Less than a decade after the first full human genome was mapped, technology has arrived to decode the full genome of a single sex cell. The ability promises to offer new insight into the causes of infertility, the development of mutations and the diversity of the human genome.

Sperm and egg cells differ from other bodily cells in that they have a single—rather than double—set of chromosomes. Researchers have successfully amplified and sequenced 91 sperm cells from a single individual, a 40-year-old man whose genome has already been sequenced and analyzed—an important factor for checking the accuracy of the sperm sequencing. They found that the sampled sperm had sustained about 23 recombinations, which help to mix up genes from the chromosomes to increase genetic diversity in offspring, and between 25 and 36 new mutations, rates that match previous estimations for those in the general population. The scientists reported the findings online July 19 in Cell.

The new capability is "going to allow us to answer a lot of questions about genome stability in the germ line," says Don Conrad, a human geneticist at Washington University School of Medicine in Saint Louis, who was not involved with the new research. The researchers found that although the man who donated the sperm already had healthy offspring, two of the sperm cells studied were each missing a full chromosome. Such mutations, however, make it less likely that a sperm cell will successfully fertilize an egg.

Until now, we have made rough estimates about genetic mutations and recombination on the population scale. "We haven't had the tools to quantify those things on a personal level," Conrad says. "This is a technological breakthrough." Stephen Quake of the Stanford School of Medicine's Department of Bioengineering and his team have been working on this project for the past decade. "We started with bacteria and worked our way up to humans," he says. They harnessed developments in the field of micro-fluidics to sequence the single cells on chips. These micro-fluidic chips allowed them to amplify the genome (with a process called multiple displacement amplification) using far less material, which reduced the odds for contamination—and thus erroneous findings—by 1,000 times, they reported.

The approach also revealed new places where mutations seem to congregate on the genome—so-called hot spots. Although the study was not designed to pinpoint particular biological signals, it demonstrates "how little we actually knew about hot spots across the genome," Quake says. And future research can use these findings—and technology—to start to probe bigger biological questions, such as "to help understand and potentially diagnose reproductive disorders, to help understand what happens when it's the man's fault," he says.

Reproductive technologists, however, will not be sequencing sperm to screen them for implantation anytime soon. The current method of sequencing destroys the sperm cell subject. Quake, however, suggests that both screening and capturing a sperm cell intact is possible under the right conditions—namely, just before a sperm cell splits through meiosis. "If you can capture them before they separate, you can sequence one and you'll know what the other is."

Sequencing for fertility—and more

The ability to sequence these single sex cells will open a new window to study infertility. "I think there are forms of infertility out there waiting to be identified that don't even have a name yet," Conrad says. He estimates that the technology could be validated and ready for clinical use within five years. The next hurdle, he says, is not technological but biological: scientists do not yet know entirely what genetic changes might be linked to various fertility challenges—a major step before diagnostic tests can be developed and rolled out.

Some couples are already testing for inherited mutations that could cause disease before an embryo is implanted in the uterus. These existing genetic tests have also made clear that there are other considerations before genome screening for sperm could become widespread. One is a "complicated legal landscape," Conrad points out. When clinicians do a full genome screen, they can find anything, such as a mutation that puts one at higher risk for a certain cancer. But it has not yet been established whether they are obligated to look for these mutations or tell patients if they find them. "Conceptually, it's straightforward to do genome sequencing," but layering on the clinical considerations and genetic counseling can make such screening thornier than it might first appear.

Sequencing a full genome from a single cell also holds promise for a variety of medical fields outside of reproduction. Quake and his team are already looking into cancer cells, which have "enormous genetic variation," he says. Cancer cells, however, have two sets of chromosomes (as do most of the body's cells), making them more difficult to genetically parse than sperm or egg cells, which have just one set of chromosomes.

Nevertheless, this technology could improve monitoring to look for specific genetic signatures of circulating cancer cells, he notes. "There's quite a bit to do," Quake says. But now that the technology is ready, "you can start thinking about those critical studies."