Circulating Tumor Fraction Estimation Using Off-Target Reads
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Solution Overview
Problem
Current liquid biopsy assays face challenges in accurately determining circulating tumor fraction estimates (ctFEs) due to cancer heterogeneity and large chromosomal copy number variations, leading to noisy variant allele fractions and inadequate representation of genomic alterations.
Innovation Solution
The method involves fitting segment coverage ratios from on-target and off-target sequence reads to integer copy states across simulated tumor fractions, allowing for accurate estimation of circulating tumor fraction in liquid biopsy samples.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If targeted-panel sequencing is used to detect genomic alterations, then sensitivity for detecting specific mutations is improved, but measurement precision of circulating tumor fraction deteriorates due to noisy variant allele fractions
Solution Approach 1:
The patent uses copy number variation (CNV) analysis as an intermediary approach to estimate circulating tumor fraction. Instead of directly relying on noisy variant allele fractions from targeted sequencing, the method uses CNV detection from the same sequencing data as a mediator to infer tumor fraction, thereby resolving the contradiction between maintaining sensitivity and improving measurement precision.
Solution Approach 2:
The patent changes the parameter being measured from variant allele fraction to copy number variation. By shifting from measuring allele frequencies (which are noisy in liquid biopsy) to measuring copy number changes (which can be more reliably detected even at low tumor fractions), the method improves circulating tumor fraction estimation while maintaining the benefits of targeted sequencing.
2Measurement precision
If comprehensive next generation sequencing analysis is performed, then detection of actionable genomic alterations is improved, but device complexity and cost increase
Solution Approach 1:
The patent makes the targeted sequencing panel serve multiple functions: it simultaneously detects specific actionable mutations and performs copy number variation analysis for circulating tumor fraction estimation. This multi-functionality eliminates the need for separate assays, reducing device complexity and cost while maintaining comprehensive genomic evaluation.
Solution Approach 2:
The patent merges variant detection and copy number analysis into a single targeted sequencing workflow. By combining these two functions that were traditionally performed separately into one unified assay, the method reduces complexity and cost while achieving comprehensive genomic characterization.
3Ease of operation
If liquid biopsy is used for non-invasive cancer monitoring, then ease of operation is improved, but measurement precision of tumor burden assessment deteriorates due to cancer heterogeneity and chromosomal variations
Solution Approach 1:
The patent uses copy number variation as an intermediary metric to bridge the gap between liquid biopsy convenience and accurate tumor burden assessment. CNV serves as a more reliable mediator than variant allele fraction in the context of cancer heterogeneity and chromosomal variations, enabling precise tumor fraction estimation from liquid biopsy samples.
Data Source
AI summary
Methods, systems, and software are provided for estimating a circulating tumor fraction (ctFE) for a test subject. Sequence reads are obtained from a panel-enriched sequencing reaction, including sequences for cfDNA fragments corresponding to probe sequences and sequences for cfDNA fragments not corresponding to probe sequences. Bin coverage values are determined from the sequences. Segments are formed by grouping adjacent bins based on similar coverage value and segment coverage values are determined based on bin coverage values for bins mapping to each segment. For each simulated ctFE in a plurality of ctFEs, segments are fitted to an integer copy state by identifying the integer copy state that best matches the segment coverage value. The circulating tumor fraction for the test subject is determined using error optimization between segment coverage values and integer copy states across the simulated ctFEs.