Do-it-yourself genomics: bad advice is bad advice

GenomeWeb's frequently entertaining Daily Scan notes that Wired magazine has a wiki which gives instructions on how to explore your own genome, including how to do your own genetic testing by home-PCRing your DNA and sending it to a contract lab for sequencing.

It isn't a very good idea, but that doesn't mean people won't try it. Doing a simple PCR really is pretty easy; I've done it in a hotel ballroom (proctoring a high school science fair sponsored by Invitrogen). Instructions for homebrew thermocyclers are surely out there; a number were published in the early days of PCR. But that doesn't mean getting good results is easy. Sticking to a purely technical level, are Wired's instructions very good?

I'd say no. I suppose I should even register to edit the wiki, but at the moment I'll limit myself to pointing out some of the technical issues that are ignored or glossed over (the material I quote below may well change, since it is a wiki).

The first obvious area is primer design. Wired's instructions are pretty simple

Designing them may be the hardest step. Look up the DNA sequence flanking your genetic marker of interest in a database like dbSNP. Pick a segment that is about 20 bases long and slightly ahead of the marker. That is your forward primer. Pick another 20ish base sequence that is behind the region of DNA that you want to study. Use a web app of your choice to find its reverse complement.

Alas, this will frequently be a recipe for disaster. As for my own qualifications for making that claim I will state that (a) I regularly design PCR amplicons in my professional life and (b) I have a much greater appreciation for my ignorance about how PCR can go awry than the average biologist. Leading the list of pitfalls is designing a primer with too low a Tm -- if those 20 nucleotides are mostly A & T, it won't work well. Second would be if the two primers will anneal to each other; you'll get lots of primer-dimer and little else. Equally bad would be a primer that can prime off itself. Third would be if the primers aren't specific to your targeted region of the genome. Prime off a conserved Alu piece and you are in real trouble.

The really silly part about this advice is that there are free primer design programs all over the internet, and some of the sites will perform nearly all of the checks mentioned above.

The rules for placement are much trickier than suggested. If you are going to sequence (and you might be sequencing heterozygous DNA; see below), then you really need the primers to be at least 50 nucleotides away from what you care about -- there is a front of unincorporated dye which often drops the quality any closer than this.

Even more of a concern is the sequence data itself. Wired makes it sound easy

Once that's done, you can buy sequencing equipment and do it yourself, or send the sample off to any one of many sequencing companies and they will do it for about five dollars.

If you are sequencing uncloned PCR products, then you are sequencing a population. If you are heterozygous for a single nucleotide, that means that nucleotide will read out as a mix -- two overlapping peaks of perhaps half height. A deletion or insertion ("indel") will make the trace "double peaked" from that spot on.

Those are the best case scenarios. If you had poor quality amplification (due to badly designed primers or just a miserable to amplify region), all those truncated PCR products will be in the sequencing mix as well -- further degrading your signal. If your SNP is in a region expanded due to copy number variation, then life is even harder.

Which gets to another point: Wired seems to be ignorant of copy number variants. Their testing recipe certainly won't work there.

The idea of untrained, emotionally involved individuals trying to interpret good genetic data is scary enough (Wired's example of celiac disease, as pointed out over at DNA and You, is a particularly problematic one); scarier is to overlay lots of ambiguity and error due to sloppy amateur technique. Hopefully, few will have the energy & funds to try it.

Just how wrong is Marilyn vos Savant?

Marilyn vos Savant is a writer of a regular column in Parade magazine. These columns address many things, but often have interesting logic puzzles. Given that she is claimed to have the highest recorded IQ ever, whole sites have sprung up to find fault with her writings. Now, I'll confess I'm always looking for an angle -- and rarely finding one.

But this past Sunday, she gave me a bit of an opening: in response to a question as to whether there are any beneficial viruses. Her response:

No. Bacteria are living one-celled microorganisms. By contrast, viruses aren’t alive in a strict sense: They are the ultimate parasites and cannot replicate without a host. They invade the cells of animals, plants and even bacteria, then either lie dormant or get into the driver’s seat and cause changes that disrupt normal cell functioning, the very essence of disease.

The first two sentences and most of the third are dead on the money: bacteria are unicellular organisms, viruses aren't considered alive & invade other cells, where they can lie dormant or immediately go crazy. However, that last bit is the clincher. Apparently Ms. vos Savant is unaware that in the bacterial world there are examples of viruses benefiting their host by bringing along useful genetic stuff. Diptheria is one example, in which the toxin (which presumably helps the bacterial host) is encoded by a virus (phage).

Are there examples outside of bacteria? I don't know of any, but I'm hardly up on my viruses. Moreover, how would we know? Suppose there were viruses which were simply neutral (or nearly so), would we have ever detected them?

Also, in a broader sense some of those phage out there may be an important ecological control on bacterial nasties. So this could be another class of "beneficial" viruses.

Just because you are a parasite doesn't mean you're guaranteed bad!

