Multiplexed Whole-Genome Library Depletion of High-Copy Sequences

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Solution Overview

Problem

Whole genome sequencing libraries contain high-copy sequences such as repetitive sequence regions and microbial DNAs, which are less informative for monogenic disease, polygenic risk stratification, or non-clinical genetic characteristics. Depleting these sequences individually from multiple samples is time-consuming and costly.

Innovation Solution

A method for preparing a depleted sequencing library involves providing a composition of nucleic acids with adaptor regions, adding removable blocker oligonucleotides that anneal to the adaptor sequences, removing non-target nucleic acids by sequence capture, and treating the composition to reduce free blocker oligonucleotides, resulting in a depleted sequencing library.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Loss of energy

If high-copy sequences are depleted individually from multiple samples, then sequencing and computational costs are reduced, but the process becomes time-consuming and costly

Engineering Contradiction:

Improvesequencing and computational costsVSAvoidtime-consuming process

Core Design Contradiction:

Loss of energyVSLoss of time

Solution Approach 1:

The patent combines multiple individual depletion reactions into a single multiplexed reaction by pooling nucleic acid samples from multiple individuals. Each sample is labeled with unique indexed adaptors and blocker molecules, allowing simultaneous depletion of high-copy sequences across all samples in one reaction, thereby reducing total time and resource consumption while maintaining cost effectiveness

Inventive Principle:

Principle #5Merging (Combining)

2Loss of energy

If high-copy sequences are depleted individually from multiple samples, then sequencing and computational costs are reduced, but the process becomes costly

Engineering Contradiction:

Improvesequencing and computational costsVSAvoidprocess complexity and cost

Core Design Contradiction:

Loss of energyVSEase of manufacture

Solution Approach 1:

The patent employs universal indexed adaptors and blocker molecules that can function across multiple samples simultaneously. The same depletion reagents and methodologies are applied to all samples in the multiplexed reaction, eliminating the need for separate depletion processes for each sample and thereby reducing overall cost and simplifying the manufacturing process

Inventive Principle:

Principle #6Universality (Multi-functionality)

3Productivity

If multiple samples are pooled together in a single reaction, then resource efficiency is improved, but adaptor self-hybridization occurs

Engineering Contradiction:

Improveresource efficiencyVSAvoidadaptor self-hybridization

Core Design Contradiction:

ProductivityVSReliability

Solution Approach 1:

The patent introduces sample-specific indexed adaptors with unique sequences for each individual sample. These unique adaptor sequences prevent self-hybridization between different samples while maintaining compatibility with the universal depletion process. Each sample's adaptors are designed to be distinct, ensuring that adaptors from different samples do not hybridize to each other, thereby maintaining reliability in the multiplexed reaction

Inventive Principle:

Principle #3Local quality

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

The method effectively reduces the proportion of high-copy sequences in the sequencing library, thereby reducing sequencing and computational costs while maintaining minimal impact on information content.

Implementation Method 1

adding removable blocker oligonucleotides that anneal to the adaptor sequences

Methodology Applied

Scientific EffectAnnealing: Annealing

Implementation Method 2

removing non-target nucleic acids from the composition by sequence capture to bait oligonucleotides

Methodology Applied

Scientific EffectHybridization capture:

Data Source

PatentUS20250290063A1Methods for depletion of high-copy sequences in multiplexed whole genome sequencing libraries

Publication Date: 2025.09.18 COLOR HEALTH INC

AI summary

A depleted sequencing library can be prepared by providing a composition comprising a heterogeneous mixture of linear nucleic acids having a first terminus and a second terminus. A first subset of target nucleic acids and a second subset of non-target nucleic acids can include a first adaptor region at the first terminus and a second adaptor region at the second terminus. A third subset of the target nucleic acids and a fourth subset of the non-target nucleic acids include the second adaptor region at the first terminus and at the second terminus. Removable blocker oligonucleotides can be added to the composition, non-target nucleic acids can be removed from the composition by sequence capture to bait oligonucleotides, and the composition can be treated to reduce a quantity of free blocker oligonucleotides that are not annealed to an adaptor sequence or to a sequence substantially complementary to an adaptor sequence.