Genomic Services Platform with Dual-Phase Genotype Imputation
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Solution Overview
Problem
Consumers face the inconvenience and cost of needing to undergo multiple genomic sequencing procedures to access various genomic services, due to the lack of a centralized repository of genomic data and limited incentives for sharing personal genomic information.
Innovation Solution
A network-based genomic services platform that processes and stores genomic sequence information, allowing users to access selected portions of this data to multiple application providers, including a bioinformatics processing pipeline with modules for read alignment, variant calling, refinement, and imputation, enabling efficient sharing and utilization of genomic data without repeated sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of operation
If a centralized repository of genomic data is established to enable access to multiple genomic services, then consumers can avoid repeated sequencing costs and administrative burdens, but data privacy and security concerns arise from centralized storage and sharing of personal genomic information
Solution Approach 1:
The patent introduces a centralized genomic data repository that acts as an intermediary between consumers and multiple application providers. The repository stores processed genomic data and enables controlled access through standardized interfaces, allowing consumers to access multiple services without repeated sequencing while maintaining data security through centralized management and access controls.
Solution Approach 2:
The system performs preliminary genomic sequencing and data processing once, storing the results in the centralized repository before consumers need to access multiple services. This preliminary action eliminates the need for repeated sequencing and processing for each service, reducing both costs and administrative burdens while enabling efficient data retrieval for various applications.
2Adaptability or versatility
If genomic data is shared across multiple entities to enable diverse genomic services, then service versatility increases, but the complexity of data management and access coordination increases
Solution Approach 1:
The centralized repository is designed with universal access capabilities that serve multiple application providers through standardized interfaces. The system stores and manages genomic data in a format that can be accessed by various types of services (medical, research, consumer applications), enabling one infrastructure to support diverse genomic services without requiring separate data management systems for each provider.
Solution Approach 2:
The patent segments the data access architecture into distinct layers: the centralized repository stores processed genomic data, while application providers access specific portions through standardized interfaces. This segmentation allows versatile service delivery while simplifying data management, as each provider interacts with a standardized interface rather than managing complex direct data sharing arrangements.
3Adaptability or versatility
If consumers undergo multiple sequencing procedures to access different genomic services, then each service can be customized specifically, but the cost and time burden on consumers increases significantly
Solution Approach 1:
The system performs comprehensive genomic sequencing and processing once in advance, storing the complete processed data set in the centralized repository. This preliminary action enables consumers to access multiple customized genomic services without undergoing repeated sequencing procedures, significantly reducing the time and administrative burden while maintaining service customization through selective data retrieval for each application.
Data Source
AI summary
Systems, platforms, methods and media for providing genomic services are disclosed. In one example, a genomic services platform comprises a network interface through which are received genomic sequence reads derived from a biological sample obtained from a user. The platform also includes a bioinformatics processing pipeline including a read alignment module configured to generate observed sequence data by aligning the sequence reads relative to a reference sequence, a variant calling module operative to identify observed variants in the observed sequence data, and a variant refinement module for producing genotype data including a set of refined variants associated with the user. A variant imputation module produces a set of imputed variants associated with the user, and is configured to receive, as input, at least some of the genotype data and separate the genotype data into high-quality and low-quality genotypes based on a genotype quality.