Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

Li, Shuo; Noor, Zorawar S.; Zeng, Weihua; Ni, Xiaohui; Yuan, Zuyang; Alber, Frank; Li, Wenyuan; Garon, Edward B.; Zhou, Xianghong Jasmine

doi:10.1101/2019.12.31.19016253

Cited by 5 publications

(7 citation statements)

References 37 publications

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“…Moreover, the shorter fragment size in ctDNA was utilised to filter out the possible clonal haematopoiesis of indeterminatepotential (CHIP)-associated genetic variants and improve the classification performance for the genetic-based approaches [89,90]. The non-random fragmentation and fragment-size information have recently been incorporated into the mutational calling algorithm specifically designed for the cfDNA [91].…”

Section: Inference Of Dna Methylation From Cfdna-fragmentation Patterns [69]mentioning

confidence: 99%

At the dawn: cell-free DNA fragmentomics and gene regulation

Liu

2021

Br J Cancer

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Epigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation status across multiple molecular layers, such as nucleosome positioning and gene expression. In this review, we revisited the computational and experimental approaches that have been recently developed to measure the cfDNA fragmentomics across different resolutions comprehensively. Moreover, cfDNA in peripheral blood is released following cell death, after apoptosis or necrosis, mainly from haematopoietic cells in healthy people and diseased tissues in patients. Several cfDNA-fragmentomics approaches showed the potential to identify the tissues-of-origin in cfDNA from cancer patients and healthy individuals. Overall, these studies paved the road for cfDNA fragmentomics to non-invasively monitor the in vivo gene-regulatory dynamics in both peripheral immune cells and diseased tissues.

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Section: Inference Of Dna Methylation From Cfdna-fragmentation Patterns [69]mentioning

confidence: 99%

At the dawn: cell-free DNA fragmentomics and gene regulation

Liu

2021

Br J Cancer

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“…Liquid biopsy has revealed an advantage over traditional gold standard tissue biopsy in its non-invasiveness, good concordance in genome profiling, and compatibility with different sample types 12,13 , thus liquid biopsy could be suitable for aiding early diagnosis 14,15 . However, somatic mutations detected from the liquid biopsy usually have lower variant allele frequency (VAF) than those from the tissue biopsy 16 , which added to the difficulty of sensitive and accurate detection of early-stage somatic mutations. Besides, liquid biopsy could offer a potential solution for longitudinal mutation profiling in diseases like minimal residual disease (MRD) 17,18 , which usually requires sensitivity down to 1:10 4 to 1:10 6 .…”

Section: Introductionmentioning

confidence: 99%

Hairpin structure facilitates multiplex high-fidelity DNA amplification in real-time PCR

Zhang

Pinto²,

Dai

et al. 2021

Preprint

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Effective polymerase chain reactions (PCR) are important in bio-laboratories. It is essential to detect rare DNA-sequence variants for early cancer diagnosis or for drug-resistance mutations identification. Some of the common detection quantitative PCR (qPCR) methods are restricted in the limit of detection (LoD) because of the high polymerase misincorporation rate in Taq DNA polymerases. High-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. Yet, there are currently no proper designs for multiplexed HiFi qPCR reactions. Moreover, the popularity of targeting highly multiplex DNA sequences requires minimizing PCR side products, as the potential of dimerization grows quadratically as the plexes of primers increases. Efforts tried before were either an add-on step, or technology-specific, or requiring high-level computing skills. There lacks an easy-to-apply and cost-effective method for dimerization reduction. Here, we presented the Occlusion System, composed of a 5’-overhanged primer and a probe with a short-stem hairpin. We demonstrated that it allowed multiplexing high-fidelity qPCR reaction, it was also compatible with the current variant-enrichment method to improve the LoD by 10-fold. Further, we found that the Occlusion System reduced the dimerization up to 10-fold in highly multiplexed PCR. Thus, the Occlusion System satisfactorily improved both qPCR sensitivity and PCR efficiency.

