of God.
Once upon a time, I would have said that my view of genetics/genomics wouldnâ€™t be much different from those who profess a faith â€” good scientists can sequester their religious beliefs from the practice of science. Unfortunately, Iâ€™ve since read Francis Collinsâ€™ new book, and that incoherent spewage of irrational lunacy is swaying me the other way, to regard religion as a toxin that corrupts good minds. The Language of God is precisely the kind of example that convinces me of the destructive failures of religious belief.
What memories do you have of Francis Collins?
Update: Sandra Porter at Discovering Biology in a Digital World remembers Dr. Collins singing about DNA with a guitar at a fund-raising dinner.
by Dr. Hsien-Hsien Lei
Posted April 8, 2008 in DNA Testing, Jobs Involving DNA, Personalities with DNA
Personal genomics company Navigenics will be hosting DNANYC in New York City starting today. The event runs from April 8 through April 17 and is meant to “celebrate the promise of genetic health.” Navigenics is now open for business and you can become a “member” for $2, 500 including first year’s subscription. The subsequent ongoing subscription rate is $250 per year.
From the press release:
Navigenics, a privately held personalized health services company, today launched Navigenics(TM) Health Compass, a new service that combines a genetic health assessment with the latest discoveries in science and medicine as well as genetic counseling. The service gives individuals information on their chances of developing up to 18 common conditions, so that with their physicians, they can obtain earlier diagnosis, delay onset or prevent the conditions altogether.
It’s a great pleasure today to share my interview with Elissa Levin, Navigenics Genetic Counseling Program Director. I’ve known Elissa since her days at DNA Direct and I think you’ll agree that her enthusiasm and knowledge of the genetic testing industry make her uniquely qualified.
Hsien Lei: At Eye on DNA, I regularly receive emails asking about career options in genetics. Can you tell us about how you came to be a genetic counselor? What do you like most about the job? What are the challenges?
Elissa Levin: I first learned about genetic counseling (GC) while I was in college studying biology and psychology. I did a fantastic summer rotation in a cytogenetics lab at CHOP, where I completely fell in love with genetics. The difficulty was that while I wanted to be connected to the basic science, I also knew that I wanted to work directly with people. Then I discovered the field of genetic counseling and it seemed like the perfect hybrid.
As I began my training as a genetic counselor, the Internet was becoming a growing information resource and seemed like a natural means of providing genetic counseling services in the future. Then, while working in General Genetics at UCSF, this concept was further reinforced as access to genetics clinics in northern California became more difficult â€“ clinics were closing, people were waiting months for appointments, traveling long distances, and some were unable to afford the time off of work, child care, travel costs, etcâ€¦ More of our pre-visit and follow-up genetic counseling services were being provided by phone (which, of course, we could not bill for). Basically, the lack of access to genetic services obviated the need to identify alternative methods for delivering genetic counseling services.
At that time an opportunity arose to establish a Web-based genetic counseling service at DNA Direct that mirrored traditional GC services. Several years later, my new challenge at Navigenics is to take my â€œvirtual genetic counselingâ€ experience and apply it to a new realm of testing â€“ whole-genome risk assessment â€“ in a professional and responsible way.
What I like most about being a GC is also its greatest challenge â€“ working with people to help them understand complex information and what it means to them and to their family. This means staying on top of new technologies, research, risk communication strategies, and creating an infrastructure to provide accurate information responsibly.
Hsien: With the number of online personal genomics companies increasing, how do you think this will affect the demand for genetic counselors? How do you think personal genomics will change a genetic counselor’s job description?
Elissa: Genomic risk assessment does not leave out the genetic counselor. In my opinion, it will actually increase the demand for genetic counselors over the coming years. In the past decade or so the role of the GC has expanded greatly â€“ out of the prenatal and pediatric clinics and into a wide range of subspecialties, research endeavors, industry, and more. I see the coming years as a continuum of this trend, but a critical one in which the opportunity to integrate genetic counseling services into primary care settings and addressing common, complex disease (as opposed to rare disease) will increase exponentially.