Turn Right on Main, Then Left at Chromosome 4

It's apparently been up since April, but I just stumbled on the Cambridge Genome Trail. Running down the main commercial spine of Cambridge from Harvard to MIT and through much of biotech country (but far enough away from my current office that I didn't see it sooner), the trail consists of large wrap-around banners on lampposts with descriptive text at street level.

The Boston area also has a permanent scale model of the solar system. I don't believe there is an atom or periodic table; perhaps they will show up in the future. Truly Quixotic would be to attempt to model the protein interactome of even a small creature -- too many interactions which are being added to too quickly!

Biotech at the Movies

I won't claim to be a connoisseur of the cinema, but I enjoy a good movie. I don't get to the cinema much, but my Netflix queue should keep me busy for a long time.

Biotechnology doesn't show up much in the movies. The reason is simple: biotech isn't very cinematic. The drama is slow and not photogenic. Most movies with a biotech angle are science fiction, with the biotech not exactly wearing a white hat: think Gattaca or Jurassic Park.

Once in a while biotech shows up in a movie which isn't generally sci fi. For example, in Family Business grandfather Sean Connery and father Dustin Hoffman are trying to convince their biologist son, Matthew Broderick (who I once had a very slight resemblance to -- twice I had strangers say I almost looked like him) to abscond with a plasmid from his company. The lab settings, as I remember, looked pretty reasonable.

At the other end of the spectrum is Mission Impossible II, which had me out of breath from laughing, though I doubt this was the intent of the director. The evil biotech company devising some devious human virus has two facilities which Tom Cruise's character must raid. The first one is in an amazing downtown high-rise -- yeah, the VCs would spring for that. The second is a cave-like seaside complex, with dripping water & bats living in the eaves. Yes, the perfect place for propagating mammalian viruses via cell culture!

If you want to see some actual biotech space, though not fitted out for such, then go watch The Spanish Prisoner. The MacGuffin driving the plot is a secret formula -- whose very field of relevance is never mentioned -- which disappears & is chased through the rest of the movie. The company digs at the beginning of the movie are at One Kendall Square, just across the courtyard from my current workplace. If I'm not mistaken, the shoot was in the space which currently houses next generation sequencing shop Helicos Biosystems. This was once Millennium space, a common history for much biotech space in Cambridge, and one group setting up there was familiar with its history & let me in on the secret. Alas, their plans for a Spanish Prisoner screening there were short-circuited by one of the first rounds of 'reshaping'.

Coincidentally, I first saw The Spanish Prisoner while flying to Europe on a Millennium business trip, though even more appropriate would have been to see it at the cinema which is part of the One Kendall Square complex. We had the space then, though I was unaware of its history. I like the movie -- the language has a distinctive rhythm of Mamet but without (if I remember correctly) the torrents of foul language that characterize some of his other movies (though I do like Glengarry Glen Ross, which should be mandatory watching before contemplating any real estate transaction!).

I'm sure this isn't a comprehensive survey of cinematic biotech. Anyone got any other favorites?

Pigs & Flies in the News

Two news items which are not earth shattering, but fun.

In time for the upcoming Year of the Pig a Chinese group has bred GFP-expressing swine. Presumably these are for some clever preclinical imaging studies, but would presumably make for some interesting dishes to eat by candlelight or during power failures. With the multitude of GFP variants around, one could have quite a lively dish!

The Scientist reports (free subscription may be required) that 30K fruit flies were released during a production of the Sarte play 'The Flies' at Brown University. I did a graduate rotation in a fly lab, and 30K flies isn't a tiny quantity (if I remember correctly, a few hundred in a bottle is about the right density, so this is a lot of bottles). I do hope the same group doesn't try to mount a production of Ionesco's Rhinoceros!

Gene Patents

Today's Parade magazine has an article titled "How Gene Patents are Putting Your Health at Risk". The topic of gene patents deserves public scrutiny & debate, but better coverage than this article.

Featured prominently (with a picture in the print edition) is Michael Crichton, whose new book has been touched on previously in this space. Crichton in particular makes a number of concrete statements, some of which are a bit dubious.

First, let's take the statement

A fifth of your genes belong to someone else. That’s because the U.S. Patent Office has given various labs, companies and universities the rights to 20% of the genes found in everyone’s DNA— with some disturbing results.

. The first sentence is just plain wrong, and given its inflammatory nature that is very poor journalism. Nobody can own your genes -- genes, as natural entities, are not themselves patentable. What can be patented are uses of information in those genes. That is a critical, subtle distinction which is too often lost. What can be patented are uses for genes, not the genes themselves, just as I could patent a novel use for water, but not water itself.

Time for the full disclosure: I am a sole or co-inventor on 11 issued gene patents (e.g. U.S. Patent 6,989,363) , many of which are for the same gene, ACE2. Many more gene patents were applied for on my behalf, but most have already been abandoned as not worth the investment. Those patents attempted to make a wide range of claims, but interestingly they missed what may be the key importance for ACE2 (we never guessed it), which is that it is a critical receptor for the SARS virus.