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“…The copyright holder for this this version posted November 11, 2021. ; https://doi.org/10.1101/2021.11.07.21265999 doi: medRxiv preprint accomplish both. For this we utilize cfSNV [12], a method we recently developed for the sensitive and accurate calling of somatic mutations in plasma samples. cfSNV specifically accommodates key cfDNA-specific properties, including the low tumor fraction, short and non-randomly fragmented DNA, and heterogeneous tumor content.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, we used clonal somatic mutations, called from the pre-treatment plasma sample or the pre-treatment tumor sample, as tumor markers. To make this selection, first tumor-derived somatic mutations are detected using cfSNV [12] from the pretreatment plasma sample; if only the pre-treatment tumor sample is available, tumor-derived mutations are the common mutations detected by Strelka2 [37] somatic and MuTect [38] in the final marker list, if its VAF is > 25% of the average of the five highest VAFs in the sample [39]. We require a minimum of 30 markers from the pre-treatment plasma sample to obtain a robust prediction.…”

Section: Identification Of Clonal Mutations In Pre-treatment Samplesmentioning

confidence: 99%

“…To monitor the pre-existing cancer, cfTrack (1) uses exome-wide somatic mutations collected in pre-treatment samples (solid tumor or blood samples) to provide a robust statistical index, then (2) models sample-specific background noise in the cfDNA sequencing data to provide an unbiased detection threshold for each patient. To monitor tumor evolution, cfTrack performs detection of exome-wide de novo tumor mutations in the post-treatment plasma samples, using our recently developed cfSNV method [12]. With exome-wide sequencing and comprehensive analysis of mutations, cfTrack can sensitively identify these previously undiagnosed patients with second primary cancers, comprehensively describe their tumor status, and enable early intervention and personalization of treatment.…”

Section: Introductionmentioning

confidence: 99%

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cfTrack: Exome-wide mutation analysis of cell-free DNA to simultaneously monitor the full spectrum of cancer treatment outcomes: MRD, recurrence, and evolution

Zeng

et al. 2021

Preprint

Self Cite

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PurposeCell-free DNA (cfDNA) offers a non-invasive approach to monitor cancer. Here we develop a method using whole-exome sequencing (WES) of cfDNA for simultaneously monitoring the full spectrum of cancer treatment outcomes, including MRD, recurrence, evolution, and second primary cancer.Experimental DesignThree simulation datasets were generated from 26 cancer patients to benchmark the detection performance of MRD/recurrence and second primary cancers. For further validation, cfDNA samples (n=76) from cancer patients (n=35) with six different cancer types were used for validating the performance of cancer monitoring during various treatments.ResultsWe present a cfDNA-based cancer monitoring method, named cfTrack. Taking advantage of the broad genome coverage of WES data, cfTrack can sensitively detect MRD and cancer recurrence by integrating signals across the known clonal tumor mutations of a patient. In addition, cfTrack detects tumor evolution and second primary cancers by de novo identifying emerging tumor mutations. A series of machine learning and statistical denoising techniques are applied to enhance the detection power. On the simulation data, cfTrack achieved an average AUC of 99% on the validation dataset and 100% on the independent dataset in detecting recurrence in samples with tumor fraction ≥0.05%. In addition, cfTrack yielded an average AUC of 88% in detecting second primary cancers in samples with tumor fraction ≥0.2%. On real data, cfTrack accurately monitors tumor evolution during treatment, which cannot be accomplished by previous methods.ConclusionOur results demonstrated that cfTrack can sensitively and specifically monitor the full spectrum of cancer treatment outcomes using exome-wide mutation analysis of cfDNA.Translational RelevanceContinuous cancer monitoring is clinically necessary for cancer patients to detect minimal residual disease (MRD), recurrence, and progression, allowing for early intervention and therapy adjustment. Cell-free DNA (cfDNA) in blood has become an appealing option due to its non-invasiveness. Until now, cfDNA-based cancer monitoring methods have been focused on deep sequencing at a few known mutations, which are however insufficient when tumors evolve or new tumors emerge. We present the method, cfTrack, which for the first time uses whole-exome sequencing (WES) of cfDNA to track the full range of cancer treatment outcomes, including MRD, recurrence, evolution, and second primary cancer. We demonstrate that, even with very low tumor fractions, cfTrack achieves sensitive and specific monitoring of tumor MRD/recurrence/evolution based on both simulation data and a cohort of cancer patients. These findings demonstrate the clinical utility of cfTrack.

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Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis

Cited by 5 publications

References 37 publications

At the dawn: cell-free DNA fragmentomics and gene regulation

At the dawn: cell-free DNA fragmentomics and gene regulation

Hairpin structure facilitates multiplex high-fidelity DNA amplification in real-time PCR

cfTrack: Exome-wide mutation analysis of cell-free DNA to simultaneously monitor the full spectrum of cancer treatment outcomes: MRD, recurrence, and evolution

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