Multiplexed SNP Sequencing for Non-Invasive HRD Detection
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Solution Overview
Problem
Conventional HRD testing methods for cancer detection are invasive, costly, and limited in sensitivity, especially when using plasma-based liquid biopsies, missing a significant subset of patients who may benefit from PARP inhibitor therapy due to the lack of genetic mutations in key HRR genes, and requiring high sensitivity and broad genomic coverage.
Innovation Solution
A method involving multiplexed PCR reactions using primer pairs to capture SNPs across target chromosome arms and genes, followed by next-generation sequencing to detect genetic instability signatures like LOH, LST, and TAI, enabling chromosome-level and gene-level analysis with high sensitivity and cost-effectiveness.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional HRD testing is performed using tissue biopsy, then detection accuracy is improved, but patient comfort and accessibility deteriorate due to invasive procedures
Solution Approach 1:
The patent uses cell-free DNA (cfDNA) as an intermediary substance that carries genetic information from the tumor to the blood plasma. By detecting HRD signatures in cfDNA through liquid biopsy, the system achieves accurate detection without requiring invasive tissue biopsy, thus resolving the contradiction between detection accuracy and patient comfort
Solution Approach 2:
The patent detects copies of genetic signatures (LOH, LST, TAI) in cfDNA that represent the tumor's genomic state. Instead of directly analyzing tumor tissue, the method analyzes circulating DNA copies that mirror the tumor's genetic instability patterns, enabling non-invasive detection with high accuracy
2Device complexity
If conventional HRD testing detects only genetic mutations in HRR genes, then test simplicity is improved, but detection completeness deteriorates by missing patients with genomic instability without HRR mutations
Solution Approach 1:
The patent segments the HRD detection into three distinct genomic signatures: Loss of Heterozygosity (LOH), Large Scale Transitions (LST), and Telomeric Allelic Imbalance (TAI). By analyzing each signature separately through targeted sequencing of specific chromosomal regions, the method comprehensively identifies HRD-positive patients while maintaining test feasibility through focused rather than whole-genome analysis
Solution Approach 2:
The patent expands detection from the traditional single dimension of HRR gene mutations to multiple dimensions by incorporating LOH, LST, and TAI signatures across different chromosomal regions. This multi-dimensional approach captures the full spectrum of genomic instability mechanisms, ensuring no HRD-positive patient is missed regardless of their specific molecular mechanism
3Measurement precision
If liquid biopsy uses broad genome coverage, then detection sensitivity is improved, but cost and complexity increase
Solution Approach 1:
The patent applies local quality by concentrating sequencing depth on specific chromosomal regions known to harbor HRD signatures (e.g., chromosome arms 1p, 3p, 4q, 5q, 6q, 10q, 13q, 14q, 17p, 18q, 22q). Rather than uniformly sequencing the entire genome, the method focuses resources on these high-yield regions, achieving high detection sensitivity while controlling cost and complexity
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 accurate and non-invasive detection of genetic instability signatures in nucleic acid samples, including those without key HRR gene mutations, facilitating personalized treatment decisions for cancer patients.
Implementation Method 1
performing a plurality of multiplexed PCR reactions using: (I) a plurality of forward and reverse primer pairs that are capable of capturing the plurality of SNPs
Implementation Method 2
using the plurality of amplicons from step (b) to generate a plurality of sequencing reads with a next-generation sequencing platform
Data Source
AI summary
Disclosed is a method of detecting signatures of genetic instability within a nucleic acid sample, comprising: (a) identifying a plurality of single nucleotide polymorphism (SNPs) at one or more pre-determined intervals across (i) one or more target chromosome arms and/or (ii) one or more target genes; (b) performing a plurality of multiplexed PCR reactions using a plurality of forward and reverse primer pairs that are capable of capturing the plurality of SNPs, wherein each primer comprises a target-specific sequence, a barcode sequence, and an adapter-specific sequence, thereby generating a plurality of amplicons; and (c) sequencing and analysing the plurality of amplicons. In particular, the signature of genetic instability is loss of heterozygosity (LOH). Also disclosed is a method of predicting and/or monitoring the response of a subject having a disorder associated with signatures of genetic stability towards treatment. In particular, the disorder is Homologous Recombination Deficiency (HRD).