Methods to compress, encrypt and retrieve genomic alignment data

Inventors

MOLYNEAUX, Adam • Ayday, Erman • Hubaux, Jean-Pierre • Garcia, Jesus • HUANG, Zhicong • Lin, Huang

Assignees

Sophia Genetics SA

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 been coded 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.

Core Innovation

The invention transposes read-based alignment information organized as a read-based alignment information data stream into a position-based alignment information data stream. In the position-based alignment information data stream, a character is a start marker for each short read, and the start marker is followed by metadata information regarding at least a nucleotide base identified at a position with an associated quality score.

The invention encodes the position-based alignment information data stream into a reference-based compressed position data stream. The encoding reduces redundancy by using reference-based compression and includes variant information as differences and quality-related and metadata information as part of the reference-based compressed position data stream.

The invention encrypts the reference-based compressed position data stream into a compressed encrypted alignment data stream. The encryption includes an order-preserving encryption scheme and encrypting sensitive information at each position, with variant information independently encrypted for each row of a data structure in storage, and it supports retrieving a subset corresponding to a genomic alignment range without decrypting an entire block.

A corresponding retrieval method receives a genomic alignment range query [Pos1, Pos2], retrieves the subset of the compressed encrypted alignment data stream corresponding to the range, decrypts the subset into a reference-based compressed position data stream corresponding to the range, and decodes the resulting reference-based compressed position data stream back into a position-based alignment information data stream for the range.

Claims Coverage

The partial content includes two independent methods: one for encoding and one for retrieval. Across these independent claims, the main inventive features focus on transposition to a position-based stream, reference-based compressed position encoding, two-part encryption combining order-preserving encryption with per-position sensitive-information encryption for privacy control, and range-subset retrieval with corresponding decryption and decoding.

Across the independent claims provided, the core claim coverage is for transforming read-based genomic alignment information into a position-based representation, reference-compressing the position-based information, encrypting the compressed data with an order-preserving encryption scheme combined with per-position sensitive-information encryption for privacy control, and retrieving, decrypting, and decoding only a subset corresponding to a requested genomic alignment range [Pos1, Pos2].

Stated Advantages

Documented Applications