Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

ABSTRACTAlterations in the genetic content, such as Copy Number Variations (CNVs) is one of the hallmarks of cancer and their detection is used to recognize tumoral DNA. Analysis of cell-free DNA from plasma is a powerful tool for non-invasive disease monitoring in cancer patients. Here we exploit third generation sequencing (Nanopore) to obtain a CNVs profile of tumoral DNA from plasma, where cancer-related chromosomal alterations are readily identifiable.Compared to Illumina sequencing -the only available alternative- Nanopore sequencing represents a viable approach to characterize the molecular phenotype, both for its ease of use, costs and rapid turnaround (6 hours).

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Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

Molecular Cancer ◽

10.1186/s12943-021-01327-5 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Filippo Martignano ◽

Uday Munagala ◽

Stefania Crucitta ◽

Alessandra Mingrino ◽

Roberto Semeraro ◽

...

Keyword(s):

Lung Cancer ◽

Cancer Patients ◽

Liquid Biopsy ◽

Copy Number ◽

Dna Analysis ◽

Copy Number Variations ◽

Nanopore Sequencing ◽

Cell Free Dna ◽

Lung Cancer Patients ◽

Free Dna

AbstractIn the “precision oncology” era the characterization of tumor genetic features is a pivotal step in cancer patients’ management. Liquid biopsy approaches, such as analysis of cell-free DNA from plasma, represent a powerful and noninvasive strategy to obtain information about the genomic status of the tumor. Sequencing-based analyses of cell-free DNA, currently performed with second generation sequencers, are extremely powerful but poorly scalable and not always accessible also due to instrumentation costs. Third generation sequencing platforms, such as Nanopore sequencers, aim at overcoming these obstacles but, unfortunately, are not designed for cell-free DNA analysis.Here we present a customized workflow to exploit low-coverage Nanopore sequencing for the detection of copy number variations from plasma of cancer patients. Whole genome molecular karyotypes of 6 lung cancer patients and 4 healthy subjects were successfully produced with as few as 2 million reads, and common lung-related copy number alterations were readily detected.This is the first successful use of Nanopore sequencing for copy number profiling from plasma DNA. In this context, Nanopore represents a reliable alternative to Illumina sequencing, with the advantages of minute instrumentation costs and extremely short analysis time.The availability of protocols for Nanopore-based cell-free DNA analysis will make this analysis finally accessible, exploiting the full potential of liquid biopsy both for research and clinical purposes.

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Detection and oncological impact of circulating tumor cells in bladder cancer patients with presence of copy number variations of circulating cell free DNA.

Journal of Clinical Oncology ◽

10.1200/jco.2018.36.6_suppl.495 ◽

2018 ◽

Vol 36 (6_suppl) ◽

pp. 495-495 ◽

Cited By ~ 1

Author(s):

Armin Soave ◽

Heidi Schwarzenbach ◽

Malte Vetterlein ◽

Jessica Rührup ◽

Oliver Engel ◽

...

Keyword(s):