It is well known that most healthcare providers are not comfortable with providing genetic information and interpretation for their patients. That is where genetic counselors become such critical players in this evolving field of genetic and genomic medicine.
GCs already have the core skills to facilitate the transition of genomic discovery into a clinical setting â€“ communicating risk information and complex genetic concepts, facilitating decision-making, and integrating personal and family medical history.
I see the field of genomic medicine as being a great opportunity for GCs, further underscoring the value of our profession as a key component of a healthcare team.
Hsien: Companies like Navigenics and DNA Direct have made genetic counseling a core offering while others like 23andMe and deCODEme have not. Do you think genetic counseling is dispensible if there’s quality online content? What do you think are the pitfalls of not offering genetic counseling to customers?
Elissa: We all know that genetics is complex and that different people have different needs â€“ some need more support in the basics, decision-making, interpretation while some need less. From my experience in â€œvirtualâ€ genetic counseling, I strongly believe that no matter how high quality the content and how interactive the tools, being able to speak with an actual, trained genetics professional makes all the difference.
Personally, Iâ€™m thrilled to continue be part of companies that value the role of the genetic counselor, since Navigenics offers GC as a core component of our services. Companies that do not offer GC services are likely to create an environment where consumers are driven to healthcare providers who may not be equipped to interpret this type of information. (This is one reason why Navigenics is committed to developing consumer-friendly tools as well as resources to educate physicians, nurses, PAs, and other providers.)
That is why I view the services offered by companies like Navigenics and DNA Direct to be a model for offering professional services in the future. The key is to set industry standards to offer accurate, responsible testing and support services to patients and providers alike. Our commitment to this goal, with GC services included as a core component of testing, is why weâ€™re actively organizing a forum to address industry standards this fall in Washington DC to include heads of industry, academia, ethics, and policy (please see our press release on April 8).
Hsien: What kind of people do you think will be the first to sign up for Navigenics?
Elissa: It is hard to say, but there are so many people who are interested in learning more about who they are on a genetic level. There is a growing trend towards people becoming more proactive about their health and wellness. Over the past few years, Iâ€™ve been hearing from an increasing number of people who want to know what health conditions they may be more likely to develop, or not, down the road.
I believe it is safe to say that those who initially choose to take the Navigenics Health Compass test will be those who are looking to maximize their health and wellness and focus their healthcare needs. As this type of testing is not yet reimbursed by insurers, initially this will likely be those who have the ability to spend healthcare dollars out of pocket. As with most new products and services, over time this type of testing will become much more accessible to larger populations.
Hsien: Given the cost, why should people get their whole genomes scanned rather than selecting a few specific genetic tests as follow-up to red flags in their family history?
Elissa: There are actually several reasons why whole genome scans can be a great tool for people. First, relying solely on family history is not a complete story for many people, and some have no such information available. Even for those who have access to family history, what we know with certainty about our familyâ€™s medical history can leave a lot to be desired.
Second, if you look at the cost of traditional, indication-specific genetic tests, the costs range from about a hundred dollars to thousands. When you look at the amount of genetic information you receive along with the number of health conditions, it becomes a very cost-effective endeavor.
Finally, the amount of information someone gets from a single genome scan is incredible! What we can provide today is a snapshot of information that has been validated in scientific studies to date. Over time, the same fundamental test will continue to provide information about new health conditions. I think itâ€™s also important to point out that Navigenics also provides ongoing genetic counseling services for anyone who chooses to have a genome-wide risk assessment. Therefore, one test today can yield an ongoing supply of reliable, genetic health-related information.
Thank you, Elissa!
