Author Archive for Joe Pickrell

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People Have A Right To Access Their Own Genetic Information

This week has seen another FDA meeting seeking guidance on how to regulate direct-to-consumer (DTC) genetic tests in the US. The meeting itself has been covered by GNZ bloggers Daniel at Genetic Future and Dan at Genomics Law Report, and its apparent outcome has sparked furious debate elsewhere. The discussion among the “independent” panel convened at the meeting appeared to converge on the proposal that all health-related genomic tests should be ordered and reported through physicians. However, the outcomes of the meeting in terms of FDA policy remain unclear, and one FDA official has indicated that decisions about the availability of genetic tests will be made on a test-by-test basis.

There is no doubt that the appropriate regulation of personal genomics tests is a complex issue, and there is a diversity of opinion about how best to achieve it within GNZ (as there is throughout the genomics community). However, there are several points we agree on:

  • Individuals have a fundamental right to access information about themselves, including genetic information. While it is important to also consider the accuracy, interpretation, validity and utility of tests, this underlying principle should guide policy.
  • There is currently no evidence that DTC genetic tests pose a danger to consumers. A recent study of over 2,000 participants in DTC testing concluded that “testing did not result in any measurable short-term changes in psychological health”. In the absence of any evidence of harm there is no justification for restricting individual autonomy.
  • DNA does not have magical powers, and does not require special treatment simply by virtue of being DNA. Genetic exceptionalism – the idea that genetics must be treated as special under the law – is an inappropriate basis for policy-making. Tests should be regulated appropriately based on their predictive power, utility and potential for harm, all of which are related concepts.
  • As DNA sequencing becomes cheaper, the line between medical and non-medical testing will continue to blur. Excessive regulation of health-related genetic tests could also unncessarily hinder the ability of people to access their entire genome sequences for other purposes (such as genetic genealogy).
  • Most clinicians do not have the appropriate knowledge to interpret genomic tests, particularly in healthy individuals. This point is almost universally agreed, even by the FDA, and has certainly been the experience of some of the GNZ members upon taking our genetic results to doctors. Physicians in general are therefore a strange choice for ‘guardians of the genome’.
  • Most early adopters of DTC genetic tests are sufficiently well-informed to understand the implications of a genomic test and interpret the results correctly. Putting a general physician between these informed individuals and their own genomes is paternalistic and unnecessary.

While the outcome of the FDA’s deliberations remain uncertain, it is clear that there will be intensive lobbying against any attempt at excessive legislation. In the worst case scenario, the fledgling and innovative personal genomics market could be crushed by the FDA. However, there is still plenty of room for a measured approach that enforces test accuracy, punishes false claims and promotes informed choices by consumers, without reducing the ability of responsible companies to continue to operate and innovate.

We urge others in the genomics community to make their voices heard on these issues. Let the FDA – and, if you’re based in the USA, your political representatives – know that regulation of genetic testing should be based on evidence, not fear, and that any attempt to unreasonably restrict your access to your own genetic information is unacceptable.

Why DTC genetic testing is good for research

I’ve been reading with interest Daniel’s coverage of the recent FDA hearings into DTC genetic testing. In this context, both he and Razib Khan are incensed by a video which seemingly shows an FDA official misleading Congress about the research done by 23andme:

You can think what you want about the value of the research done to date by 23andme [1], but in my mind, there’s one simple reason why the sorts of participant-driven research they’re doing can only be a good thing: all research is driven by curiosity, and the people most curious about a disease or trait are those who have it. While people may think of the academic research community as a machine with endless resources and limitless motivation, it’s not. People work on things they think are interesting; they sometimes follow “trendy” topics, or move into fields with more grant money, or get bored of a given problem and move on. So if the research in the trait you’re most interested in isn’t moving fast enough for you, well, tough luck.

Recall that one of the key players in the discovery of the gene for Huntington’s disease was a foundation started by a man whose wife had the disease (startlingly, the current president of the foundation apparently accused DTC companies of “raping” the human genome during the present FDA hearing). Recall also that James Lupski, curious about the cause of his Charcot-Marie-Tooth disease, simply sequenced his own genome to find it. These are simply well-connected and trained people driven to find a gene involved in a disease. Patient communities that currently exist are also curious and driven, but in many cases are dealing with complex diseases that are amenable to genetics only with large sample sizes and extensive organization; what these communities can now do is outsource, in a sense, their research to 23andme (see, eg., 23andme’s Parkinson’s study). For scientific knowledge, this can only be a good thing.

