Studying Copy Number Variations in Cell-Free DNA: The Example of AR in Prostate Cancer

2018 ◽  
pp. 95-103
Author(s):  
Samanta Salvi ◽  
Valentina Casadio
Keyword(s):  
Prostate Cancer ◽  
Copy Number ◽  
Copy Number Variations ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Copy number variations in urine cell free DNA as biomarkers in advanced prostate cancer

Oncotarget ◽  
2016 ◽  
Vol 7 (24) ◽  
pp. 35818-35831 ◽  
Author(s):  
Yun Xia ◽  
Chiang-Ching Huang ◽  
Rachel Dittmar ◽  
Meijun Du ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Copy Number ◽  
Advanced Prostate Cancer ◽  
Copy Number Variations ◽  
Cell Free Dna ◽  
Free Dna

Quantifying copy number variations in cell-free DNA for potential clinical utility from a large prostate cancer cohort.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 5072-5072
Author(s):  
Ekkehard Schütz ◽  
Mohammad R Akbari ◽  
Julia Beck ◽  
Howard B. Urnovitz ◽  
William Zhang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Copy Number ◽  
Area Under The Curve ◽  
Roc Curves ◽  
Copy Number Variations ◽  
Male Population ◽  
Cell Free Dna ◽  
Free Dna ◽  
Statistical Separation

5072 Background: Prostate cancer (PrCa) is the most frequent non-dermatological malignancy in the male population. Genomic instability resulting in copy number variation (CNV) is a hallmark of malignant transformation. CNV traces from tumors in cell-free DNA (cfDNA) of prostate cancer patients may be identified through massive parallel sequencing (MPS) of serum DNA. These CNV traces may be biomarkers of cancer with clinical applications for screening and follow-up. Methods: DNA was extracted from serum of 205 PrCa patients (Gleason 2 to10), 207 age matched male controls (HC), 10 men with benign hyperplasia (BPH) and 10 with prostatitis (PiS). DNA was amplified using random primers, tagged with a unique molecular identifier per sample, sequenced on a SOLiD system and aligned to the human genome (Build 37). Hits were counted in sliding 100kbp intervals and normalized. Using a random-resampling procedure, genomic regions showing copy number variations in cfDNA that distinguish PrCa from HC were selected. A model using 20 cfDNA regions was cross-validated and used as cfDNA biomarker. Receiver operator characteristics (ROC) curves were calculated for assessment of diagnostic performance by means of area under the curve (AUC). Results: To assess whether CNVs in cfDNA are indicative of PrCa, the number of regions with significant CNV deviation was counted in a first subset of 82 PrCa. Using only the number of regions as measure resulted in an AUC of 0.81 (0.7 – 0.9, p<0.001). Therefore, all samples were used to select regions (n=80) in random resampling (50/50). These regions were used to define a highly significant 20-regions model using five rounds of 10-fold cross-validation (AUC: 0.85±0.7; p< 10-7). This final model discriminated between PrCa and HC with an AUC of 0.92 (0.87 – 0.95) reaching a calculated accuracy of 83%. Both BPH and PiS could be distinguished from PrCa using the cfDNA CNV biomarker with a predicted accuracy of 90%. Conclusions: MPS revealed that only a limited number of chromosomal regions showing CNVs are necessary to achieve statistical separation between prostate cancer and controls. This technique may prove to be clinically useful for screening and follow up of men with prostate cancer.

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

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.

Copy number variations in AR-associated and DNA repair genes from plasma cell-free DNA of metastatic CRPC patients.

2016 ◽  
Vol 34 (2_suppl) ◽  
pp. 281-281 ◽  
Author(s):  
Ratish Gambhira ◽  
Elisa M. Ledet ◽  
Aryeneesh Dotiwala ◽  
Diptasri Mandal ◽  
A. Oliver Sartor
Keyword(s):  
Prostate Cancer ◽  
Dna Repair ◽  
Cancer Progression ◽  
Copy Number ◽  
Genetic Alterations ◽  
Copy Number Variations ◽  
Dna Repair Genes ◽  
Prostate Cancer Progression ◽  
Free Dna ◽  
Repair Genes

