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Fast and safe retrieval method, device and storage medium for dna sequence

A technology of sequence indexing and sequence, which is applied in the fields of fast and safe retrieval of DNA sequences, devices and storage media, and can solve the problems of not covering life insurance, long-term care insurance, etc.

Inactive Publication Date: 2018-10-19
KONINKLJIJKE PHILIPS NV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, GINA does not cover life insurance, disability insurance, and long-term care insurance

Method used

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  • Fast and safe retrieval method, device and storage medium for dna sequence
  • Fast and safe retrieval method, device and storage medium for dna sequence
  • Fast and safe retrieval method, device and storage medium for dna sequence

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Embodiment Construction

[0018] Disclosed herein is a method for indexing DNA sequences (or more generally, genomic sequences, e.g., DNA sequences, RNA sequences, etc.) using finite memory tree source models such as (e.g., fixed-order or variable variable order) Markov models, context tree weighted (CTW) models (an illustrative approach used in this paper), etc. An index record against the DNA sequence is then constructed, including models and parameters. The estimated codeword length obtained by applying the same limited memory tree model to the query DNA sequence then serves as a basis for quantification, compared to the codeword length estimated by direct modeling of the query DNA sequence using CTW. A comparative measure that evaluates the similarity of query and index DNA sequences. For example, codeword length comparisons are computed using mutual information measures such as entropy or information gain (IG) or similar means.

[0019] This method preserves the privacy of patients whose DNA seq...

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Abstract

Retrieves a sequence model from a sequence index. The sequence models model DNA or RNA sequences stored in a database, and each include a limited memory tree source model and parameters for the limited memory tree source model. One or more DNA or RNA sequences stored in the database are identified as most similar to the query DNA or RNA sequence based on the fit of the retrieved sequence model to the query DNA or RNA sequence. The sequence model may be a context tree weighted (CTW) model wherein Sx refers to the context tree model for the DNA or RNA sequence x stored in the database and refers to the context tree model Sx parameters. Said fitting for each CTW model can comprise using said CTW model to calculate a codeword length for said query DNA or RNA sequence y.

Description

technical field [0001] The following relates to genome sequence indexing, storage, retrieval, processing, labeling, and related tasks, and to aspects such as patient privacy and medical data security, and to applications such as medical diagnosis, medical screening, etc. Although described with illustrative reference to deoxyribonucleic acid (DNA) sequences, the following also applies in conjunction with genomic sequences such as DNA sequences, ribonucleic acid (RNA) sequences, and the like. Background technique [0002] DNA sequencing has many existing and anticipated commercial, medical, and scientific applications, such as the diagnosis of cancer and other conditions, medical screening for genetic diseases, personalized medical treatments, personalized drug design, genetic anthropology, and the study of evolution , genealogy research, forensic human identification, etc. In the medical field, clinical trials and genome-wide association studies are typical tools for evalua...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/22G06F19/28G16B50/40G16B30/00G16B50/50
CPCG06F16/2246G06F16/24561G16B30/00G16B50/00G16B50/40G16B50/50
Inventor T·伊格纳坚科
Owner KONINKLJIJKE PHILIPS NV