Many of the gene patents do illustrate a key shortcoming of current patent law. When filing a gene patent, we (and all the other companies) tried to claim all sorts of uses for the information in the gene. These sorts of laundry lists are the equivalent of being able to buy as many lottery tickets for free. A rational system would penalize multiple claims, just as multiple testing is penalized in experiment designs. The patent office should also demand significant evidence for each claim (they may well do this now; I am no expert on the current patent law).

Another one of Crichton's claims deserves at least some supporting evidence, plus it confuses two distinct concepts in intellectual property law

Plus, Crichton says, in the race to patent genes and get rich, researchers are claiming they don’t have to report deaths from genetic studies, calling them “trade secrets.”

First, just because some idiots have the chutzpah to make such claims doesn't mean they are believed or enforceable. Second, such claims have nothing to do with gene patents -- such claims could exist in any medical field. Finally, trade secrets and patents are two different beasts altogether. In a patent, the government agrees to give you a monopoly on some invention in return for you disclosing that invention so others may try to improve on it; a trade secret must be kept secret to retain protection and should someone else discover the method by legal means, your protection is shot.

The on-line version also includes a proposed "Genetic Bill of Rights". I would propose that before enacting such a bill, one think very carefully about the ramifications of some of the proposals.

Take, for example,

Your genes should not be used in research without your consent, even if your tissue sample has been made anonymous.

. What exactly does this mean? What it will probably mostly mean is that the thicket of consent hurdles around tissue samples will get thicker. Does this really protect individual privacy more, or is it simply an impediment which will deter valuable research? Will it somehow put genetic testing of stored samples on a different footing than other testing (e.g. proteomic), in a way which is purely arbitrary?

Another 'right' proposed is

Your genes should not be patented.

.
First, an odd choice of verb? "Should"? Isn't that a bit mousy? Does that really change anything? And what, exactly, does it mean to patent "your genes"?

On the flip side, I'm no fan of unrestricted gene patenting. All patents should be precise and have definite bounds. They should also be based on good science. Patents around the BRCA (breast cancer) genes are the most notorious, both because they have been extensively challenged (particularly in Europe) and because the patent holders have been aggressive in defending them. This has led to the strange situation in (at least part of) Europe where the patent coverage on testing for breast cancer susceptibility depends on what heritage you declare: the patent applies only to testing in Ashkenazi Jews.

In a similar vein, I can find some agreement with Crichton when he states

During the SARS epidemic, he says, some researchers hesitated to study the virus because three groups claimed to own its genome.

It is tempting to give
non-profit researchers a lot of leeway around patents. However, the risk is that some such researchers will deliberately push the envelope between running research studies and running cut-rate genetic testing shops. Careless changes to the law could also hurt companies selling patented technologies used in research: if a researcher can ignore patents for genetic tests, why not for any other patented technologies.

Gene patents, like all patents, are an attempt by government (with a concept enshrined in the U.S. Constitution) to encourage innovation yet also enable further progress. There should be a constant debate as to how to achieve this. Ideas such as 'bills of rights', research exemptions, the definitions of obviousness and prior art, and many other topics need to be hashed over. But please, please, think carefully before throwing a huge stone, or volley of gravel, into the pool of intellectual property law.

One Company I'm Not Sending My Resume To

On some site today a Google ad caught my eye -- alas I cannot remember why -- and I found a site for NEXTgencode. However, it doesn't take long to realize that this isn't a real company . The standard links for a real biotech company, such as 'Careers', 'Investors', etc. are missing.

Clicking around what is there leads to a virtual Weekly World News of imaginative fabrications, though some have previously been presented as true by places that should know better, such as the BBC. I think I saw an item on grolars (grizzly-polar bear hybrids) in the press as well. Also thrown in is a reference to the recently published work: "Humans and Chips Interbred Until Recently".

Various ads show products in development. My favorite ad is the one for Perma Puppies, which never grow old or even lose their puppy physique (though their puppy isn't nearly as cute as mine was!). There's also the gene to buy with the HUGO symbol BLSHt.

The giveaway is the last news article, which describes a legal action by the company

Michael Crichton's book "Next" claims to be fiction, but its story line reveals proprietary informaiton of Nextgencode, a gene manipulation company.

Surprise! "Next" will be released at the end of the month.

When I read Andromeda Strain as a kid, I fell hook, line & sinker for a similar ploy in that book -- all of the photos were labeled just like the photos of real spacecraft in books on NASA ("Photo Courtesy of Project SCOOP"). It took some convincing from older & wiser siblings before I caught on.

Going back over the news items with the knowledge of who is behind it was revealing. Crichton has become noted for throwing his lot in with global warming skeptics. "Burn Fuel? Backside Fat Powers Boat" is the tamer of the digs; another item suggests Neanderthals were displaced by the Cro-Magnon due to the Neaderthals environmentalist tendencies.

Well, at least it's a tame fake -- a fake company purely to hawk a book. Sure beats the shameless hucksters who set up companies to peddle fake cures (we have stem cell injections to cure hypochondria!) to desperate patients.