Misha Angrist's Blog

August 10, 2012

A note from PLOS Blogs Community Manager Victoria Costello: We’re sad to see Misha Angrist leave our blog roster but we’ve been honored to host the last two years’ of his Genomeboy posts, which will remain here on PLOS Blogs for our readers to find and enjoy into the future.  Misha blends mastery of genetics with a clear ethical compass, a keen wit, and a big heart – with all of these qualities evident in his last post for us, titled A Mayan Discovery, about a crowdsourced effort to uncover the cause of one little girl’s rare genetic disorder. We wish him well in his next blogging endeavor.


Egrets…I’ve had a few. But then again…


Aw shucks. If there’s one emotion I’ve associated with Genomeboy since its original launch, it’s sheepishness. Ach, you know, I had such ambitions: I would post regularly and fervently, I would be Part of the Conversation. And sure, I’ve had my moments but let’s not soft-pedal it: I am an inconsistent blogger at best. Time and again I’ve read something and thought “I should blog about that” only to have the idea and impulse evaporate in an instant. Thus has Genomeboy come to be enveloped by peeling paint and the sound of crickets. My congenial hosts at PLOS have indulged my sloth and quasi-functional ADHD for almost two years. They have higher expectations as well they should. I appreciate their unflagging support and willingness to stick with me.


Like so many other folks I have assorted demands that only seem to multiply: a family and a day job and students and grants and articles and meetings and a dog and even a band of sorts (!) calling my name. As well they should. In no way am I complaining–this is how life is and mine is blessed in all kinds of ways. But I have not made sustained blogging a part of it for quite a long time and so I think it’s only fair that I stop taking up space in the Hotel PLOS.


I expect I will continue to cause trouble and make noise in various public forums. As a reader, however, I will not abandon this one. I am deeply indebted to my fellow PLOS bloggers both for their sublime literary gifts and especially for their sense of community. As always I look forward to whatever they do next.


I cannot express how grateful I am to you for reading and hanging out.


Good night and good luck.


 



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Published on August 10, 2012 05:53 • 52 views

July 26, 2012


Thanks to a mutual friend (hi Fred!), last night I had the pleasure of hearing, meeting and dining with Sir Gary Brooker, singer and co-writer of “A Whiter Shade of Pale,” and leader of the criminally underrated British band Procol Harum. He was in outstanding voice, which was remarkable given not only his age (67), but the fact that he fractured his skull in late May (on his birthday!), was in critical condition for a while, and almost had to cancel this entire tour. He was a total mensch and keen to chat about the Olympics and the ridiculous things the games have , exploits from days of yore, science fiction, and anything else. He and his wife of 44 years, Franky, could not have been more charming. Clearly he didn’t get the memo that rock stars are supposed to be self-absorbed and stand-offish. Thanks and godspeed, Sir G.



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Published on July 26, 2012 14:32 • 27 views

July 25, 2012


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Published on July 25, 2012 03:20 • 29 views

July 20, 2012

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Published on July 20, 2012 05:09 • 19 views

July 17, 2012

Maya is a four-year old delight. She’s wiggly and giggly and has a partner in crime, her dog Parker. She loves animals, other kids, being naughty, and life as a whole.


She has also undergone multiple operations, does not speak, and is developmentally delayed. No one knows why. As her mother Dana wrote a couple of weeks ago, “When you’ve been looking for the answer for three and a half years, you don’t really expect one anymore.”


But maybe the search is nearing an end. With fundraising and logistical help from the Rare Genomics Institute, researchers at Yale have sequenced Maya’s exome, i.e., the entire protein-coding part of her genome. They appear to have identified a de novo (not seen in the parents) nonsense (one that presumably causes no protein to be made) mutation in a gene implicated in fetal and childhood development. As far as anyone knows, this particular variant has never been seen before, though, as RGI founder Jimmy Lin says, much remains to be done.


What is arguably just as impressive is that this exome sequencing was crowdfunded: RGI solicited donations on its website and within six hours raised more than $3500. If you’re so inclined (and it will make you feel good, I swear), Gram is within striking distance!