Are any Eye on DNA readers Navigenics Health Compass members? Please share your story in the comments or email me!
by Dr. Hsien-Hsien Lei
Posted February 3, 2008 in DNA Fun, Personalities with DNA
A fun conversation I saw on the Sinfest forums about Craig Venter’s genome:
Dro: My father was reading Craig Venter’s autobiography. I flipped it open to see if there was anything interesting about sequencing the genome. I read, “My Ph.D. committee was amazed by the length and rigor of my thesis”. Put down book.
mouse: a little thesis envy there, dro?
wish i could remember where i saw it – back when venter was sequencing the human genome, someone put up a poll on “who is the unidentified individual whose dna is being sequenced?” – and the choices were a) craig venter; b) craig venter or c) craig venter.
man doesn’t seem to have any self-esteem problems.
FYI, Sinfest is a webcomic by Tatsuya Ishida.
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 wasâ€”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)
by Dr. Hsien-Hsien Lei
Posted December 6, 2007 in DNA and Disease, Eye on DNA Headlines, Personalities with DNA
- Congratulations to Dr. Elizabeth Blackburn of UCSF who has won the L’ORÃ‰AL-UNESCO For Women in Science Award. She is a pioneer in telomere and telomerase research and is also a strong contender for a Nobel Prize.
Dr. Blackburn’s research examines the function of the enzyme as it relates to cell aging and mutations that can cause cancer. During DNA synthesis, telomerase restores the ends of eukaryotic chromosomes, called telomeres, and Dr. Blackburn’s research has found that mutant variations of telomerase impair cell division, which can contribute to aging and cancer.
- The Economist explores consumer genomics and genetic sequencing in this week’s issue.
- Nine genetic markers for schizophrenia have been uncovered using whole genome homozygosity association (WGHA) analysis. Published in PNAS, the study genotyped 500,000 markers in 178 schizophrenia cases and 144 healthy controls.
Four of these 9 “risk ROHs” contained or neighbored genes associated with schizophrenia (NOS1AP, ATF2, NSF, and PIK3C3).
- Four times as many imprinted genes have been identified in a recent study at Duke University. Most of the imprinted genes found in this study are within genomic regions associated with cancer, diabetes, autism, and obesity.
- A small study of 102 men and 101 women found that those with one form of the AVPR1a gene were more likely to be generous when playing an online game involving money. Israeli researchers found that those with generous AVPR1a gene variant gave away 50% more money on average. I wonder if deCODEme or 23andMe will find that a disproportionate number of their customers have the “generous” AVPR1a genetic variation.
by Dr. Hsien-Hsien Lei
Posted November 30, 2007 in DNA Testing, Personalities with DNA
As promised, here’s my exclusive interview with Jorge Conde, President and CEO of Knome – the latest company to offer personal genome services. Jorge is a graduate of Harvard Business School and also holds an MS from the Harvard-MIT Division of Health Sciences and Technology (HST) and a Bachelor’s degree in Biology from The Johns Hopkins University. He previously worked in business development at Helicos Biosciences as well as other life sciences companies. Jorge is clearly motivated and energized by the promise of personal genomics. He’s an up-and-coming player in the field who’s one to watch!
Hsien: Knome claims to be the first company to offer whole-genome sequencing and analysis to private clients but it certainly won’t be the last. How will Knome distinguish itself from competitors like Navigenics, 23andMe, and (to an extent) The Personal Genome Project?
Jorge: We’re focusing on whole-genome sequencing now because we believe that this is the approach that will drive personal genomics forward. An advantage for us to being first is that, from inception, we’ve built our platform and services specifically around whole-genome applications. And because we’re initially focusing on a limited number of clients, we can provide first-in-class service â€“ customized and personalized to each individual client.
We’ve also spent a considerable amount of time thinking about our responsibilities as a personal genomics company. At Knome, we’ve taken a novel approach to ensuring that our clients’ genomic information remains private and secure. We’ve built our platform to completely avoid centralized storage of databases containing sensitive genomic information. As you can imagine, these databases could prove to be very tempting targets.
