January 11, 2009
Genetic Assays About Ourselves

Noted Harvard psychologist and author Steven Pinker has an article in the New York Times Magazine entitled My Genome, My Self. He explores the relationship between your DNA sequence and your personal identity.

Last fall I submitted to the latest high-tech way to bare your soul. I had my genome sequenced and am allowing it to be posted on the Internet, along with my medical history. The opportunity arose when the biologist George Church sought 10 volunteers to kick off his audacious Personal Genome Project. The P.G.P. has created a public database that will contain the genomes and traits of 100,000 people. Tapping the magic of crowd sourcing that gave us Wikipedia and Google rankings, the project seeks to engage geneticists in a worldwide effort to sift through the genetic and environmental predictors of medical, physical and behavioral traits.

Parenthetically, I think the Personal Genome Project is an excellent idea. DNA sequence information is becoming so cheap so far that our biggest problem is how to compare the genetic data of a large number of people against many characteristics about them. Lots of genetic variations make only small contributions to traits. So picking out those influences is very difficult. A large sample size of people is needed to give scientists decent odds of picking up on which genetic variants make a difference in which trait.

The Personal Genome Project is an initiative in basic research, not personal discovery. Yet the technological advance making it possible — the plunging cost of genome sequencing — will soon give people an unprecedented opportunity to contemplate their own biological and even psychological makeups. We have entered the era of consumer genetics. At one end of the price range you can get a complete sequence and analysis of your genome from Knome (often pronounced “know me”) for $99,500. At the other you can get a sample of traits, disease risks and ancestry data from 23andMe for $399. The science journal Nature listed “Personal Genomics Goes Mainstream” as a top news story of 2008.

The $99,500 service doesn't offer utility commensurate to the money at this point because we do not know the functional significance of the vast bulk of the locations in the genome that differ from one person to the next. Still, if you are rich why not get the full picture? You'll find out more quickly for each new genetic discovery whether it matters to you.

In order to keep costs down the 23andMe folks do not check for as many genetic differences. They focus more on telling you about genetic variants suspected or known to be useful or at least revealing. Their disease risk info might spur you to get tested more often for some form of cancer for which you have higher risk (early detection being great for raising the chance of a cure). Or you might look at your test results and resolve to try harder to make lifestyle and diet choices to reduce your risk of heart disease. I also think their ancestry analysis could be especially interesting for adopted people and others who do not know much about where their ancestors came from.

Pinker says we can make use of genetic information without going crazy about it (my phrasing, not his).

Though the 20th century saw horrific genocides inspired by Nazi pseudoscience about genetics and race, it also saw horrific genocides inspired by Marxist pseudoscience about the malleability of human nature. The real threat to humanity comes from totalizing ideologies and the denial of human rights, rather than a curiosity about nature and nurture. Today it is the humane democracies of Scandinavia that are hotbeds of research in behavioral genetics, and two of the groups who were historically most victimized by racial pseudoscience — Jews and African-Americans — are among the most avid consumers of information about their genes.

I think we are going to find lots of ways to use genetic information and this will fragment into different industries. Lots of people will write software to analyze genetic data for different purposes. For example, there'll be a mini-industry on genes and diet. There'll be another on ancestry tracing. There'll be still another on genetics and sports. Is there a way to compensate for your genes with drugs to make you perform just as well as someone who has better genes for swimming or tennis? Companies will look for ways.

DNA won't just get translated into static information to ponder. You will ask how best to interact with your DNA. That'll involve drug development, diet, exercise, and perhaps creation of environments that complement your genetic profile.

Of course, some answers from genome sequencing will not be pretty. Pinker has decided not to be told whether he carries a variant of the apolipoprotein E gene (APOE) that increases risk of Alzheimer's disease. It is understandable to not want to know about something that you can't do anything about. But as the decades go by and more effective treatments get developed for a long list of diseases some of the highly undesirable genetic variants will get matched up with useful treatments. So learning about your worst genetic variants won't carry as much a sense of futility and loss as is the case today. There is one case where genetic knowledge can be used today: testing before pregnancy. Turns out, there's a new company which specializes in pre-pregnancy genetic testing. They ask on their web site "Thinking about starting a family?".

The genes analyzed by a new company called Counsyl are more actionable, as they say in the trade. Their “universal carrier screen” is meant to tell prospective parents whether they carry genes that put their potential children at risk for more than a hundred serious diseases like cystic fibrosis and alpha thalassemia. If both parents have a copy of a recessive disease gene, there is a one-in-four chance that any child they conceive will develop the disease. With this knowledge they can choose to adopt a child instead or to undergo in-vitro fertilization and screen the embryos for the dangerous genes. It’s a scaled-up version of the Tay-Sachs test that Ashkenazi Jews have undergone for decades.

How does this work? First a couple gets tested. If they do not have any of the problematic genetic variations which this company screens for then they can start a pregnancy the old fashioned way. If they do have variations which could cause genetic diseases in offspring they then have some choices to make. But the point is they really do have choices they can make. As Pinker says, this is actionable information.

As biotechnology and biomedical science advance we will find many more ways in which we can respond to genetic knowledge about ourselves and take useful decisions. But already today we can make decisions about reproduction based on genetic tests. Granted, those tests do not cover every way that genes can affect health or other qualities of offspring. But a genetic screen for known well characterized genetic diseases is a good start.

I wonder whether small Amish populations that have high rates of a few genetic diseases would be willing to do matchmaking based on genetic data. They might not be willing to use IVF and pre-implantation genetic diagnosis (PGD) for embryo selection. But for those mutations which are only harmful when there are two copies then matchmaking could be used to avoid marriages between pairs who carry the same harmful genetic variant. Something like the Counsyl test could help to reduce the frequent of genetic diseases in the Amish or other populations that have higher frequencies of genetic diseases.

Share |      Randall Parker, 2009 January 11 11:54 PM  Biotech Assay Services

David Govett said at January 12, 2009 8:18 AM:

Of what value is a person's genome without the associated epigenome?

Carl Shulman said at January 12, 2009 9:09 AM:

"I wonder whether small Amish populations that have high rates of a few genetic diseases would be willing to do matchmaking based on genetic data."

That's what many religious Jews already do, using a blinded system, where the test results of the individuals are not revealed, just whether the match has two recessives.

Dog of Justice said at January 13, 2009 1:33 AM:

In a more rational world, I would have voluntary euthanasia plans drawn up in the face of stuff like bad APOE news. As is, I'd have to judge whether my friends and family at the time would be okay with such a cold approach.

Of what value is a person's genome without the associated epigenome?

Er, perfect information is only needed if you want to be cloned or something. There's still a large, and rapidly increasing, number of valid statistical conclusions you'd be able to draw with just your genome.

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