Methods to compress, encrypt and retrieve genomic alignment data

Abstract

A genomic data decoder may jointly compress and encrypt genomic data alignment information while preserving the privacy of sensitive genomic data elements at retrieval stage. Genomic data alignment information organized as a read-based alignment data stream may be transposed into a position-based alignment data stream. The position-based alignment information may be encoded into a reference-based alignment data stream. The reference-based alignment data stream may be encrypted with a combination of order-preserving encryption of the genomic position information and symmetric encryption of the reference-based alignment differential data. Differential encoding and entropy coding schemes may further compress the reference-based alignment data stream. The resulting compressed and encrypted stream may be indexed and stored in a biobank storage unit. A genomic data decoder may efficiently retrieve, decrypt and decode a specific subset of the resulting compressed and encrypted stream without leaking information on the other genomic data subsets in the resulting stream.

What is claimed is: 
     
         1 . A method to encode genomic data alignment information organized as a read-based alignment information data stream, comprising the steps of:
 Transposing, with a processor, the read-based alignment information data stream into a position-based alignment information data stream;   Encoding, with a processor, the position-based alignment information data stream into a reference-based compressed position data stream;   Encrypting, with a processor, the reference-based compressed position data stream into a compressed encrypted alignment data stream.   
     
     
         2 . The method of  claim 1 , wherein encoding the position-based alignment information data stream into a reference-based compressed position data stream comprises a step of differential encoding. 
     
     
         3 . The method of  claim 2 , wherein differential encoding comprises recording, for each position in the reference-based compressed position data stream, the alignment differences relative to the alignment reference sequence. 
     
     
         4 . The method  claim 1 , wherein encoding the position-based alignment information data stream into a reference-based compressed position data file further comprises a step of entropy coding. 
     
     
         5 . The method of  claim 1 , wherein encrypting the reference-based compression position data stream into a compressed encrypted alignment data stream comprises a step of encrypting the position information with an order-preserving encryption scheme. 
     
     
         6 . The method of  claim 1 , wherein encrypting the reference-based compression position data stream into a compressed encrypted alignment data stream comprises a step of encrypting the position-based alignment information with a symmetric encryption scheme. 
     
     
         7 . The method of  claim 6 , wherein the symmetric encryption scheme is a stream cipher. 
     
     
         8 . The method of  claim 7 , wherein the symmetric encryption scheme is a block cipher operating in a stream cipher mode. 
     
     
         9 . A method to retrieve genomic data alignment information from a compressed encrypted alignment data stream, recorded on a storage unit, comprising the steps of:
 Receiving a genomic alignment range query [Pos1, Pos2] from a genomic data analysis system;   Retrieving from the storage unit, with a processor, the subset of the compressed encrypted alignment data stream corresponding to the genomic alignment range [Pos1, Pos2] in the compressed encrypted alignment data stream;   Decrypting, with a processor, the compressed encrypted alignment data stream into a reference-based compressed position data stream corresponding to the genomic alignment range [Pos1, Pos2];   Decoding, with a processor, the reference-based compressed position data stream into a position-based alignment information data stream corresponding to the genomic alignment range [Pos1, Pos2].   
     
     
         10 . The method of  claim 9 , further comprising the step of reverse transposing, with a processor, the position-based alignment information data stream into a read-based alignment information data. 
     
     
         11 . The method of  claim 9 , wherein retrieving the subset of the compressed encrypted alignment data stream for the genomic alignment range [Pos1, Pos2] comprises retrieving the symmetric encrypted data and the metadata stored in data blocks between the order-preserving encrypted position associated with Pos1 and the order-preserving encrypted position associated with Pos2. 
     
     
         12 . The method of  claim 11 , wherein decrypting the compressed encrypted alignment data stream into a reference-based compressed position data stream corresponding to the genomic alignment range [Pos1, Pos2] comprises symmetric decryption of the symmetric encrypted data between the order-preserving encrypted position associated with Pos1 and the order-preserving encrypted position associated with Pos2. 
     
     
         13 . The method of  claim 12 , wherein the symmetric decryption scheme is a stream decipher. 
     
     
         14 . The method of  claim 12 , wherein the symmetric decryption scheme is a block decipher operating in a stream decipher mode. 
     
     
         15 . The method of  claim 9 , wherein decoding the position-based alignment information data stream into reference-based compressed position data stream comprises a step of entropy decoding. 
     
     
         16 . The method of  claim 9 , wherein decoding the position-based alignment information data stream into reference-based compressed position data stream comprises a step of differential decoding.