281 Background: Cell-free DNA (cfDNA) present in the plasma of advanced cancer patients can reflect tumor related genetic alterations. Recent data suggests copy number variations (CNVs) in AR-associated and DNA repair pathway genes play a potential role in prostate cancer progression. Here, we performed sequencing of cfDNA from 13 mCRPC patients to evaluate its potential in elucidating tumor related genetic variations. The long-term goal of our project is to correlate cfDNA derived genetic alterations with prostate cancer progression and/or therapeutic resistance/responses. Methods: cfDNA was isolated from 13 advanced mCRPC patient plasma samples using the Qiagen circulating nucleic acid kit. 100ng of cfDNA was utilized for library construction; and the libraries were paired-end sequenced on the Illumina HiSeq 2000. The resulting data was analyzed using the GATK best practices bioinformatics pipeline and the visualized using the SNP & Variation Suite v8.x. Results: The bioanalyzer profiles of cfDNA derived from mCRPC patients is highly fragmented with an average fragment size of 306-605bp. Although, several CNVs were found across the genome, we focused analysis on CNVs related to AR associated and DNA repair genes. Our preliminary analysis of cfDNA, despite low sequencing depth, shows full or partial amplifications in AR (13/13), and other genes including FOXA1, NCOR1, NCOR2 and/or PIK3CA (7/13) and NCOR2 (10/13). For DNA repair genes partial/full amplifications were present in BRAC1, BRAC2, ATM, CDK12, MLH1 and/or MSH2 (7/13). Deletions are less reliably detected in the highly fragmented cfDNA. The majority of these CNVs have been reported in the WGS studies from metastatic CRPC tissue derived genomic DNA (cBioPortal). We are currently validating cfDNA genomic alterations by comparing it to germ line DNA derived via qPCR. Conclusions: Our preliminary study indicates that AR and DNA repair related genetic alterations could be found in the cfDNA derived from metastatic CRPC patients. This warrants more detailed examination of these cfDNA genetic alterations for identifying clinically relevant issues in mCRPC patients.

Plasma cell free DNA (cfDNA) based somatic aberrations detected in treatment naïve metastatic hormone sensitive prostate cancer (mHSPC), hormonally ablated mHSPC and metastatic castration resistant prostate cancer (mCRPC) states and their impact on survival.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 5047-5047
Author(s):  
Manish Kohli ◽  
Winston Tan ◽  
Tiantian Zheng ◽  
Amy Wang ◽  
Calvin Wong ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Plasma Cell ◽  
Copy Number Variations ◽  
Cell Free Dna ◽  
Androgen Ablation ◽  
Free Dna ◽  
Impact On Survival ◽  
Treatment Naïve ◽  
The Impact ◽  
Somatic Aberrations

5047 Background: We identified plasma cell free DNA (cfDNA) based copy number variations (CNV); single nucleotide variants (SNVs) & TMPRSS-ERG fusion in four sub states of metastatic prostate cancer (mPCa) and determined the impact on survival. Two mHSPC cohorts included treatment naïve, gp-1 and mHSPC patients (pts) responding to chronic androgen ablation (AA) (gp-2). Two mCRPC cohorts included mHSPC pts with PSA relapse on chronic AA (gp-3) and a clinically progressive mCRPC cohort post AA (gp-4). Methods: Enrollment of mPCa pts was performed from 2009-14 who were followed until 2018. Plasma from collected blood was used for extracting cfDNA. NGS was performed using Illumina HiSeq X for a preselected target panel of 129 genes including DNA damage repair genes. Statistical analyses of genomic aberrations were performed in R 3.5.1 and Cox proportional-hazard models were used for survival analyses. Results: A total of 255 pts were enrolled with 215 having adequate cfDNA that passed NGS QC. Median study follow up was 90.2 (Range:73;99) months. The table highlights pts in each gp with CNV, SNV, fusion events. ARamplification was higher in mCRPC gps3&4 (20/103 pts) compared to 3/106 pts in mHSPC gps1&2 (p < 0.001) and was prognostic for poor survival in mCRPC (p < 0.001;HR:3.34; 95%CI: 1.9-5.76). 54/103 pts in gp3&4 had SNVs in TP53 compared to 34/106 pts in mHSPC gps1&2 (P < 0.01). SNVs in APC, AR, CDK12 and BRIP1 were also increased in gps3&4 (p < 0.01). Gp1 mHSPC pts with SNVs in ATM/ CHEK2 had shorter response to AA (p < 0.001; HR:3.66; 95%: CI:1.81-7.39). Conclusions: Plasma cfDNA based somatic aberrations are detected with increased prevalence in mHSPC to mCRPC states. The ease of specimen collection and the need for molecular profiling in mPCa increases its potential for clinical applications in pt care. [Table: see text]

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

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 495-495 ◽  
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.

5-hydroxymethylcytosine as a liquid biopsy biomarker in mCRPC.