Bladder Cancer ◽

Cancer Patients ◽

Tumor Cells ◽

Circulating Tumor Cells ◽

Copy Number ◽

Copy Number Variations ◽

Chromosome 8 ◽

Cell Free Dna ◽

Free Dna ◽

Circulating Cell Free Dna

495 Background: To investigate detection and oncological impact of circulating tumor cells (CTC) in bladder cancer patients with presence of copy number variations (CNV) of circulating cell-free DNA (cfDNA) treated with radical cystectomy (RC). Methods: Secondary analysis of 85 bladder cancer patients, who were prospectively enrolled and treated with RC at our institution between 2011 and 2014. Blood samples were obtained preoperatively. For CTC analysis, blood was analyzed with the CellSearch system (Janssen). cfDNA was extracted from serum using the PME DNA Extraction kit (Analytik Jena). Multiplex ligation-dependent probe amplification (MLPA) was carried out to identify CNV of cfDNA. In a single reaction MLPA allows analyzing CNV in 43 chromosomal regions containing 37 genes. Results: MLPA was suitable for characterization of CNV in 72 patients (84.7%). Data on CTC was available for 45 of these patients (62.5%). In total, 7 patients (15.6%) had CTC with a median CTC count of one (IQR: 1-3). In 21 patients (46.7%), one to 6 deleted or amplified chromosomal regions were detected with a median CNV count of 2 (IQR: 1-2). Overall, most changes were located in the genes CDH1, RIPK2 and ZFHX3 in 8 patients (17.8%), 6 patients (13.3%) and 5 patients (11.1%). Chromosomal aberrations were most frequently found on chromosome 8 in 8 patients (17.8%). Overall, presence of CTC was not associated with CNV status. However, presence of CTC was associated with copy number losses in miR-15a (p = 0.011). Patients with CTC had reduced recurrence-free survival (RFS) compared to patients without CTC (p = 0.012). In combined Kaplan-Meier analysis, patients with CTC plus presence of CNV had reduced cancer-specific survival (CSS) and RFS compared to patients without CTC but with presence of CNV (p≤0.035). In addition, patients with CTC plus presence of CNV had reduced RFS compared to patients without CTC and without presence of CNV (p = 0.028). Conclusions: CTC and CNV of various genes are detectable in peripheral blood of bladder cancer patients. The presence of CTC seems to be associated with CNV of specific genes. CTC have a negative impact on survival in patients with and without presence of CNV.

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Cell-free DNA copy number variations in plasma from colorectal cancer patients

Molecular Oncology ◽

10.1002/1878-0261.12077 ◽

2017 ◽

Vol 11 (8) ◽

pp. 1099-1111 ◽

Cited By ~ 27

Author(s):

Jian Li ◽

Rachel L. Dittmar ◽

Shu Xia ◽

Huijuan Zhang ◽

Meijun Du ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Patients ◽

Copy Number ◽

Copy Number Variations ◽

Dna Copy Number ◽

Dna Copy Number Variations ◽

Cell Free Dna ◽

Free Dna ◽

Colorectal Cancer Patients

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A novel decision tree model based on chromosome imbalances in cell-free DNA and CA-125 in the differential diagnosis of ovarian cancer

The International Journal of Biological Markers ◽

10.1177/1724600821992356 ◽

2021 ◽

pp. 172460082199235

Author(s):

Weina Zhang ◽

Yu-min Zhang ◽

Yuan Gao ◽

Shengmiao Zhang ◽

Weixin Chu ◽

...

Keyword(s):

Ovarian Cancer ◽

Differential Diagnosis ◽

Decision Tree ◽

Copy Number ◽

Malignant Tumors ◽

Copy Number Variations ◽

Ca 125 ◽

Benign Tumors ◽

Cell Free Dna ◽

Free Dna

Objective: CA-125 is widely used as biomarker of ovarian cancer. However, CA-125 suffers low accuracy. We developed a hybrid analytical model, the Ovarian Cancer Decision Tree (OCDT), employing a two-layer decision tree, which considers genetic alteration information from cell-free DNA along with CA-125 value to distinguish malignant tumors from benign tumors. Methods: We consider major copy number alterations at whole chromosome and chromosome-arm level as the main feature of our detection model. Fifty-eight patients diagnosed with malignant tumors, 66 with borderline tumors, and 10 with benign tumors were enrolled. Results: Genetic analysis revealed significant arm-level imbalances in most malignant tumors, especially in high-grade serous cancers in which 12 chromosome arms with significant aneuploidy ( P<0.01) were identified, including 7 arms with significant gains and 5 with significant losses. The area under receiver operating characteristic curve (AUC) was 0.8985 for copy number variations analysis, compared to 0.8751 of CA125. The OCDT was generated with a cancerous score (CScore) threshold of 5.18 for the first level, and a CA-125 value of 103.1 for the second level. Our most optimized OCDT model achieved an AUC of 0.975. Conclusions: The results suggested that genetic variations extracted from cfDNA can be combined with CA-125, and together improved the differential diagnosis of malignant from benign ovarian tumors. The model would aid in the pre-operative assessment of women with adnexal masses. Future clinical trials need to be conducted to further evaluate the value of CScore in clinical settings and search for the optimal threshold for malignancy detection.

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