Parallel Dataverses: Doppelgangers in Medicine and Recreation

Dr. Egon Spengler: There’s something very important I forgot to tell you.
Dr. Peter Venkman: What?
Dr. Egon Spengler: Don’t cross the streams.
Dr. Peter Venkman: Why?
Dr. Egon Spengler: It would be bad.

Some regulatory regimes in the United States, like those in the state of New York, require laboratories that receive and analyze any tissue specimen for any purpose to adhere to standards of clinical medicine. The laboratories are, for example, required to follow quality measures defined by the Clinical Laboratory Improvement Amendments (CLIA). Furthermore, individual citizens are prohibited from ordering laboratory services directly. They must, instead, work through a state-appointed and licensed physician if they seek to obtain personal biological data.

This restriction does not depend on the intended use of the data. An individual who wants to have the DNA in their saliva analyzed for recreational purposes, like genealogy or ancestry or education, still must work through a physician.

This has resulted in the paradoxical situation of non-clinical, clinical genetic testing. “Don’t cross the streams,” Dr. Egon Spengler would say. Well, the streams are already crossed and its time, I think, to uncross them. Biological data for non-medical purposes needs a paradigm distinct from the medical domain.

Here are a few reasons why this proposal should be strongly considered:

(1) Physicians are overburdened as it is, there is no need from them to be involved in recreational activities like genetic genealogy.

(2) Ditto for governmental regulatory bodies that are charged with ensuring the quality and safety of medical products and practices.

(3) Autonomy of individuals is being restricted unjustly.

(4) Enforcing clinical standards on non-clinical activities puts an unfair burden on individuals who may want to specifically avoid clinical implications of genetic sequence data, which might include the discovery of a medically relevant genotype (e.g., male infertility and genealogy testing) and health insurance liabilities.

So, what do you think? Should uncrossing the streams be an initiative we support? What are other reasons why this may or may not be a good idea?

3 modes of sharing genetic information

In order to understand the risks of obtaining and sharing personal genetic information, a few words are in order about the different types of sharing that are possible.

In general, there are three modes for sharing genetic information.

1) No disclosure

This might be referred to as the cupboard drawer strategy. A person gets sequenced, their data is shipped to them on a DVD, and they stick this DVD in the cupboard drawer. Data is kept private and not shared at all. Not very useful.

Conceivably, one day there might be software available for home computers, for those who are paranoid about sharing their genetic data but still seek knowledge that may be gained from genomic interpretation.

2) Controlled disclosure

Medicine, recreation, and the advancement of science are all reasons for sharing personal genetic information. Giving access permissions to specific individuals or groups of individuals, including organizations, is called controlled disclosure. Individuals with access permission will be responsible for being good data stewards.

Examples of data stewards might be:

3) Uncontrolled disclosure

This category of information describes the situation that personal genetic data is made publicly available, by publishing on a website for example. To be clear, publishing a personal genome sequence on a public website may be a conscious act, and is controlled in that way, but once the data is in a public forum where anyone has access, disclosure itself becomes more or less uncontrolled.

Uncontrolled disclosure also describes any situation where access is gained by individuals without explicit permission, through hacking or the carelessness of a data steward for example.

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This month I am doing an extended meditation about the risks of obtaining and sharing personal genome sequences. This exercise will be cathartic for me. Beyond that, I hope it may help to reorient the conversation about risks into something that one day might resemble practical guidance for individuals considering obtaining and sharing personal genetic information.

Best Sentence I Read Today on “Onlineness”

“Controlling your life online isn’t about a set of guidelines for everyone to follow. It’s about being aware of where you might be giving up control and making conscious decisions.”

This is taken from an excellent meditation by Vanessa Fox on living life online (she tagged the post “onlineness” which I had to look at a couple times to find the root word).

One topic she touched on briefly is how a person’s online activity can reach beyond the individual and touch the lives of others. What is acceptable practice in these circumstances? People disagree. Here is a clip:

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Nom de Ome: A pseudonym for your genome

How common will genomic pseudonyms be in 25 years? When might a person choose to use a Nom de Ome?

In some sense, the Human Genome Project’s human genome reference sequence has a nom de ome (which is “human genome reference sequence”). This sequence was generated mostly from a tissue sample donated by an anonymous male from Buffalo, NY. This volunteer was likely solicited from a newspaper article that ran in the Buffalo News on March 23, 1997. Here are the opening words from that article:

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The gene is dead…oh wait…alive but sloppy

The concept of the gene almost died this morning. I was just sitting at my desk minding my own business, reading a journal article when, blam!, the gene was dead. Well almost — turned out to be more of a near death experience. I’m sorry to report there was no white light or anything mysterious like that. But there was coffee, so thats good.

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Can a personal genome sequence get a creative commons license?

The short answer is no. There is a long essay waiting to be written here. But for now, I can say that the reason it will not work is because there is no clear legal foundation to build a license on top of when it comes to sequence data. Creative Commons licenses have copyright to build on. Material Transfer Agreements (MTAs) have good old fashioned property law to build on (turns out important things still exist outside of the bitsphere). A personal genome sequence is, well, just bits. (Update: Or lifebits? I love the term)

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False Alarm: The Celebrity Meme

There is this meme that has been going around about how “celebrity genomics” is in some way very naughty and should be avoided. This meme keeps popping up since it was first inaugurated in a news article by Erika Check entitled “Celebrity genomes alarm researchers”. Here were some of the quotes from that article:

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Richter Scale and Your Genomic Portfolio

The field of personal genomics needs a richter scale. This scale would provide a mechanism for giving each new genomic association a score, maybe from 1-10, based on some criteria such as penentrance, actionability, and validity. Existing genetic tests should be scored as well. Commercially available tests might have additional criteria, like whether there is an FDA-approved test or whether the test is reimbursed.

The higher the score the “better” the association or test. A low score might indicate that the association is very likely just “noise” regardless of the fact that it was all over your morning newspaper.

This scale will be very handy once you have a copy of your own genome. Let’s be honest, if you’re sipping on your morning cup of coffee, reading the paper, and see an article about a newly discovered “gene for alzheimer’s” or “snp for sudden stroke”…you’re going to be compelled to run over to your computer to see if your genome possesses that genetic variant. Without a good way to quickly judge the relevance of the news article, journalistic sensationalism may have you running over to your computer several times a day. That doesn’t sound like a very good use of time, does it?

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Can I see some ID?

Should there be a minimum age requirement for personal genome sequencing? If so, what age?

Or maybe that question is irrelevant — or only relevant for the next decade or two. Future generations might get sequenced at birth (or maybe even prior to birth via PGD). That might leave no individual choice about personal sequencing, in which case, maybe there will be regulations about the minimum age for disclosure of personal genomic data to individuals. 13? 18? 21? 30? What age?

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Oh the horror

I just looked at Jim Watson’s genome I think. Thats not the scary part. What is shocking to me is how much work we have to do in order to make a user interface to human genomes that doesn’t make my head spin.

Sequencing is quickly becoming the easy the part. A freshly liberated ladder is of little help if I can’t figure out how to use it. We need more genomic cartographers.

The Genomic Cartographer:
1 part bioinformatician
1 part beautician
mix and serve

Update: This Genome Browser is looking promising.

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