In the 1970s and 1980s, before safety measures were in place to screen out tainted blood, people with hemophilia were routinely exposed to HIV-infected blood products. Most of those patients became infected and later died of AIDS, but a significant minority -- some 20 percent of those who were almost certainly exposed to the virus repeatedly -- did not.
Now, David Goldstein, director of the IGSP's Center for Human Genome Variation, and his colleagues think that the complete genome sequences of those fortunate few will be key in the search for rare genetic variants that offer significant protection from HIV. Indeed, such host resistance to HIV is uncommon, existing in only a small percentage of the general population. It has been traced, in part, to the presence of genetic variants linked to the ability to block infection.
"But these known variants explain only a very small amount of the differences among individuals exposed to the HIV virus," says Goldstein. "We think there are probably other, much rarer variants that also play a role. We just haven't had the right setting or tools to find them. But now we do," supported by a $3 million grant from the Bill & Melinda Gates Foundation.
Goldstein's group will sequence the full genomes of 50 HIV-resistant people with hemophilia whose ability to ward of the infection can't be explained by previously identified protective gene variants.
As of mid-December, they had already completed the first of those genomes at a moderate level of coverage. Given that other efforts to sequence human genomes to date have focused on sampling "normal" individuals representing different geographical regions, that first sequence is notable in and of itself; it will become the first complete "human disease genome" known to science, IGSP Associate Investigator Kevin Shianna says. Ultimately, they expect to churn out all 50 complete human genome sequences over a period of six months, a feat made possible by seven next-generation sequencing machines known as Illumina Genome Analyzers.
"One way to look at it is that we will be generating the equivalent of a Human Genome Project every week," Goldstein said. "We're gearing up now to produce data in volumes that are absolutely unprecedented."
A Deluge of Data
That quantity of data presents major challenges. With genome-wide association studies (GWAS), there are a fixed number of possible variations researchers can always rely on, and even that can be overwhelming because there are millions of them.
Illumina Genome Analyzers will be used to sequence 50 human genome in six months.
That's where Goldstein team member Dongliang Ge, now a new IGSP faculty member, enters the picture. Ge developed software called Sequence Variant Analyzer to sort out the absolute overload of information to come from the new whole-genome sequencing studies.
The data coming from the next-generation sequencing machines in the Genome Analysis Facility that Shianna runs will enter a streamlined pipeline for analysis, Ge explains.
The Analyzer will filter through variants in search of those with potential functional relevance, automatically assigning each to one of 16 possible categories. For instance, it will determine which changes alter the makeup of a protein or which insert a "stop" in a location that would cause complete loss of a protein or even which might lead to changes in other functional entities in the genome. They'll also be able to detect immediately which variations have been seen before and which are unique. Researchers interested in particular pathways, such as those important to the functioning of the immune system, can easily filter the variation to find the relevant bits.
"We think we can catch just about anything we know about," Ge says.
Goldstein agrees, adding that the new tool essentially encapsulates the "theory of everything. It takes everything we know about the human genome to find those variants with potential functional relevance."
Eventually, they'll narrow the list of contenders down by comparing the 50 HIV-resistant genomes to one another and to control sequence from participants in the 1000 Genomes Project, an international effort designed to create the most detailed picture so far of human genome variation by sequencing 1,000 individuals from all over the world.
The Case of the Missing Heritability
The ongoing study is just the beginning of a broader effort by Goldstein's team to investigate what is still a very new idea: that even common diseases are caused in large part by rare changes in the genome. The idea has arisen from the realization that previous studies of common disease have turned up disappointingly little in the way of common genetic causes.
"There have now been comprehensive screens for common variants for most common diseases, and I believe we've gotten out most of what's to be had," Goldstein says. "We are left with a dark matter problem. If you assess heritability, it's high for everything. Then you look at common variation and we're missing a lot of the genetic control. It could be some other phenomenon masquerading as heritability, but I think it's relatively rare and highly penetrant things that are now missed."
In support of such a notion, a recent report in Science, which included Goldstein as a collaborator, found new genetic variants associated with schizophrenia, all of which are rare deletions or duplications in the genome.
The approach the IGSP team is taking now in HIV resistance -- sequencing the complete genomes of people with extreme characteristics -- may be the best way to find such rare and elusive genetic variants. Shianna said they also plan to do a whole-genome sequencing study of people with schizophrenia who are resistant to treatment. They have plans on the horizon to sequence people at the extremes of cognition, including a group with well-documented "photographic" memories, meaning that they have essentially perfect recall of everything that has ever happened to them. And, in the HIV realm, Goldstein's group will also sequence people at another extreme: those who immediately progress to AIDS almost as soon as they become infected with HIV.
This new approach to genomics will no doubt be an important tool in many cases, says Greg Wray, director of the IGSP's Center for Evolutionary Genomics and overseer of the IGSP's core DNA sequencing facility. But it won't necessarily apply in all instances.
"For some diseases, the rare stuff will be critical," Wray says. "Given the costs, the big challenge will be to determine which diseases are best approached from this perspective. In some cases GWAS or microarrays that measure gene expression may be all we need to know. There are a growing number of approaches and no one will be right in every case."
While Goldstein agrees, he and his team are confident that the new approach will soon lead them to new HIV-resistance variants. And though few people may carry them, those variants could prove to have incredible significance for many more individuals.
"We hope this project will yield new information that will help us to further understand disease resistance and to identify new targets and guidance for drug and vaccine development," says Goldstein. "Rare human genetic variation is a new frontier for discovery."