Dataset Information

Integrating genomic features for non-invasive early lung cancer detection.

ABSTRACT: Radiologic screening of high-risk adults reduces lung-cancer-related mortality^1,2; however, a small minority of eligible individuals undergo such screening in the United States^3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)⁵, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent. Compared with tumour-derived mutations, clonal haematopoiesis mutations occur on longer cfDNA fragments and lack mutational signatures that are associated with tobacco smoking. Integrating these findings with other molecular features, we develop and prospectively validate a machine-learning method termed 'lung cancer likelihood in plasma' (Lung-CLiP), which can robustly discriminate early-stage lung cancer patients from risk-matched controls. This approach achieves performance similar to that of tumour-informed ctDNA detection and enables tuning of assay specificity in order to facilitate distinct clinical applications. Our findings establish the potential of cfDNA for lung cancer screening and highlight the importance of risk-matching cases and controls in cfDNA-based screening studies.

SUBMITTER: Chabon JJ

PROVIDER: S-EPMC8230734 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Integrating genomic features for non-invasive early lung cancer detection.

Chabon Jacob J JJ Hamilton Emily G EG Kurtz David M DM Esfahani Mohammad S MS Moding Everett J EJ Stehr Henning H Schroers-Martin Joseph J Nabet Barzin Y BY Chen Binbin B Chaudhuri Aadel A AA Liu Chih Long CL Hui Angela B AB Jin Michael C MC Azad Tej D TD Almanza Diego D Jeon Young-Jun YJ Nesselbush Monica C MC Co Ting Keh Lyron L Bonilla Rene F RF Yoo Christopher H CH Ko Ryan B RB Chen Emily L EL Merriott David J DJ Massion Pierre P PP Mansfield Aaron S AS Jen Jin J Ren Hong Z HZ Lin Steven H SH Costantino Christina L CL Burr Risa R Tibshirani Robert R Gambhir Sanjiv S SS Berry Gerald J GJ Jensen Kristin C KC West Robert B RB Neal Joel W JW Wakelee Heather A HA Loo Billy W BW Kunder Christian A CA Leung Ann N AN Lui Natalie S NS Berry Mark F MF Shrager Joseph B JB Nair Viswam S VS Haber Daniel A DA Sequist Lecia V LV Alizadeh Ash A AA Diehn Maximilian M

Nature 20200325 7802

Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, ...[more]

PMID: 32269342

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Project description:Background: Clinical outcomes of bladder cancer (BC) are tightly associated with the stage and grade of the initial diagnosis of BC because early detection is clearly important for patients with BC. However, the diagnostic capability of current detection methods, such as urinary cytology, cystoscopy, imageology method, and several urine-based tests, is inadequate for early detection of BC. The objective of our study is to discover novel biomarkers for detecting BC at an early stage, called non-muscle invasive (NMI) BC, using liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based metabolomics. Methods: First, morning midstream urine samples were collected from healthy adult and NMIBC patients. The LC-HRMS-based metabolomics were applied to distinguish the NMIBC group without hematuria from the controls (gender- and age-matched volunteers with normal clinically healthy index), low-grade NMIBC from the controls, and high-grade from low-grade NMIBC. Results: A total of 284 subjects were enrolled in our study including 117 healthy adults, 80 NMIBC patients without hematuria, and 87 NMIBC patients with hematuria. The metabolite panel including dopamine 4-sulfate, MG00/1846Z,9Z,12Z,15Z/00, aspartyl-histidine, and tyrosyl-methionine was found in a discovery set, which showed the predictive ability to distinguish the NMIBC group from the control group with an area under the curve (AUC) of 0.838 in an external validation set. The AUC of the panel for low-grade NMIBC samples, which consisted of 3-hydroxy-cis-5-tetradecenoylcarnitine, 6-ketoestriol, beta-cortolone, tetrahydrocorticosterone, and heptylmalonic acid, was 0.899. The sensitivity and specificity were 0.881 and 0.786, respectively. The AUC of the panel for distinction of low-grade NMIBC with and without hematuria against high-grade NMIBC with and without hematuria were 0.827 and 0.755, respectively. In addition, metabolites involved in tryptophan metabolism were upregulated in the urine of high-grade NMIBC patients when compared with low-grade NMIBC patients with the presence or absence of hematuria. Conclusion: The NMIBC urine metabolic profiling was able to assist in the early detection of BC. Panels of metabolites were discovered to have a potential value for high-grade NMIBC and low-grade NMIBC diagnosis as well as for NMIBC grading distinction.

Dataset Information

Integrating genomic features for non-invasive early lung cancer detection.

Publications

Integrating genomic features for non-invasive early lung cancer detection.

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