Contrived Nucleic Acid Samples for Sequencing Validation

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Solution Overview

Problem

Obtaining sufficient cell-free nucleic acid (cfNA) samples with known, predetermined characteristics for process validation in nucleic acid sequencing is challenging due to high costs, limited availability, and biological variability.

Innovation Solution

The development of contrived nucleic acid samples with specific, known physical and chemical characteristics, such as fragment length and methylation profiles, which can be produced in quantities sufficient for validating large-scale sequencing processes.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If biological cfNA samples are obtained from individuals for process validation, then the samples have natural biological characteristics, but the samples are expensive, scarce, and lack uniform known qualities

Engineering Contradiction:

Improveknown characteristicsVSAvoidsample quantity

Core Design Contradiction:

ReliabilityVSQuantity of substance

Solution Approach 1:

The patent creates artificial copies of biological cfNA samples by synthesizing nucleic acid fragments that replicate the size distribution, GC content, and other physical characteristics of natural cfNA. These synthetic copies can be produced in unlimited quantities with known, predetermined properties, eliminating the scarcity and cost issues of biological samples while maintaining the necessary biological-like characteristics for validation

Inventive Principle:

Principle #26Copying

Solution Approach 2:

The patent systematically controls and adjusts parameters of synthetic nucleic acid samples including fragment size distribution, GC content, and sequence composition to match or exceed the characteristics of biological cfNA. By precisely controlling these parameters during synthesis, the patent produces samples with uniform known qualities that are suitable for process validation

Inventive Principle:

Principle #35Parameter changes

2Quantity of substance

If artificial nucleic acid samples are used for process validation, then the samples are available in sufficient quantities, but the samples lack specific biological characteristics such as methylation profiles and fragment length distributions

Engineering Contradiction:

Improvesample quantityVSAvoidcharacteristic accuracy

Core Design Contradiction:

Quantity of substanceVSManufacturing precision

Solution Approach 1:

The patent applies local quality by introducing specific modifications to particular regions of synthetic nucleic acid fragments. For example, methylation is applied to specific cytosine residues at defined frequencies, and fragment length distributions are engineered to match biological patterns. This allows the synthetic samples to have both abundant quantity and accurate local biological characteristics

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The patent creates composite nucleic acid samples by combining synthetic fragments with controlled modifications. The samples incorporate multiple characteristics including specific size distributions, GC content profiles, and chemical modifications like methylation, hydroxymethylation, and formylation. This composite approach enables the samples to simultaneously possess abundant quantity and high manufacturing precision for multiple biological characteristics

Inventive Principle:

Principle #40Composite materials

3Adaptability or versatility

If biological samples are used for validation, then the samples have natural variability, but the variability makes it difficult to assess process accuracy with known standards

Engineering Contradiction:

Improvebiological representativenessVSAvoidprocess accuracy assessment

Core Design Contradiction:

Adaptability or versatilityVSMeasurement precision

Solution Approach 1:

Instead of accepting biological variability as given and trying to measure against it, the patent inverts the approach by creating samples with predetermined, known characteristics. The synthetic samples have defined methylation levels, known fragment distributions, and controlled sequence compositions. This inversion allows the samples to serve as known standards against which process accuracy can be precisely measured, while still maintaining biological representativeness

Inventive Principle:

Principle #13The other way round (Inversion)

Data Source

PatentUS20250122575A1Sequence process validation methods and compositions

Publication Date: 2025.04.17 FREENOME HOLDINGS INC

AI summary

The present disclosure provides methods and systems for preparing and using contrived nucleic acid samples for process validation and control. The contrived nucleic acid samples have prescribed specific physical and chemical characteristics, and are present in quantities sufficient to validate and confirm large-scale sequencing processes. Method validation may require known samples to confirm expected outcomes of the processes being validated. The inherent biological variability of biological samples obtained from individuals may not be suitable for the rigid requirements of process validation. The contrived biological samples described herein may approximate the complexity and biological features of a biological sample in a known and defined manner that may be controlled accordingly for the processes being validated.