genomeboy.com

Once again patients are told they can’t handle the truth (subscription only):

“The worry,” says Bill Thies, vice president of medical and scientific relations at the Alzheimer’s Association, is that patients may react to positive results in “inappropriate” ways. “Will they become fully depressed?” he says. “If that’s the case, then you’re going to obscure any public-health benefit.”

God forbid an Alzheimer’s diagnosis ever bums anyone out…Anyway, thankfully, not everyone presumes to know what’s best for you. And they appear to have actual science on their side:

“What we’ve been showing is that we can disclose APOE to people who are interested and they do not seem to have a whole lot of ill effects,” said Dr. Robert C. Green, a director of the study and a professor of neurology, genetics and epidemiology at Boston University. “There is some temporary increase in distress at six weeks, but at six months it’s gone.”

Some want the information to make financial and legal arrangements in case they become demented, and some who find out that they have e4 start trying to take better care of themselves. Not surprisingly, those who find out they do not have e4 are relieved, even though it does not guarantee that they are in the clear.

“Not everyone wants to know, but the people who want to know really want to know, and they have their own reasons,” Dr. Green said. “I think it’s a little patronizing for the medical establishment to say, ‘We could give you that test, but we don’t think you can handle it.’”

As Hsien observes, everyone’s blogging about their $1000 personal variomes…so I confess to feeling a little sheepish posting yet another breathless update about the PGP. On the other hand, it beats wrapping Christmas presents…

• The Church lab-invented, Danaher-manufactured Polonator — the high-speed sequencing platform that will, um, soon be used to sequence our 20,000 genes — is now available for purchase (hurry and and you can leave it under the tree…some assembly required…).
• The Affymetrix SNP chip has been done on most of the PGP-10. I know you’re all dying to know my relative risk for restless legs syndrome.
• The Church/Danaher team has put its hat in the ring for the X-Prize. This means the PGP-10 will almost certainly have their complete genomes sequenced in the next 1-2 years. Which means we won’t have to scratch that check for $350k. Which means more money left over to buy my kids bobblehead dolls. Yay!
• The PGP is also exploring the transcriptome. George reports that his lab has improved its protocol for converting skin-derived fibroblasts to pluripotent stem cells. For those who want to know why: “We have been doing allele-specific quantitative RNA sequencing assays, since we feel that this is complementary to sequencing the non-coding regions and in many ways preferable to standard RNA assays of tissues from individuals. This provides an assay for nearly all cis-elements (enhancers, promoters, splicing signals, RNA termination, poly-A sites, etc.).”
• In the next couple of months, I expect the PGP-10 will reconvene in Boston, at which time we will:
  • receive our initial sequence data and help in interpreting it
  • donate skin samples for stem cell studies
  • donate saliva for microbiome sequencing (”Look, Ma, it’s my very own E. coli!”)
  • complete phenotypic questionnaires
  • learn more about the plans to scale up to 100,000

Things may be quiet here for a while (yes yes, what else is new?). For now, Nat, Frank and I would like to toast you with a wish for peace on earth and good will toward almost everyone…

Two caveats on the PGP consent form: our genomes could be used to a) claim [our] relatedness to infamous villains and (b) make synthetic DNA and plant it at a crime scene. I was reminded of these by Ari Shapiro’s excellent series on NPR, The Ethics of DNA Use. Some money excerpts from Part I:

Law-enforcement groups like to say that giving police a DNA sample is no different from giving police your fingerprint, but Tania Simoncelli of the ACLU says DNA is far more personal than a fingerprint. A DNA sample “contains a great deal of information. It could be about susceptibility to disease, as well as your family history,” Simoncelli says. “This is private, personal information about you that goes far beyond just your identification.”

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Courts have said little about how much of a right people have to keep…genetic material private…”Traditionally, the law has been that if you abandon your DNA, you lose it,” says Barry Scheck, co-director of The Innocence Project.

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The Washington Supreme Court ruled six to three that “police are allowed to use some deception, including ruses, for the purpose of investigating criminal activity.”

“No recognized privacy interest exists in voluntarily discarded saliva,” the court found.

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But let’s not forget to give props to phenotypes:

…[A]s Harvard professor and DNA expert David Lazer points out, police can learn at least as much about us through other means as they can through our DNA.

“One could build a very detailed profile of every single individual based on the information they make freely available through credit card use, through cell phone use, through paying taxes and the like,” Lazer says. “It’s very difficult to hide in this life that we live in the grid.”

[Jason] Bonham’s volcanic fills on Nobody’s Fault But Mine confirmed that there are some things that can be transmitted only through DNA.

Led Zeppelin: Immutable.

(Image from The New York Times)