eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-Free DNAs in Blood

Zou, Jinfeng; Wang, Edwin

doi:10.1016/j.gpb.2017.01.004

Cited by 18 publications

(11 citation statements)

References 41 publications

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“…The clinical usefulness of ctDNA analysis is confirmed by the recent approval by the Food and Drug Administration of the cobas EGFR Mutation Test v2 as a blood-based diagnostic tool for the detection of epidermal growth factor receptor ( EGFR ) mutations and selection of non-small cell lung cancer patients who are candidates for erlotinib treatment 8 . Also, algorithms have been proposed for non-invasive diagnosis and discrimination of cancer type based on copy number variation in ctDNA 9 .…”

Section: Introductionmentioning

confidence: 99%

KRAS and BRAF mutations in circulating tumour DNA from locally advanced rectal cancer

Sclafani

Chau

Cunningham

et al. 2018

Sci Rep

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There are limited data on circulating, cell-free, tumour (ct)DNA analysis in locally advanced rectal cancer (LARC). Digital droplet (dd)PCR was used to investigate KRAS/BRAF mutations in ctDNA from baseline blood samples of 97 LARC patients who were treated with CAPOX followed by chemoradiotherapy, surgery and adjuvant CAPOX ± cetuximab in a randomised phase II trial. KRAS mutation in G12D, G12V or G13D was detected in the ctDNA of 43% and 35% of patients with tumours that were mutant and wild-type for these hotspot mutations, respectively, according to standard PCR-based analyses on tissue. The detection rate in the ctDNA of 10 patients with less common mutations was 50%. In 26 cases ctDNA analysis revealed KRAS mutations that were not previously found in tissue. Twenty-two of these (84.6%) were detected following repeat tissue testing by ddPCR. Overall, the ctDNA detection rate in the KRAS mutant population was 66%. Detection of KRAS mutation in ctDNA failed to predict prognosis or refine patient selection for cetuximab. While this study confirms the feasibility of ctDNA analysis in LARC and the high sensitivity of ddPCR, larger series are needed to better address the role of ctDNA as a prognostic or predictive tool in this setting.

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Section: Introductionmentioning

confidence: 99%

KRAS and BRAF mutations in circulating tumour DNA from locally advanced rectal cancer

Sclafani

Chau

Cunningham

et al. 2018

Sci Rep

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“…In future researches, we attempt to quantify and computationally dissect clones from tumors and conduct clone-based analysis, in order to decipher the evolutionary dynamics of tumor clonal networks during confined-lymphnode transition 41 , 42 . Additionally, circulating tumor cells (CTCs) and cell-free DNAs (cfDNAs) in blood samples could also be used to discover the promising biomarkers and promising therapeutic targets 43 . The underlying molecular mechanism during confined-lymphnode transition might surprise us with its great value in cancer research.…”

Section: Discussionmentioning

confidence: 99%

Identification of prognostic genes through expression differentiation during metastatic process in lung adenocarcinoma

Yang

2017

Sci Rep

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Cancer is a highly complicated biological process due to large scale heterogeneity. Identification of differentially expressed genes between normal and cancer samples is widely utilized in the discovery of prognostic factors. In this study, based on RNA sequencing data of lung adenocarcinoma, we focused on the expression differentiation during confined (with neither lymph node invasion nor distant metastasis) primary tumors and lymphnode (with only lymph node invasion but not distant metastasis) primary tumors. The result indicated that differentially expressed genes during confined-lymphnode transition were more closely related to patient’s overall survival comparing with those identified from normal-cancer transition. With the aid of public curated biological network, we successfully retrieved the biggest connected module composed of 135 genes, of which the expression was significantly associated with patient’s overall survival, confirmed by 9 independent microarray datasets.

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“…Random Forest and its extension are widely used in the recent research of disease diagnosis. Ada, a variates of Random Forest was used in cfDNA discrimination of cancer types [25]. A sparse regression-based random forest was designed to predict the Alzheimer's disease [26].…”

Section: Random Forest With Balanced Subsamplingmentioning

confidence: 99%

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

Pei

et al. 2020

J Transl Med

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Background: Sepsis remains a major challenge in intensive care units, causing unacceptably high mortality rates due to the lack of rapid diagnostic tools with sufficient sensitivity. Therefore, there is an urgent need to replace time-consuming blood cultures with a new method. Ideally, such a method also provides comprehensive profiling of pathogenic bacteria to facilitate the treatment decision. Methods: We developed a Random Forest with balanced subsampling to screen for pathogenic bacteria and diagnose sepsis based on cell-free DNA (cfDNA) sequencing data in a small blood sample. In addition, we constructed a bacterial co-occurrence network, based on a set of normal and sepsis samples, to infer unobserved bacteria. Results: Based solely on cfDNA sequencing information from three independent datasets of sepsis, we distinguish sepsis from healthy samples with a satisfactory performance. This strategy also provides comprehensive bacteria profiling, permitting doctors to choose the best treatment strategy for a sepsis case. Conclusions: The combination of sepsis identification and bacteria-inferring strategies is a success for noninvasive cfDNA-based diagnosis, which has the potential to greatly enhance efficiency in disease detection and provide a comprehensive understanding of pathogens. For comparison, where a culture-based analysis of pathogens takes up to 5 days and is effective for only a third to a half of patients, cfDNA sequencing can be completed in just 1 day and our method can identify the majority of pathogens in all patients.

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eTumorType, An Algorithm of Discriminating Cancer Types for Circulating Tumor Cells or Cell-Free DNAs in Blood

Cited by 18 publications

References 41 publications

KRAS and BRAF mutations in circulating tumour DNA from locally advanced rectal cancer

KRAS and BRAF mutations in circulating tumour DNA from locally advanced rectal cancer

Identification of prognostic genes through expression differentiation during metastatic process in lung adenocarcinoma

Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA

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