Tag Archive for 'personal genomics'

Direct-to-consumer genetic test results in a clinical setting: a case report

Dr Neeta Tailor is an anaesthetist working at the Royal Gwent Hospital in Wales. Dr Tailor recently treated a friend of Genomes Unzipped members (referred to here as Patient X) who required emergency surgery following some unusual and fairly horrible complications (believe me, I’ve seen the photos!) from wisdom tooth removal. The remarkable thing about this case: prior to surgery the patient volunteered information about her potential drug responses based on her 23andMe profile, including variation in one gene that could have had a profound effect on her response to a standard muscle relaxant. Dr Tailor kindly agreed to write up her experience in this guest post.

For those interested in the genetic details: Patient X’s 23andMe results suggest she is heterozygous for the rs1799807 SNP, which induces an aspartate to glycine change in the BCHE gene and is associated with a substantially prolonged apnea (loss of breathing) following administration of succinylcholine. This is one of three separate mutations in the BCHE gene tested by 23andMe. Although in this case the clinicians had already decided independently to avoid the use of succinylcholine, it’s intriguing to think about how rapidly this type of information could become useful to clinicians – and what steps will need to be taken to ensure DTC genetic testing results are trustworthy enough to justify their consideration in this kind of emergency setting. [DM]


Anaesthesia is classically described as the pharmacologically induced triad of amnesia (memory loss), analgesia (pain reduction) and the loss of muscle reflexes. Patients usually come across anaesthetists during their pre-operative anaesthetic assessment; we are the ones telling you that our job is to pop you off to sleep, although it is usually more complicated than that!

The patient described below works in the world of genetics and invited me to describe her case in order to illustrate how pharmacogenomics and person specific genetic characteristics may affect the choice of general anaesthesia.

A 37 year old woman (Patient X) was booked onto the emergency theatre list on a Sunday morning. The planned operation was incision and drainage of an infected haematoma in the cheek, an unusual complication which had developed quickly over 48 hours following the extraction of a wisdom tooth by her own dentist. By the time she was admitted to hospital, she had extensive facial swelling, not just of her gum, but also the whole of the left side of her face from her forehead to her neck. In addition, she had reduced jaw movement, as well as limited mouth opening of less than one finger breadth. She was also feeling quite unwell having vomited during the night and her blood tests showed raised markers of infection. She was in pain requiring several different types of analgesia.

This presentation in itself poses some difficulty. One of our jobs as anaesthetists involves administering drugs to cause unconsciousness which subsequently requires maintenance of a patent airway using either a mask, an airway device that sits above the vocal cords, or by a tube in the trachea. We usually then maintain unconsciousness using an inhaled volatile anaesthetic via the chosen device.

During this operation we knew we were going to need to share the airway with our maxillo-facial surgery colleagues performing the procedure. To ensure the optimal outcome for all (an anaesthetised patient for us and access to the mouth for the maxfax team), a tube in the trachea was the most ideal option. However, to get to the trachea, we have to get in the mouth and get a good view of the vocal cords and this is where the potential problem could arise.
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A case study in personal genomics

I have no strong family history of any disease, despite having 7 blood aunts and uncles and countless cousins. So when I sent my spit off to 23andMe at the start of the Genomes Unzipped project, I was expecting something very similar to Caroline’s experience: a 5% increase in risk here, a 2% decrease in risk there, nothing that would really tell my anything about my health.

However, this was not my experience. Along with a pretty interesting Y haplogroup, I also had three unexpected and potentially worrying health results. I am a cystic fibrosis carrier, a hemochromatosis compound heterozygote, and have a strongly elevated risk of age-related macular degeneration. This cocktail of genetic disease certainly was not what I came to the test expecting!

After some thinking, I decided to take my test results to my GP, and see if there was any advice or testing he would recommend. In the end, my GP referred me to a clinical geneticist, which started a cascade of appointments which in turn led to a number of important changes in how I treat my own health.

What was most interesting is how the whole experience got me thinking about my health as something I am in charge of. I have since made a number of important life-style changes, some of them directly related to my genotyping results, some more generally to improve my overall health.

The point of this post is just to go through some of the experiences, what I have learned about specific conditions, and what changes I have made to my life since. In some sense, I feel like my experience is a case-study in what good outcomes can come from personal genomics, both for specific conditions, and more generally for how genetic data can change your own approach to your health.

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Cracking non-coding variation, carrying cystic fibrosis, and more Alzheimer’s prediction

Daniel and Luke attended the Biology of Genomes conference at Cold Spring Harbour last week. The talks did not have a huge amount of direct relevance to personal genomics, but did show some real quantum leaps in understanding the function of the non-coding DNA that makes up most of our genomes. Understanding mutations that lie outside of coding DNA is largely a prerequisite for transitioning to whole-genome sequencing for personal genomics, as most of the variation that drives genetic differences between people appears to lie there. As we’ve said before, one of the powerful aspects of sequencing is that it allows you to get at the aspects of your DNA that are unique to you, but that is only really useful (and a lot cooler) if we know what this unique variation does. Biology of Genomes showed us that that dream is closer now than it has ever been before.

