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Background Graft-versus-host disease (GVHD) results from recognition of host antigens by donor T cells following allogeneic hematopoietic cell transplantation (AHCT). Notably, histoincompatibility between donor and recipient is necessary but not sufficient to elicit GVHD. Therefore, we tested the hypothesis that some donors may be “stronger alloresponders” than others, and consequently more likely to elicit GVHD. Methods and Findings To this end, we measured the gene-expression profiles of CD4+ and CD8+ T cells from 50 AHCT donors with microarrays. We report that pre-AHCT gene-expression profiling segregates donors whose recipient suffered from GVHD or not. Using quantitative PCR, established statistical tests, and analysis of multiple independent training-test datasets, we found that for chronic GVHD the “dangerous donor” trait (occurrence of GVHD in the recipient) is under polygenic control and is shaped by the activity of genes that regulate transforming growth factor-β signaling and cell proliferation. Conclusions These findings strongly suggest that the donor gene-expression profile has a dominant influence on the occurrence of GVHD in the recipient. The ability to discriminate strong and weak alloresponders using gene-expression profiling could pave the way to personalized transplantation medicine., The donor gene expression profile appears to have a dominant influence on the occurrence of graft-versus-host disease in the recipient., Editors' Summary Background. Human blood contains red blood cells, white blood cells, and platelets, which carry oxygen throughout the body, fight infections, and help blood clot, respectively. Normally, blood-forming (hematopoietic) stem cells in the bone marrow (and their offspring, peripheral blood stem cells) continually provide new blood cells. Tumors that arise from the bone marrow (such as leukemia and lymphoma, two types of hematopoietic tumor) are often treated by a bone marrow or peripheral blood stem cell transplant from a healthy donor to provide new blood-forming stem cells, as a follow-up to chemotherapy or radiotherapy designed to eradicate as much of the tumor as possible. This procedure is called allogeneic hematopoietic cell transplantation (AHCT)—the word allogeneic indicates that the donor and recipient are not genetically identical. When solid organs (for example, kidneys) are transplanted, the recipient's immune system can recognize alloantigens (proteins that vary between individuals) on the donor organ as foreign and reject it. To reduce the risk of rejection, the donor and recipient must have identical major histocompatibility complex (MHC) proteins. MHC matching is also important in AHCT but for further reasons. Here, donor T lymphocytes (a type of white blood cell) can attack the skin and other tissues of the host. This graft versus host disease (GVHD) affects many people undergoing AHCT despite MHC matching either soon after transplantation (acute GVHD) or months later (chronic GVHD). As an aside, the transplant may also act against the tumor itself—this is known as a graft versus leukemia effect. Why Was This Study Done? GVHD can usually be treated with drugs that damp down the immune system (immunosuppressive drugs), but it would be preferable to avoid GVHD altogether. Indeed, GVHD continues to be the leading cause of nonrelapse mortality following AHCT. Unfortunately, what determines who will develop GVHD after MHC-matched AHCT is unclear. Although GVHD only develops if there are some mismatches in histocompatibility antigens between the donor and host, it does not inevitably develop. Until now, scientists have mainly investigated whether differences between ACHT recipients might explain this observation. But, in this study, the researchers have examined the donors instead to see whether differences in their immune responses might make some donors stronger “alloresponders” than others and consequently more likely to cause GVHD. What Did the Researchers Do and Find? The researchers used a molecular biology technique called microarray expression profiling to examine gene expression patterns in the T lymphocytes of peripheral blood stem cell donors. From these patterns, they identified numerous genes whose expression levels discriminated between donors whose MHC-identical transplant recipient developed GVHD after AHCT (GVHD+ donors) and those whose recipient did not develop GVHD (GVHD− donors). The researchers confirmed that the expression levels of 17 of these genes discriminated between GVHD+ and GVHD− donors using a second technique called quantitative reverse transcriptase polymerase chain reaction. Many of these genes are involved in TGF-β signaling (TGF-β is a protein that helps to control the immune system), cell growth, or proliferation. The researchers also identified four gene pairs that interacted with each other to determine the likelihood that a given donor would induce GVHD. Finally, the researchers computationally retested their data and showed that the measurement of expression levels of each of these genes and of the four interacting gene pairs could correctly identify a donor sample likely to cause GVHD in up to 80% of samples. What Do These Findings Mean? These findings provide the first evidence that the donor's gene expression profile influences the development of GVHD in the recipient after AHCT. The researchers suggest that a “dangerous donor” (strong alloresponder) is a key factor in determining whether GVHD occurs after AHCT and propose that gene expression profiling of donor T lymphocytes might identify those donors likely to cause GVHD. Before this approach can be used to reduce the incidence of GVHD after AHCT, these findings need to be confirmed in many more donors. Also, the development of a test that is accurate enough for clinical use—one that does not miss dangerous donors but does not discard too many safe donors—may require the identification of larger groups of interacting genes. But, if it survives further investigation, the concept of a dangerous donor could represent an important advance in transplantation medicine, one that could help clinicians select low-risk donors for AHCT and tailor patients' immunosuppressive drug regimens according to their donor-determined risk of GVHD. Additional Information. Please access these Web sites via the online version of this summary at http://dx.doi.org/doi:10.1371/journal.pmed.0040023. • The National Marrow Donor Program provides information for patients and physicians on all aspects of hematopoietic stem cell transplantation, including GVHD • The MedlinePlus encyclopedia has pages on bone marrow transplants, GVHD and transplant rejection • The US National Cancer Institute has a factsheet on bone marrow and peripheral blood stem cell transplantation