PART 01
The more monitoring sites, the higher the sensitivity
During the MRD detection process, there are significant differences in the mutation profiles of patients with different cancer types. Similarly, there is also heterogeneity in mutations among different patients with the same cancer type. The mutations monitored by the individualized panel are more accurate than those by the fixed panel. In the monitoring of the individualized panel, the detection sensitivity is affected by various factors, including the amount of input DNA sample, the library conversion efficiency, the sequencing depth, and the number of target mutations. Among them, expanding the number of target mutations is crucial for improving sensitivity.
1. A study on lung cancer MRD based on CAPP-seq found that when tracking the information of a single mutation, the MRD detection sensitivity was only 58%; however, when tracking all the mutations carried by the patient, the MRD sensitivity could be increased to 94% [1].
2. A study based on MRDetect showed that the width of sequencing can replace the depth of sequencing to overcome the limitation of the small number of ctDNA fragments in plasma. When there are fewer mutation sites of concern, it is possible that there are no fragments supporting the target SNV in the tested sample, and even ultra-deep targeted sequencing cannot detect the mutation signal [2].
3. In a study on the performance of ctDNA MRD detection, in a simulation experiment with the selection of 10-150 sites for detection, it was found that when the ctDNA abundance is high (≥0.5%), the sensitivity is not affected by the number of detection sites. However, when the abundance is less than 0.01%, the sensitivity increases significantly with the increase in the number of detection sites [3].
All the above studies suggest that increasing the breadth of MRD detection coverage and monitoring a larger number of gene mutations can increase the detection probability of gene mutations of tumor origin, and thus improve the sensitivity and accuracy of MRD detection.
PART 02
WES + Individualized MRD Panel
In actual detection, the large TMB cohort study by Foundation Medicine shows that the median TMB value for all populations is 3.6 mutations/Mb, and the specific values vary significantly depending on the type of cancer [5]. Based on this, it is difficult to screen all the variant sites of patients for MRD tracking through a large tumor panel. Therefore, in the current cohort studies of MRD detection, the tumor-informed customized panel scheme based on WES is still the main choice, and its remarkable effects have been confirmed in clinical applications [6-8].
In response to this, iGeneTech, based on the tumor-informed analysis strategy, combining the advantages of the depth differences of Aigene WES V3 Human Whole Exome Tumor Edition, as well as years of experience in panel customization, has launched an overall solution for ctDNA MRD. By combining the free customized synthesis of individualized MRD panels, it promotes the clinical application of MRD detection.
PART 03
Zero Cost for Individualized MRD Panel Customization
While increasing the number of individualized MRD detection sites, the high customization cost for each patient is undoubtedly one of the main limiting factors in the actual implementation and promotion of clinical detection applications. In response to this, as a domestic provider of targeted capture reagents and solutions, iGeneTech has vigorously launched an MRD free customization solution with up to 150 probes per panel, and ensures stable and excellent performance. Compared with the conventional column-based single probe synthesis solution, it can quickly meet the customization needs for a large sample size while minimizing the cost.
PART 04
Full-process Reagent Solution
In the entire chain of MRD detection, through years of independent research and development of supporting reagents and application expansion in different scenarios, iGeneTech has formed a complete set of solutions covering sample extraction, library construction, capture, and bioinformatics analysis. At the same time, each link can be stably and efficiently used in combination with automated equipment.
PART 05
Display of Actual Measurement Data
Based on iGeneTech's MRD panel synthesis solution and full-process reagents, 7 MRD panels with different target sites synthesized in the same batch were randomly selected for capture performance testing. The actual measurement data show that stable and excellent capture performance can be obtained for different panels and different sites. At the same time, in the performance test of low-frequency mutation detection, even with a mutation frequency as low as 0.01%, the mutation information of 4 out of 8 mutation sites can still be stably detected.
Figure 1. Data performance of capture testing using different MRD panels. Capture testing was performed using 7 MRD panels each containing 37 probes. The single hybridization library input amount was 750 ng, and sequencing was conducted on the NovaSeq 6000 platform with PE150 mode.
Figure 2. Detection statistics of known mutation sites in 8 positive reference materials at mutation frequencies of 0.001%-0.1%. Horizon ctDNA reference materials (HD780) with mutation frequencies of 0.1%, 0.01%, and 0.001% were used for library construction with a 50 ng input amount. A random MRD Panel containing 37 probes was used for capture. The sequenced data were analyzed using the UMI pipeline established by iGeneTech®. The number of detected mutations after single-end correction was statistically analyzed.
Founded in 2014, iGeneTech is the first domestic company focusing on targeted capture solutions. Relying on three independent core intellectual property technical platforms—NGS probe hybridization, multiplex PCR, and high-throughput OligoPools synthesis—it has independently developed supporting reagent solutions over the past decade. Especially in MRD detection technology solutions, iGeneTech continues to innovate, working with partners to enhance performance, reduce costs, and develop more flexible and effective technical solutions, providing comprehensive support for deepening clinical application and popularization.
References
1. Chaudhuri A A , et al. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling[J]. Cancer Discovery, 2017, 7(12):1394-1403.
2. Zviran A, et al. Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring[J]. Nature medicine, 2020, 26(7): 1114-1124.
3. Seung-Bum, Ryoo,Sunghoon, Heo,Yoojoo, Lim et al. Personalised circulating tumour DNA assay with large-scale mutation coverage for sensitive minimal residual disease detection in colorectal cancer.[J] .Br J Cancer, 2023, 129: 0.
4. Chalmers Z R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden[J]. Genome medicine, 2017, 9: 1-14.
5. Chalmers Z R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden[J]. Genome medicine, 2017, 9: 1-14.
6. Kotani D, Oki E, Nakamura Y, et al. Molecular residual disease and efficacy of adjuvant chemotherapy in patients with colorectal cancer. Nat Med. 2023;29(1):127-134.
7. https://doi.org/10.1016/j.annonc.2023.09.1749
8. https://ascopubs.org/doi/abs/10.1200/JCO.2023.41.4_suppl.213
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