For a (somewhat technical) account of some of the conference talks, you can read Luke’s blog posts over at Genetic Inference (along with a signficiantly less technical post about chipmunks and wood cabins), and Matthew Herper has a lay-friendly post on his Forbes blog. As has become standard, Twitter was an important way of disseminating knowledge live during talks, and Keith Bradnam and EpiExperts wrote about this aspect. [LJ]

Since GNZ started, Luke has actually been holding back writing about his many and varied genomics woes, and his resulting quest for bodily health, mostly for lack of time. However, one part of this has leaked out somewhat: he has recently given an interview to fellow blogger Elaine Westwick about being one of the two cystic fibrosis carriers in Genomes Unzipped. Read the interview at Elaine’s blog The Stuff of Life. [LJ]

On a similar subject to our recent post about calculating Alzheimer’s risk, over at Genomics Law Report Dan has written a detailed post about the regulatory challenges ahead for both direct-to-consumer and clinical tests for Alzheimer’s. [LJ]

Last chance to submit comments to the FDA about DTC genetics

Today is the last day to submit comments to the FDA about the future of regulation of direct-to-consumer genetic testing, and, by extension, the future of personal genomics. I would strongly urge anyone reading this blog to submit a comment; the FDA needs to hear the full diversity of opinions and facts on this subject to make an informed decision.

Have you or your family taken a DTC genetic test, and can explain your experiences, either positive or negative? Are you a scientist working on human genetics and have thoughts about the scientific merits of the tests? Are you a clinician, and have insights into how individual’s having direct access to their own genetic information will effect your practice? Are you an ethicist, social scientist or public health professional with opinions about the rights of individuals to access their genetic data, or the impacts such access will have on society or public health? Write a hundred words or so and submit them to the FDA.

You can submit comments via this form; remember, today is the last day before comments close. You can see the comments that have already been submitted here.

For more coverage on this round of comments, see posts by Dan, Daniel and Razib. You may also like to reread our consensus statement about the FDA’s recent investigations.

Using 23andMe to confirm identical twinnery, and a chance to tell the FDA what you think about DTC genetics

Over at Daily Kos, Michael Convente shares a fascinating story of using 23andMe data to pin down the precise relationship he has with his twin brother Matt. When Mike and Matt were born, the obstetrician told their mother that the presence of two separate placentas indicated that the brothers were non-identical (fraternal) twins – yet their incredibly similar appearance while growing up (see photo on left) suggested otherwise. Testing with 23andMe confirmed what the brothers had always suspected: that they are in fact identical twins. This is a useful reminder of the non-medical value of accessible genetic information: when it comes to unravelling these kinds of family mysteries, direct access to large-scale genetic data can be a powerful tool. [DM]

Readers who care about access to genetic information (i.e. all of you) and who are concerned about the potential effects of regulation on this access and on innovation in the field in general will soon have an opportunity to make their voices heard. Thanks to the efforts of Dan Vorhaus and others, the FDA has agreed to reopen the opportunity for public submissions while it deliberates on its next move following the agency-sponsored meeting on direct-to-consumer genetics last month. The submissions docket is apparently due to reopen today, and will remain open to submissions until the 2nd of May – so you all have a month to get your opinions in there. You’ll hear more from us about the process of submitting to the docket over the next week or so. [DM]

On a related note, genetic counsellor Christine Patch and academic (and Unzipped guest blogger) Barbara Prainsack have penned a response to the above-mentioned FDA meeting for BioNews. Patch and Prainsack provide a welcome note of nuance to the discussion; their final two paragraphs are worth quoting in full:
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Analysing your own genome, bloggers respond to the FDA and more reporting on bogus GWAS results

Razib Khan, more known for his detailed low-downs of population biology and history, has written an important post on Gene Expression, explaining in careful detail exactly how to run some simple population genetic analysis on public genomes, as well as on your own personal genomics data. The outcome of the tutorial is an ADMIXTURE plot (like the one to the left), showing what proportion of your genome comes from different ancestral populations. This sort of analysis is not difficult, but it can often be hard to know how to start, so Razib’s post gives a good landing point for people who want to dig deaper into their own genomes.

This tutorial also ties in to some political ideas that Razib has been talking about since the recent call to allow access to genomic information only via prescription. If you are worried about losing access to your genome, one option is to ensure that you do not require companies to generate and interpret your genome. As sequencing, genotyping and computing prices fall, DIY genetics becomes more and more plausible. Learn to discover things about your own genome, and no-one will be able to take that away from you. [LJ]

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Guest post by Razib Khan: My personal genome

I’ve been following Razib Khan’s scholarly and analytical exploration of his family’s genetic history – using data from 23andMe – over at Gene Expression with increasing fascination. When last week he noted that his findings appeared to be (finally) converging on a consensus, I asked if he’d be willing to summarise his journey for Genomes Unzipped readers. Here it is. –DM.

