Integrated digital error suppression for improved detection of circulating tumor DNA

Newman, Aaron M.; Lovejoy, Alexander F.; Klass, Daniel M.; Kurtz, David M.; Chabon, Jacob J.; Scherer, Florian; Stehr, Henning; Liu, Chih Long; Bratman, Scott V.; Say, Carmen; Zhou, Li; Carter, Justin N.; West, Robert B.; Sledge, George W.; Shrager, Joseph B.; Loo, Billy W.; Neal, Joel W.; Wakelee, Heather A.; Diehn, Maximilian; Alizadeh, Ash A.

doi:10.1038/nbt.3520

Cited by 902 publications

(1,022 citation statements)

References 50 publications

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“…The same authors recently re-engineered their approach by combining a digital error suppression (iDES) technique to reduce background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. This combination of techniques resulted in a 15-fold improvement in respect to sensitivity [30]. This example shows that detection of unknown biomarkers within a screening procedure in stage 1 tumor patients is currently at the technical limits of known methods, and that only a combination of bioinformatics and sophisticated molecular techniques will solve this problem.…”

Section: Deep Sequencing-based Approaches/ Ngs-based Methodsmentioning

confidence: 93%

Detection and characterization of circulating cell free tumor DNA in cancer patients with malignant solid tumors. Liquid biopsy: a new tool in molecular pathology?

Hinrichsen

Dworniczak

Wachter

et al. 2016

LaboratoriumsMedizin

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Abstract:The term liquid biopsy comprises methods of blood-based analysis of nucleic acids, which are increasingly under discussion in oncology and personalized medicine, and are already applied in individual cases. The analysis of tumor markers, which in certain tumor diseases can be found as protein markers in vast amounts in the blood, constitutes a primary form of liquid biopsy. Cell-free circulating DNA fragments in the blood (ctDNA), which reflect the genetic profile of a tumor cell and are released in different ways by the tumor, represent a new class of more specific and sensitive biomarkers that can be correlated with the dynamics of the tumor disease. New technologies based on PCR and sequencing techniques pave the way for diagnostic approaches to define molecular tumor characteristics, not only in tumor tissue but also in the blood, by analyzing cell-free circulating DNA.The combination of molecular profiling of the tumor with ctDNA analytics by liquid biopsy is a promising step in the advancement of precision medicine.

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Section: Deep Sequencing-based Approaches/ Ngs-based Methodsmentioning

confidence: 93%

Detection and characterization of circulating cell free tumor DNA in cancer patients with malignant solid tumors. Liquid biopsy: a new tool in molecular pathology?

Hinrichsen

Dworniczak

Wachter

et al. 2016

LaboratoriumsMedizin

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“…This number can be measured by calculating the ratio of the detected individual molecules after sequencing to the total approximate number of DNA molecules that enter the assay. Over last five years, this metric improved from around 30% in 2011 (86) to more than 60% in 2016 (89).…”

Section: Error Suppression Methodsmentioning

confidence: 99%

“…In our own data, (Assouline and colleagues, in review) we have directly inferred mutations from ctDNA libraries using a similar error suppression strategy at levels as low as 1% across a broad gene panel. An interesting combination approach termed "integrated digital error suppression" (iDES) was described in 2016 by Newman and colleagues (89). The authors redesigned their previously published Capp-Seq panel (81) to integrate molecular barcoding into their workflow.…”

