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- Type of Document: M.Sc. Thesis
- Language: Farsi
- Document No: 51684 (05)
- University: Sharif University of Technology
- Department: Electrical Engineering
- Advisor(s): Maddah-ali, Mohammad Ali; Motahari, Abolfazl
- Abstract:
- DNA sequence is the lifetime private information of each individual: it can reveal personal traits, health status, and medical risk of that individual, it can be abused by entities such as insurance companies, it can be used for identity theft, etc. Unfortunately, due to cost, regulations, or some restrictions, we may not be able to complete DNA sequencing in-house and have to outsource it to some unreliable companies in some foreign countries.This would compromise the DNA privacy from the beginning. This would raise the question that how we can guarantee the DNA privacy in the process of sequencing.Here we propose a solution for private DNA sequencing by exploiting the fact that the process of sequencing consists of two phases: (1) reading, i.e. identifying the sequence of genomes in each fragment of DNA. (2) reconstruction i.e. concatenation of the read fragments of DNA and forming the entire sequence. In the proposed solution, the reading step which is technological and expensive is outsourced, and the reconstruction step which is computational is done locally on trusted machines. We artificially increase the ambiguity at the reading machines such that the reconstruction step is impossible to be executed there. To increase the ambiguity, in a pooled sequencing framework, we add the fragments of individuals with known sequence of DNA to the pools of fragments of individuals with unknown sequences. On top of that, in one solution, we distribute the reading task among several sequencers, and collect all the results to complete the reconstruction task at a local processing unit. This will increase the knowledge gap between the processing unit and each sequencer, and allows us to complete the reconstruction at the processing unit, while limiting the information leakage at each sequencer. In another solution, we use only one sequencer, with some structured (lattice based) solution, where this structure is lost at the sequencer due to the added ambiguity
- Keywords:
- Genome Analysis ; Security ; DNA Sequencing ; Read
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