[1] To date, the novel associations discovered by 23andme are in hair morphology, freckling, photic sneeze reflex, and “asparagus anosmia”. What these things have in common is that they’re biologically interesting, but not particularly medically interesting; it’s pretty much only curiosity that would drive you to map these traits. Medical researchers tend to scoff at this sort of thing; I think it’s actually pretty cool.

Our favourite papers of 2010

To celebrate the end of the blogging year here at Genomes Unzipped, we wanted to spend a bit of time reminiscing about the papers we enjoyed the most in 2010. Feel free to add your own suggestions in the comments!

Joe: Mice, men, and PRDM9. A key goal in evolutionary biology is to identify the mechanisms leading to speciation. One way to get at that goal is to identify genes that cause sterility or reduced fitness in hybrids between species or diverged populations. In mammals, exactly one such gene has been identified to date: the DNA-binding protein PRDM9. This year, three groups working on a seemingly different problem–deciphering the molecular mechanisms by which recombination shuffles genetic variation between generations–stumbled across an important gene in this process: PRDM9. Variation in this gene influences recombination patterns in both mice and humans, and is responsible for the dramatic differences in recombination patterns between humans and chimpanzees. Is it a simple coincidence that a gene which influences recombination also appears to have a role in speciation? Time will tell.

Parvanov et al. (2010) Prdm9 Controls Activation of Mammalian Recombination Hotspots. Science. DOI: 10.1126/science.1181495.

Baudat et al. (2010). PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice. Science. DOI: 10.1126/science.1183439.

Myers et al. (2010). Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination. Science. DOI: 10.1126/science.1182363.

Daniel: Whole-genome sequencing to develop personalised cancer assays. The area of medicine where the transforming power of new DNA sequencing technologies is moving the fastest is in cancer diagnostics and therapy. There were many studies relevant to this field in 2010 (with a fair proportion featuring on the excellent MassGenomics blog), but this paper was a simple, elegant example: the authors performed low-coverage whole-genome sequencing of four tumour samples, identified large genomic rearrangements present in the tumour cells but not in the patient’s healthy tissue, and then designed personalised, quantitative assays measuring the proportion of cells carrying these rearrangements in the patients’ blood. These assays allowed them to track, almost in real time, how the patients’ cancers responded to various therapies, like so:

Leary et al. (2010) Development of personalized tumor biomarkers using massively parallel sequencing. Science Translational Medicine. DOI: 10.1126/scitranslmed.3000702.
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The cell is a messy place: understanding alternative splicing with RNA sequencing

Though this site is largely dedicated to discussions of personal genomics, I’d like to use this post to discuss some of my recent work (done with Athma Pai, Yoav Gilad, and Jonathan Pritchard) on mRNA splicing. Our paper, in which we argue that splicing is a relatively error-prone and noisy process, has just been published in PLoS Genetics [1].

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Friday Links

A quick note about the Reader Survey; we are going to stop taking responses at the end of Saturday (Pacific Time). If you haven’t already done so, please fill out the survey now.

A couple of interesting articles this week on the Personal Genome Project and public genomics in general. Mark Henderson at the Times has an opinion piece (behind a paywall, I’m afraid) about Misha Angrist‘s book Here Is A Human Being (see also this review from The Intersection), and in the Duke Magazine Mary Carmichael has an in-depth feature on the work of George Church, with some interesting history of the early days of the PGP.

One aspect that comes out of these articles is how those who take part in public genomics projects are starting to own the unknown unknowns. They accept that they cannot anticipate all the risks of making their data public, but are willing to take the risk of exposing themselves to these unknown risks, and in doing so turn them into knowns. Another aspect is the sheer number of individuals who want to sign up to have their data published online: 15,000 people have expressed interesting in being part of the PGP, despite initial NIH concerns the no-one would want to take part at all. This also chimes with research presented at ASHG this year, showing that members of the public are more concerned with contributing to scientific knowledge, and, crucially, getting access to their own genetic data than they are about the potential risks that such data could expose them too. [LJ]

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Am I partly Jewish? An unexpected turn of events

In my last post, I discussed how I used 23andMe data to test hypotheses about my ancestry. In particular, I was intrigued by Dienekes Pontikos’s result suggesting that I (and my colleague Vincent) might be partly Ashkenazi Jewish. Ultimately, however, I concluded that his algorithm was not properly modeling my southern European ancestry (inherited from one Italian grandparent), and that this was leading to a spurious result.