I’ve always been interested in genetics, anthropology, and history. Many may perceive me to be a collector of obscure facts, but summing up infinitesimals does produce something substantial in aggregation. One of the most influential books in my life has been History and Geography of Genes. So with that, the shift from classical markers to uniparental lineages, and now to the dense SNP-chips, has been a boon for my own intellectual interests which reside in part at the intersection of history and population genetics.

However, I’ve never been deeply curious as to the history of my own personal genome. I’m not adopted. All four of my grandparents were ethnic Bengalis, albeit from relatively diverse communal backgrounds. I look typically South Asian. Genealogy has never been a family fascination, and I’m going to be honest and admit that until five years ago I didn’t even know the names of my grandparents (in the Bengali language there are distinctive terms for maternal and paternal grandparents, so this wasn’t needed). Both sides of my family are from the Comilla district of Bengal, and that’s all I really cared about (and I didn’t care that much, I don’t put much stock in “heritage” as determinative).

As for other yields of personal genomics, I was skeptical. My parents have many siblings, and many, many, cousins. I had a general sense of my risks for diseases through an inspection of the pedigree of my family and their medical histories. Additionally, many of the risk alleles have been identified in European study populations, and I wasn’t totally sure about the between-population portability of these inferences. And I won’t even address the fact that effect size of many of the markers isn’t something to shout home about.

But last spring Daniel alerted me to the 23andMe “DNA Day” sale. It was affordable, and at that point enough of the readers of my weblog had been typed that I kept getting questions as to my own background (e.g., my family has the title Khan, so there was a question as to whether I carried the “Genghis Khan haplotype”). So I bit. At the time I recall emailing Dan and being excited that I’d be told I likely had brown eyes and was 75% “European” and 25% “Asian.” When my results came back, I was in for a mild surprise. The proportion to the left are calculated by 23andMe’s “ancestry painting” algorithm. As you can see, I’m more than 25% “Asian.” My initial reaction was that this seemed a touch high, but no worries, I would ask around and see which other South Asians had such a high value. After dozens of instances of “gene sharing,” the answer came back: none.
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A decade of genomics, 60 new genomes, parenthood and sharing genetic data, and more on data return

To celebrate 10 years since the back-to-back publications of complete human genomes in Science and Nature, Science has published series of articles looking back at the last 10 years of genomics, and forward to the future. The article contains short essays from Francis Collins and Craig Venter, the former talking about some of the successes of medical sequencing (including giving a name and photograph to the exome-sequenced IBD patient I discussed a few weeks ago), and the latter discussing how far we still have to go before genomics can reach its potential. Baylor’s Richard Gibbs talks about how the large-scale technical discipline of genomics and the biological subject of genetics are starting to re-merge, after the Human Genome Project saw the two diverging, and there is an oddly inspiring comment from theologian Ronald Cole-Turning about how genomics is redefining our vision of humanity.

Of particular interest is an article by Eliot Marshall on why genomics hasn’t yet had a large effect on medical practice, and what needs to be done to allow the genomic revolution to trickle into medical care. He argues that scientists and doctors need to meet each other half way; scientists need to focus more on showing the direct clinical utility of genomics, whereas doctors need to be more ready to accept new technologies and discoveries, and adapt the way they practice medicine to make full use of them. [LJ]

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Digging deeper into my disease risk

When Daniel first asked me if I wanted to be involved in Genomes Unzipped, I was one of the more hesitant participants.  I weighed up the pros and cons, but in the end what sold me was that after almost a decade of curiosity I finally had the opportunity to find out my genotype for the hereditary haemochromatosis (HH) variants in the gene HFE.  But things didn’t unfold quite how I’d expected, and I’m still left with some unanswered questions about HH in my family.

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Saturday Links

Due to a communication breakdown, no-one wrote a Friday Links post yesterday, so today we have a Saturday Links to make up for it.

Steve Hsu has a very appropriately named post, News from the future, about the Beijing Genomics Institute. The BGI is the largest genome sequencing center in China, and one of the largest in the world, and is growing faster than any other, and loading up on a shedload of high-tech HiSeq machines.

Steve reports that the BGI are claiming that their sequencing rate will soon be at 1000 genomes per day, with a cost of about $5k (£3.2k) each. To put a slight downer on these amazing numbers, he clarifies that this might be referring to 10X genomes, which would realistically mean ~300 high quality genomes a day, at $15k (£9.6). Either way, if you want to keep an eye on how fast whole-genome sequencing is progressing, perhaps with an eye to when you’re ready to shell out to get your own done.

A question for the comments: how cheap would a whole-genome sequence have to get before you’d order one?

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