DNA Sequencing Data Management System for Privacy-Compliant Sample Processing

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Solution Overview

Problem

Conventional systems for processing biological samples require reprocessing or additional sampling for subsequent tests, which is inefficient and may violate privacy and regulatory standards.

Innovation Solution

A sample processing production line that includes a genomic DNA extractor, a target amplifier, and a sequencer, along with a sample information management system (SIMS) and a quality control database, which allows for the extraction, amplification, and analysis of DNA, and the storage and aggregation of results, including additional tests not initially requisitioned, while maintaining patient anonymity.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Adaptability or versatility

If conventional systems reprocess samples for subsequent tests, then additional tests can be performed, but processing time and resource consumption increase

Engineering Contradiction:

Improvecapability to perform additional testsVSAvoidprocessing time

Core Design Contradiction:

Adaptability or versatilityVSLoss of time

Solution Approach 1:

The system performs comprehensive DNA extraction and amplification of all possible test targets from a single sample in advance, before any specific test requisition is made. This preliminary processing creates a pool of amplified DNA components that can be rapidly analyzed for any number of different tests without requiring additional sample processing steps.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The amplification process is designed to generate DNA components for multiple potential tests simultaneously, making the processed sample universally usable for various different test requisitions. A single sample processing workflow produces results that can serve multiple different testing purposes.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Adaptability or versatility

If conventional systems store and reprocess sample portions, then additional testing is enabled, but system complexity and storage requirements increase

Engineering Contradiction:

Improvecapability for subsequent testingVSAvoidsample management complexity

Core Design Contradiction:

Adaptability or versatilityVSDevice complexity

Solution Approach 1:

The system extracts and separates the DNA amplification step from the sample storage requirement. By amplifying all necessary DNA components during the initial processing and storing only the digital test results and data, the system eliminates the need to physically store and manage multiple sample portions for different tests.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The system creates digital copies of test results and stores them in a database, replacing the need for physical sample storage. The amplified DNA components are used immediately for testing, while the results are preserved digitally for future retrieval and additional testing without requiring the original sample.

Inventive Principle:

Principle #26Copying

3Adaptability or versatility

If full sequencing data is stored for all markers, then future analysis flexibility is improved, but data storage and privacy management complexity increase

Engineering Contradiction:

Improvefuture analysis flexibilityVSAvoidprivacy information management

Core Design Contradiction:

Adaptability or versatilityVSLoss of information

Solution Approach 1:

The system extracts only the specific test results requested by the requisition from the full sequencing data and stores those in the database. The complete raw sequencing data for all markers is not stored, but rather only the relevant results for the specific tests ordered are retained, reducing privacy management complexity while maintaining future analysis flexibility for the same test types.

Inventive Principle:

Principle #2Taking out (Extraction)

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

Enables efficient and privacy-compliant processing of biological samples by performing a full set of tests on initial samples, storing additional results for future analysis, and delivering only requisitioned data to clients, while allowing for future notifications and updates based on new data availability.

Implementation Method 1

a genomic DNA extractor configured to extract DNA from a biological sample

Methodology Applied

Scientific EffectDNA extraction:

Implementation Method 2

a target amplifier configured to amplify components of the extracted DNA

Methodology Applied

Scientific EffectDNA amplification:

Data Source

PatentUS8600683B2Systems and methods for obtaining and managing sequencing data

Publication Date: 2013.12.03 LABORATORY CORPORATION OF AMERICA HOLDINGS INC

AI summary

Systems and methods for biological sample processing are described. A production line extracts genomic DNA from a biological sample, amplifies target components of the sample and produces sequence data for markers from the amplified components. The markers are associated with tests identified in a requisition received with the sample and some markers may be associated with unrequisitioned tests. A sample information management system (SIMS) controls and monitors the production line and subsequent analysis of the results using information in a quality control (QC) database to validate the results. A repository comprising the QC database and a research database receives and aggregates the results without identifying the source of the sample. A portal may be provided to provide access to the research database to a plurality of external contributors. Contributors can selectively provide additional research data and data can be processed using data mining and curation tools.