Biblio

Personalized medicine performs diagnoses and treatments according to the DNA information of the patients. The new paradigm will change the health care model in the future. A doctor will perform the DNA sequence matching instead of the regular clinical laboratory tests to diagnose and medicate the diseases. Additionally, with the help of the affordable personal genomics services such as 23andMe, personalized medicine will be applied to a great population. Cloud computing will be the perfect computing model as the volume of the DNA data and the computation over it are often immense. However, due to the sensitivity, the DNA data should be encrypted before being outsourced into the cloud. In this paper, we start from a practical system model of the personalize medicine and present a solution for the secure DNA sequence matching problem in cloud computing. Comparing with the existing solutions, our scheme protects the DNA data privacy as well as the search pattern to provide a better privacy guarantee. We have proved that our scheme is secure under the well-defined cryptographic assumption, i.e., the sub-group decision assumption over a bilinear group. Unlike the existing interactive schemes, our scheme requires only one round of communication, which is critical in practical application scenarios. We also carry out a simulation study using the real-world DNA data to evaluate the performance of our scheme. The simulation results show that the computation overhead for real world problems is practical, and the communication cost is small. Furthermore, our scheme is not limited to the genome matching problem but it applies to general privacy preserving pattern matching problems which is widely used in real world.

Since the first whole-genome sequencing, the biomedical research community has made significant steps towards a more precise, predictive and personalized medicine. Genomic data is nowadays widely considered privacy-sensitive and consequently protected by strict regulations and released only after careful consideration. Various additional types of biomedical data, however, are not shielded by any dedicated legal means and consequently disseminated much less thoughtfully. This in particular holds true for DNA methylation data as one of the most important and well-understood epigenetic element influencing human health. In this paper, we show that, in contrast to the aforementioned belief, releasing one's DNA methylation data causes privacy issues akin to releasing one's actual genome. We show that already a small subset of methylation regions influenced by genomic variants are sufficient to infer parts of someone's genome, and to further map this DNA methylation profile to the corresponding genome. Notably, we show that such re-identification is possible with 97.5% accuracy, relying on a dataset of more than 2500 genomes, and that we can reject all wrongly matched genomes using an appropriate statistical test. We provide means for countering this threat by proposing a novel cryptographic scheme for privately classifying tumors that enables a privacy-respecting medical diagnosis in a common clinical setting. The scheme relies on a combination of random forests and homomorphic encryption, and it is proven secure in the honest-but-curious model. We evaluate this scheme on real DNA methylation data, and show that we can keep the computational overhead to acceptable values for our application scenario.