(Photo from Uncommon Sense)


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Published on July 17, 2012 10:36 • 24 views

June 19, 2012

In PLoS Medicine Basu et al report on a systematic meta-analytic comparison of private and public health care systems in low- and middle-income countries such as Viet Nam, Namibia, Tanzania, Sri Lanka, Bangladesh, India and Peru. They extracted data from 102 publications and divided their findings into six health care-system themes: accessibility and responsiveness; quality; outcomes; accountability, transparency, and regulation; fairness and equity; and efficiency.


Yes, meta-analyses are fraught with all sorts of hazards and require all sorts of caveats. But what did the authors find? Private health care systems were less likely to publish data reflecting their performance and tended to serve people in higher socioeconomic classes. Public sector health care systems were less likely to be responsive to patients and more likely to lack equipment, medications, and trained health care workers. Both public and private sector systems lacked accountability and transparency. Duh.


Private health care systems were more apt to deliver low-quality care, to be less efficient (!), to pose greater risks of complications and to incentivize (yeah that’s a word) unnecessary testing and treatment. Sound familiar? Providers in the private sector more frequently violated medical standards of practice and had poorer patient outcomes…but they were more timely and hospitable. Yeah baby!



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Published on June 19, 2012 19:57 • 28 views

June 17, 2012

Last week I was at the National Cancer Institute Think Tank on the Identifiability of Genomic Data and Biospecimens, a gathering of a few dozen people aimed at hashing out how human tissue and genomic data should be handled in the era of dirt-cheap DNA sequencing and ubiquitous sharing of information. It was fascinating, exhilarating, frustrating and exhausting.


The current rules that govern how tissue and data are managed, whether by design or not, encourage the severing of the links between research participants and those who study them. As most of y’all know, I think this is a mistake, and in my keynote speech I said as much to my colleagues in Rockville:


My position is this: genetic privacy is a red herring. That’s not to say that it’s not important or that it should be abolished, but let’s look at it for what it is: a legacy of the abuses perpetrated by the 20th-century eugenics movement that has become a convenient way to limit institutional liability. It begins from the premises that data about human beings 1) can be kept private; and 2) should be kept private. At all costs. Lock it up and throw away the key unless, you know, someone might die and we might get sued. It makes no allowances for where the locus of control over this information lies or whether it should change, let alone whether it can change. But we are here today because we are up against a new reality: Traditional genetic privacy cannot assimilate a Facebook-driven world, let alone one driven by empowered patients and research participants who suddenly have an array of choices.


 



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Published on June 17, 2012 17:02 • 24 views

June 4, 2012


In April I attended the Genomes Environments Traits conference, along with a couple hundred other people, many of whom were and are participants in the Personal Genome Project. This was the first year that GET felt more like a coming-out party than a cultish gathering of fringe -omics enthusiasts.  Yes, there was still a bit of a dewy-eyed utopianism  and yes, there were some people there who didn’t seem to fully grasp what the PGP is about, but the point is: they were there. They were invited to a meeting with the researchers who were studying them and the meeting was free. It was, to borrow a phrase, “…an opportunity to foster symmetry of knowledge and learning processes between purported experts and non-experts.”


At GET participants had the chance to participate in various additional studies, including this one:


Autodesk and Iowa State University conducted real-time 3D video scans of the faces of attendees at the GET Conference. As part of the exhibit, a fun experiment was tried where attendees were asked to make different faces for about 10 seconds, always the same faces, so that the data could be compared later. This fun exhibit could have a concrete real world application in the future tied to the newest scientific innovation in connection to the Personal Genome Project.


That’s my psychedelic punim above. And yes, this kind of stuff is actually useful in the clinical realm.



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Published on June 04, 2012 05:54 • 40 views

May 27, 2012

Durham–the whole Triangle really–has so many amazing bands…like this one.