Security is further strengthened by keeping control in the hands of those that value it most. Using our platform, our clients control how their information is accessed and shared, and they retain full ownership over their own genomic information â€“ after all, they’re paying us to help them understand their genome and not to take possession of their DNA.
Hsien: At this point in time, it’s far easier to sequence the genome than to understand it. How does Knome plan to organize genomic information and make it directly relevant to the average consumer?
Jorge: We’ll be talking much more about this in the near future, but clearly this is central to the service we will be providing to our clients. Broadly speaking, there are two key challenges to relating whole genome information to the average consumer.
The first, of course, is making sense of all the research that is currently out there and staying current on new information as it becomes available. Of course, we want to be sure that our analyses accurately and responsibly represent the best and most current scientific knowledge, and we’re working with teams of leading bioinformaticians, geneticists and clinicians to tackle this challenge.
The second challenge will be to communicate inherently complex, and often inconclusive, information in a way that the average consumer can understand. As you know, our genomes provide a wealth of information about us but there are very few yes/no answers, so it will be critical that our clients understand what this information may tell us â€“ and what it cannot tell us. Our focus on individualized interpretation and consultation services will enable us to establish a direct line of communication with them to help guide them.
And because a client’s whole-genome will have already been sequenced, we will be able to update our analyses as our understanding improves.
Hsien: In the Knome FAQ, it seems that the company is positioning itself as a comprehensive genome services company, including both medical genetic information along with ancestry and genealogy. How are these two sides of genetic testing compatible?
Jorge: We want our clients to understand that our genomes can tell us more about ourselves than just our risk for developing disease. Our ancestry and genealogy make up a very important part of who we are, and this is an application that the average consumer can appreciate and enjoy. That said, our initial focus will be on medical genetic information analysis and interpretation services. In the future, we hope to develop ancestry, genealogy and other novel applications.
Hsien: What kind of person do you think will be a first generation Knome customer? What kind of person do you think will benefit most from whole genome sequencing?
Jorge: Pricing for our service starts at $350,000, so our first generation clients will of course need to have the financial means to use our services. That said, these early adopters will also be pioneers in the personal genome revolution and will be amongst the first people in history to be fully sequenced. These participants will be on the cutting edge of science and medicine. They will have access to the latest information as it becomes available and those that are willing to learn as we learn (and can appreciate risk prediction and the changing nature of our scientific understanding) will be best positioned to benefit.
We also hope to attract people who have a personal desire to contribute to expanding the scientific frontier, which is why we also offer each client the option of allowing researchers to have access to their anonymous sequenced genome. But, as I mentioned previously, while we hope that a significant percentage of our customers choose to participate, it is certainly not required.
Hsien: What do you think are the biggest obstacles to overcome in the personal genome revolution?
Jorge: Clearly there are many challenges today to fully realizing the potential of personal genomics. The most immediate obstacle is the cost of sequencing. Fortunately, some very smart people are out there working to solve this problem. The next challenge will be to enhance our understanding of human genetic variation, and we believe Knome is well-positioned to make a significant contribution here. And, of course, the overarching obstacle will be how we as a society deal with the legal, privacy and ethical issues surrounding the use, and potential misuse, of personal genomic information.
Thanks for taking the time to answer these questions, Jorge! I cannot believe that it is now possible to get our genomes sequenced without signing up to be a research subject.
Update: David Hamilton of Venture Beat has more on Knome.
by Dr. Hsien-Hsien Lei
Posted November 21, 2007 in DNA Podcasts and Videos, Personalities with DNA
J. Craig Venter visits Google’s Mountain View, CA headquarters to discuss his book, “A Life Decoded: My Genome: My Life.” This event took place on November 12, 2007 as part of the Authors@Google series.
I wanted my sister to ask Dr. Venter if he had ever read Eye on DNA but she had a meeting to go to afterwards.
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