Section: Error Suppression Methodsmentioning

confidence: 99%

Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies

Volik¹,

Alcaide

Morin

et al. 2016

Molecular Cancer Research

300

235

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Precision oncology is predicated upon the ability to detect specific actionable genomic alterations and to monitor their adaptive evolution during treatment to counter resistance. Because of spatial and temporal heterogeneity and comorbidities associated with obtaining tumor tissues, especially in the case of metastatic disease, traditional methods for tumor sampling are impractical for this application. Known to be present in the blood of cancer patients for decades, cell-free DNA (cfDNA) is beginning to inform on tumor genetics, tumor burden, and mechanisms of progression and drug resistance. This substrate is amenable for inexpensive noninvasive testing and thus presents a viable approach to serial sampling for screening and monitoring tumor progression. The fragmentation, low yield, and variable admixture of normal DNA present formidable technical challenges for realization of this potential. This review summarizes the history of cfDNA discovery, its biological properties, and explores emerging technologies for clinically relevant sequence-based analysis of cfDNA in cancer patients. Molecular barcoding (or Unique Molecular Identifier, UMI)-based methods currently appear to offer an optimal balance between sensitivity, flexibility, and cost and constitute a promising approach for clinically relevant assays for near real-time monitoring of treatment-induced mutational adaptations to guide evidence-based precision oncology.

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“…However, there is a paucity of cfDNA data sets large enough to evaluate the similarity of tumor-initiating alterations ("truncal drivers") in solid tumor cancers to those found in the cfDNA of advanced cancer patients. Among the various methods available for cfDNA analysis, targeted panel deep-sequencing assays that utilize extensive errorcorrection methods provide the depth (sensitivity) and genomic breadth necessary to optimally survey tumor-derived genomic alterations in plasma cfDNA, even at low allelic fractions (12)(13)(14)(15).…”

Section: Introductionmentioning

confidence: 99%

The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients

Zill

Banks

Fairclough

et al. 2018

Clinical Cancer Research

307

249

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Running title: Somatic genomic landscape of circulating tumor DNA Keywords: circulating tumor DNA, tumor heterogeneity, resistance, genomic landscape, cfDNA clonality Financial support: The study was funded by and conducted at Guardant Health, Inc. No additional grant support or administrative support was provided for the study. *Corresponding author:Stephen R. Fairclough Translational relevanceThis study describes genomic alterations from the largest cell-free circulating tumor DNA cohort to date, as derived from regular clinical practice. The high prevalence of resistance alterations found in advanced, treated cancer patients necessitated accurate methods for determining mutation clonality and driver/resistance status from plasma. We provide such methods, thereby extending the utility of cell-free DNA sequencing analysis. Our finding of an association between estimated circulating tumor DNA (ctDNA) levels and tumor mutational burden ascertained from plasma suggests that ctDNA level is likely an important variable to consider for immunotherapy applications of ctDNA analysis. Although cell-free DNA can provide a summary of tumor heterogeneity across multiple metastatic sites in a patient, our findings of high variability in ctDNA levels across patients, and its impact on variant detection, highlight the need for an improved understanding of factors influencing ctDNA levels and safe methods for maximizing them at the time of ctDNA testing. AbstractPurpose: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants.Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types. To facilitate interpretation of the genomic complexity of circulating tumor DNA in advanced, treated cancer patients, we developed methods to identify cfDNA copy-number driver alterations and cfDNA clonality.Results: Patterns and prevalence of cfDNA alterations in major driver genes for non-small cell lung, breast, and colorectal cancer largely recapitulated those from tumor tissue sequencing compendia (TCGA and COSMIC;, with the principle differences in alteration prevalence being due to patient treatment. This highly sensitive cfDNA sequencing assay revealed numerous subclonal tumor-derived alterations, expected as a result of clonal evolution, but leading to an apparent departure from mutual exclusivity in treatment-naïve tumors. Upon applying novel cfDNA clonality and copy-number driver identification methods, robust mutual exclusivity was observed among predicted truncal driver cfDNA alterations (FDR=5x10 -7 for EGFR and ERBB2), in effect distinguishing tumor-initiating alterations from secondary alterations. Treatment-associated resistance, including both novel ...

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Integrated digital error suppression for improved detection of circulating tumor DNA

Cited by 902 publications

References 50 publications

Detection and characterization of circulating cell free tumor DNA in cancer patients with malignant solid tumors. Liquid biopsy: a new tool in molecular pathology?

Detection and characterization of circulating cell free tumor DNA in cancer patients with malignant solid tumors. Liquid biopsy: a new tool in molecular pathology?

Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies

The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients

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