For One Baby, Life Begins with Genome Revealed
How a California father made an end run around medicine to decode his son’s DNA.
An infant delivered last week in California appears to be the first healthy person ever born in the U.S. with his entire genetic makeup deciphered in advance.
His father, Razib Khan, is a graduate student and professional blogger on genetics who says he worked out a rough draft of his son’s genome early this year in a do-it-yourself fashion after managing to obtain a tissue sample from the placenta of the unborn baby during the second trimester.
“We did a work-around,” says Khan, 37, who is now finishing a PhD in feline population genetics at the University of California, Davis. “There is no map for doing this, and there’s no checklist.”
The idea of sequencing fetuses is extremely new and sensitive. Khan, who had no real medical reason to learn his son’s DNA code, says sequencing his son in utero “was more cool than practical.” He did it to show where technology is headed and because he likes “pushing the envelope.”
Khan is already well known in genetics circles as a conservative blogger who publishes provocative views on genetics, race, and reproduction, most recently at the Unz Review, and has also criticized government regulation of DNA testing. Among his most frequent predictions over the last few years: sequencing of fetuses will soon become routine, like it or not. “The future is here, deal with it,” he wrote on his blog in May.
Sequencing DNA has become so cheap and easy that its routine use in pregnancy, as a way to get a broad view of a fetus’s health, is starting to look inevitable. “In five years we will be offering [genome] sequencing for all routine pregnancies in the first trimester,” predicts Art Beaudet, chairman of molecular genetics at Baylor College of Medicine. He says Baylor is developing plans to begin offering so-called exome sequencing, or decoding of the key parts of the genome, during pregnancy for some couples.
What’s still not settled is the ethics of prenatal sequencing—or the question of who gets to control the data. In fact, that debate has barely begun. It’s such a new idea that the American College of Medical Genetics and Genomics, which sets guidelines for medical geneticists, still has no position on it, says Diana Bianchi, executive director of the Mother Infant Research Institute at Tufts University.
The problem is too much information. Unlike a targeted test—say, a lab exam for a single condition—genome sequencing reveals every gene. In effect, it provides a test for over 3,000 inherited disorders as well as information about genes associated with higher risks of developing certain disorders. For example, a mutation in one gene, known as APOE, strongly predicts a person’s likelihood of developing Alzheimer’s disease in old age. Right now, however, many doctors remain opposed to doing predictive genetic tests on children for diseases that occur only in adulthood.
Gathering such information on fetuses in utero is even more controversial. That is because discovery of a bad mutation could lead parents to an “irrevocable action” such as an abortion, says Bianchi. Yet DNA isn’t always destiny—sometimes a person has a genetic defect but no symptoms.
All that makes doctors reluctant to delve into a fetus’s DNA makeup without good reason. Khan says he met resistance from his family’s genetic counselor and testing labs. “They did try to discourage us. Like, ‘Why would you do it? There are no protocols. There are no reasons,’” he says. “They do not want infants born sequenced.”
Several experts contacted by MIT Technology Review, including Beaudet and Bianchi, could point to only a single published report (here) of a child born with its genome already decoded. That case, in 2012, involved a baby who suffered from severe genetic problems and survived only 10 days. Researchers at Massachusetts General Hospital, where the research was done, says they have since sequenced about five more fetuses, but only as part of medical research studies on abnormalities. Scientists in China also claim to have obtained rough-draft sequences from IVF embryos, which were brought to term, though details of their procedure are not clear.
“My guess is that a few people may have done this privately already,” says Jay Shendure, an expert in fetal genomics at the University of Washington. “But this is the only case where someone is being public about it. I think it’s going to become a lot more common.”
The reason for that, says Shendure, is that the cost of gathering DNA data is plummeting: decoding all six billion letters in a person’s genome now costs only a few thousand dollars. Other tests that provide a coarse map of a person’s genetic makeup, called a genotype, cost only $99. That means that more people are exploring DNA—and for reasons doctors may not always agree with or be able to control.
Regulatory tensions have been growing over who gets to interpret gene data. Last year, the U.S. Food and Drug Administration barred the genetics company 23andMe, which is backed by Google, from marketing its $99 direct-to-consumer genotype test, saying it made unproven health claims by telling people what science says about their genes. Now consumers who want that sort of information about themselves can’t easily get it unless a doctor is involved.
On his blog, Khan has called access to DNA data a “right” that government and doctors are trying to squelch. If medicine insists on blocking access to gene data, he warned in 2011, consumers might be forced to generate the data on their own, perhaps by purchasing used sequencing machines and running them in their homes or in shared labs. “How dare the government question your right to know the basic genetic building blocks of who you are,” he wrote.
Khan had been determined to learn about his child’s genome in advance since soon after his wife became pregnant last year. To do so, he needed a sample of the growing baby’s DNA. Getting hold of it wasn’t easy. He and his wife decided to have a test called CVS, in which a biopsy of tissue was taken from her placenta, which shares the fetus’s DNA. Her doctor shipped it off to a lab called Signature Genomics, in Spokane, Washington, for a standard test that looks for missing, duplicate, or broken chromosomes.
The test came back normal. But Khan wanted more information. He asked for the raw data. When Signature declined, he began badgering the company to send what was left of the sample to his Davis laboratory. “They did not want to give it back,” he says. “No one really knew how to go about it. I realized I am on my own here.”
In fact, Signature routinely returns samples to doctors for further testing, says Britt Ravnan, one of the company’s lab’s directors. “What was unusual in this case was that it was not the patient or the physician asking for the sample, but the patient’s husband,” she says. Signature held onto the sample until Khan eventually got his wife and her doctors to fill out the right paperwork. Then it shipped the baby’s DNA to him in California. “Once it leaves our building, it’s not up for us to decide what the patient does with it,” says Ravnan.
Ravnan, a specialist in chromosome analysis, says she is “absolutely sympathetic” to Khan’s wish to know more about his son. “That is his right—it’s his information, his fetus’s information, and you don’t want to be paternalistic about it,” she says. On the other hand, she cautions, DNA testing in an academic lab could easily generate misleading results. “I worry a little bit that without a lot of experience in interpreting the sequence data on a clinical basis, he might overinterpret or misinterpret things,” she says.
When Khan got the DNA earlier this year, he could have ordered simple tests for specific genes he was curious about. But why not get all the data? “At that point, I realized it was just easier to do the whole genome,” he says. So Khan got a lab mate to place his son’s genetic material in a free slot in a high-speed sequencing machine used to study the DNA of various animal species. “It’s mostly metazoans, fish, and plants. He was just one of the samples in there,” he says.
The raw data occupied about 43 gigabytes of disk space, and Khan set to work organizing and interpreting it. He did so using free online software called Promethease, which crunches DNA data to build reports—noting genetic variants of interest and their medical meaning. “I popped him through Promethease and got 7,000 results,” says Khan.
Promethease is part of an emerging do-it-yourself toolkit for people eager to explore DNA without a prescription. It’s not easy to use, but it’s become an alternative since the FDA cracked down on 23andMe. To log in, a user has to click on several warnings, including one that cautions not to make reproductive decisions without a doctor.
Exploring his son’s genome several months before he was born, Khan found few surprises. He’s just a regular kid. “It’s mostly pretty boring. So that is good,” he says.
Khan makes few apologies for bypassing gatekeepers or for making decisions on behalf of his son. He says, “Our attitude is that you make a lot of decisions for your kids, including ones that may seem sketchy in hindsight.”