I was wrong.
Continue reading ‘Am I partly Jewish? An unexpected turn of events’

Am I partly Jewish? Testing ancestry hypotheses with 23andMe data

I agreed to make my 23andMe genotyping results publicly available as part of GNZ without a moment’s hesitation. This is in part because I knew the results were actually a bit dull (in a good way, I suppose) – I’m not at vastly increased or decreased risk for any diseases (based on research so far), and I was unsurprised to find out that I have blue eyes. I was also unsurprised that 23andMe identified me as most likely of north European ancestry.

Several hours after we released our data, however, I was pointed to a post where Dienekes Pontikos wrote about the results of running all our data through his ancestry prediction program. While just about everyone was quite confidently predicted to be almost entirely of northwestern European descent, this analysis gave me a point estimate of 20% Ashkenazi Jewish ancestry. Within hours, several people had asked me about this, and I had no real response. So I decided to take a look at the data myself; some basic analyses are below.
Continue reading ‘Am I partly Jewish? Testing ancestry hypotheses with 23andMe data’

Friday Links

Over at 23andMe’s blog The Spittoon, Stanford genetics professor Uta Francke has a great point-by-point dissection of the new policy statement of the European Society of Human Genetics on direct-to-consumer genetic testing. Francke doesn’t shirk from explaining that this statement should be seen in the context of an ongoing turf war between traditional geneticists and DTC upstarts:

For example, organizations like ESHG, the American Society of Human Genetics (ASHG), and the American College of Medical Genetics (ACMG) were created to represent the interests of their professional membership, similar to the American Medical Associations (AMA) for physicians. Any claims to act in the public interest by protecting people from potentially damaging genetic information may reflect a fear of the new consumer-driven healthcare system that, as in the case of DTC genetic testing, may circumvent the professional establishment. Insisting on individual professional counseling in the pre-testing and post-testing phase can be interpreted as an attempt to ensure continued involvement of board-certified genetics professionals. [DM]

In PLoS Genetics, researchers report that a SNP associated with risk for colorectal cancer likely exerts its effect by modifying the expression level of a nearby gene. Previous studies on a different region associated with both prostate and colorectal cancer revealed a similar mechanism (see here, for example). This contributes to growing molecular evidence that SNPs with long-range regulatory effects might be generally important in disease. [JP]

Kevin Davies’ superb new book The $1000 Genome is now available on Amazon. Keith Robison has already posted his review, and I’ll have my full thoughts here on Genomes Unzipped soon – but for now I’ll just say that Davies’ long and extensive experience working the genomics beat really pays off, with both a wealth of inside information and juicy anecdotes about the key players in the field. Well worth a read for anyone interested in modern genomics (i.e. everyone reading this post). [DM]

Dan Koboldt of MassGenomics has a useful review of the recent Cold Spring Harbor Personal Genomes meeting. He pulls out four key themes emerging from the conference: new estimates of human mutation rates, more sequencing of cancer genomes, studies of genome regulation and epigenetics, and an explosion of exome sequencing in both severe and common diseases. [DM]

Our own Dan Vorhaus reports on the utterly bizarre decision by Health and Human Services (HHS) Secretary Kathleen Sebelius and NIH Director Francis Collins to discontinue the Secretary’s Advisory Committee on Genetics, Health, & Society (SACGHS). Inexplicably, Sebelius and Collins argued that “the major topics related to genetic and genomic technologies had been successfully addressed by the committee through its comprehensive reports and recommendations over the years”. Vorhaus notes diplomatically that “it is clear that even those issues SACGHS investigated in detail have not been resolved with any meaningful degree of finality”. [DM]

Detecting positive natural selection from genetic data

As humans expanded out of Africa into the rest of the world, they adapted to a whole host of new habitats, pathogens, and food sources. In recent years, there has been an explosion of interest in identifying the specific genetic loci underlying these adaptations using whole genome genotyping (and now sequencing). In this post, I’ll outline some of the basic principles of how these methods work.

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How widespread personal genomics could benefit molecular biology

While the majority of the buzz surrounding personal genomics has to do with prediction of disease risk and other medical applications, there’s clearly the potential for these sorts of technologies to influence basic science as well. In this post, I’ll lay out one such potential application: the use of personal genomics in understanding basic molecular biology, in particular the biology of transcriptional regulation in humans.

Continue reading ‘How widespread personal genomics could benefit molecular biology’


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