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Published on May 27, 2012 16:20 • 18 views

May 25, 2012

25 May 2012


Amy Gutmann, PhD

Chair, The Presidential Commission for the Study of Bioethical Issues

1425 New York Avenue NW

Suite C–100

Washington, DC 20005


Re: Comments on the ethical issues raised by the ready availability of large-scale human genome sequence data, with regard to privacy and data access and the balancing of individual and societal interests


Dear Dr. Gutmann:


Thank you for guiding The Presidential Commission for the Study of Bioethical Issues’ consideration of the ethical issues raised by the ready availability of large-scale human genome sequence data. That the Commission is willing to take up such an acutely important issue and in doing so to hear testimony from citizens outside of the ossified academic bioethics community (e.g., Genomera CEO Greg Biggers) gives me hope.


My message is a simple one and it echoes closely the one conveyed by two notable patient activists. Genetic Alliance President and CEO Sharon Terry has launched a campaign called “That’s My Data!” (I might have said, “Those Are My Data!,” but no one asked for my grammatical input). And “terminal” cancer patient Dave deBronkart (aka “e-Patient Dave”) has, in no uncertain terms, demanded: “Gimme my damn data!”


Whether Terry and deBronkart are talking about controlling access to their own biospecimens, genomic research data derived from those biospecimens, secondary findings of clinical import, secondary findings of no apparent clinical import, or even raw sequence data, is not necessarily clear to me. But I would argue that neither does it matter: they are entitled to do any and all of the above. Those samples and that information were derived from them and whether the setting was a research laboratory, a clinical laboratory or a garage is mostly beside the point. If anyone “owns” that information and those tissues, it is the people from whom it came. Not only have they subsidized the genomic research that has made such sample and data collection possible, but they have given of their time, consented to risk, and placed their faith in a research enterprise that, with few exceptions, cannot make ingenuous promises of health benefits other than in some vague “future.” Meanwhile in the clinical setting, at this moment laboratories are charging thousands of dollars for exome sequencing and in many (most? all?) cases not granting patients (or their physicians) access to their entire exomes. This “ostrich paradigm” is neither just nor sustainable.


The most salient counterargument, of course, is that granting patients and research participants unfettered access to their samples and data/results will pose too great a burden on researchers and clinicians. I am not naïve: what I propose will not be easy. It will require years, a wholesale change in culture, and a discrete break with our longstanding American tradition of genetic determinism.


But the status quo has already been shown to be untenable. We know from multiple studies that DNA is inherently identifiable, yet the present Common Rule/HIPAA-based system presumes to share de-identified data with everyone except the patients and participants themselves (I see this in IRB meetings every month). Is it not impossible to frame such an approach as one that maximizes participant/patient autonomy?


Embedded in the PCSBI’s request for comment on the widespread availability of DNA sequence data is a fallacious assumption: that individual and societal interests must be “balanced.” I don’t think one needs to be a fire-breathing libertarian to contend that, at some level, individual interests are societal interests. Consider amniocentesis. As recounted by Ruth Schwartz Cowan in her book Heredity and Hope, amniocentesis was not routinely offered to pregnant women over the age of 35 until such women who were not offered amniocentesis and subsequently gave birth to babies with severe anomalies began to sue doctors and hospitals. It is not hard to imagine a lab or investigator being similarly targeted for litigation after choosing to withhold DNA sequence information from a patient or research participant who goes on to develop a serious genetic disease that full disclosure might have mitigated.


The reality is that the cost and technical barriers to generating sequence data have fallen to the point where large societal institutions—research universities, clinical laboratories and commercial firms—can no longer keep such data and knowledge enclosed. There is a reason that entities like the Personal Genome Project and PatientsLikeMe that collect biological data without guarantees of privacy and confidentiality—but with unprecedented participant access and involvement—have grown exponentially over the last five years.


I hope the Commission will acknowledge such realities as it confronts the postgenomic world. I thank you for your consideration.


Sincerely,


Misha Angrist, PhD, MFA



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Published on May 25, 2012 11:25 • 24 views