2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 148-148
Author(s):  
Martin Sjöström ◽  
Shuang Zhao ◽  
Eric Jay Small ◽  
Yuhong Ning ◽  
Corinne Maurice-Dror ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Overall Survival ◽  
High Risk ◽  
Liquid Biopsy ◽  
Copy Number ◽  
Whole Genome ◽  
Cell Free Dna ◽  
Free Dna ◽  
Disease Specific

148 Background: 5-hydroxymethylcytosine (5hmC) is an epigenetic modification which regulates gene expression and is associated with active transcription. The optimization of 5hmC sequencing in cell-free DNA (cfDNA) could therefore enable assessment of gene activity through a liquid biopsy. We aimed to investigate the 5hmC landscape of metastatic castration-resistant prostate cancer (mCRPC) and to evaluate the potential of 5hmC modifications in cfDNA as biomarkers of outcome in mCRPC patients. Methods: Genome-wide 5hmC modifications were analyzed with a low-input whole-genome 5hmC sequencing method based on selective chemical labeling in DNA from 93 mCRPC tissue biopsies previously profiled with whole-genome sequencing (WGS), RNA-sequencing and whole-genome bisulfite sequencing (WGBS). In addition, we analyzed 64 cell-free DNA (cfDNA) samples, from men with mCRPC before first-line abiraterone or enzalutamide, with both 5hmC sequencing and a conventional targeted ctDNA panel assessing common genomic alterations. Results: In mCRPC tissue samples, 5hmC enrichment was more strongly associated with gene expression than promoter methylation or copy number. Among cancer hallmark pathways, the androgen response genes had the strongest association between 5hmC and gene expression, suggesting a disease specific marking of gene activation. 5hmC patterns in cfDNA could be used to estimate the circulating tumor DNA fraction (ct-fraction), which was prognostic for overall survival (tertiles of ct-fraction, HR = 1.6 95%CI 1.1-2.3, p = 0.007). Further, 5hmC levels were indicative of gain of oncogene activity (such as AR, MYC, and PIK3CA) and loss of tumor suppressor gene activity (such as RB1, TP53 and BRCA2). The number of alterations, by 5hmC levels, of common drivers of mCRPC was prognostic for overall survival, also after adjusting for ct-fraction (adjusted p = 0.00001), and the prognostic value of common alterations detected by 5hmC sequencing versus conventional targeted ctDNA sequencing was similar. Finally, 5hmC levels in cfDNA of genes not significantly altered by copy number gain or loss (and thus not routinely included in targeted ctDNA sequencing assays), such as TOP2A and EZH2, identified a high-risk subgroup of mCRPC, which was highly prognostic for overall survival independent of ct-fraction (adjusted HR = 1.8 95%CI 1.2-2.8, p = 0.007). Conclusions: 5hmC in mCRPC tissue demonstrated an association with gene expression that was highest for prostate cancer driver genes, highlighting the ability to track disease-specific biology. 5hmC in cfDNA from men with mCRPC can be used to estimate the ct-fraction of the sample, infer activity gain and loss of common drivers of mCRPC, and identify high-risk groups of mCRPC based on alterations not commonly detected with conventional ctDNA sequencing, showing its potential as a liquid biomarker. Further studies are aimed at optimizing and validating 5hmC-based biomarkers in larger cohorts.

scholarly journals The landscape of copy number variations in classical Hodgkin lymphoma: a joint KU Leuven and LYSA study on cell-free DNA

2021 ◽  
Vol 5 (7) ◽  
pp. 1991-2002
Author(s):  
Lieselot Buedts ◽  
Iwona Wlodarska ◽  
Julio Finalet-Ferreiro ◽  
Olivier Gheysens ◽  
Luc Dehaspe ◽  
...  
Keyword(s):  
Hodgkin Lymphoma ◽  
Copy Number ◽  
Early Stage ◽  
Read Depth ◽  
Metabolic Tumor Volume ◽  
Genetic Alterations ◽  
Copy Number Variations ◽  
Classical Hodgkin Lymphoma ◽  
Cell Free Dna ◽  
Free Dna

Abstract The low abundance of Hodgkin/Reed-Sternberg (HRS) cells in lymph node biopsies in classical Hodgkin lymphoma (cHL) complicates the analysis of somatic genetic alterations in HRS cells. As circulating cell-free DNA (cfDNA) contains circulating tumor DNA (ctDNA) from HRS cells, we prospectively collected cfDNA from 177 patients with newly diagnosed, mostly early-stage cHL in a monocentric study at Leuven, Belgium (n = 59) and the multicentric BREACH study by Lymphoma Study Association (n = 118). To catalog the patterns and frequencies of genomic copy number aberrations (CNAs), cfDNA was sequenced at low coverage (0.26×), and data were analyzed with ichorCNA to yield read depth-based copy number profiles and estimated clonal fractions in cfDNA. At diagnosis, the cfDNA concentration, estimated clonal fraction, and ctDNA concentration were significantly higher in cHL cases than controls. More than 90% of patients exhibited CNAs in cfDNA. The most frequent gains encompassed 2p16 (69%), 5p14 (50%), 12q13 (50%), 9p24 (50%), 5q (44%), 17q (43%), 2q (41%). Losses mostly affected 13q (57%), 6q25-q27 (55%), 4q35 (50%), 11q23 (44%), 8p21 (43%). In addition, we identified loss of 3p13-p26 and of 12q21-q24 and gain of 15q21-q26 as novel recurrent CNAs in cHL. At diagnosis, ctDNA concentration was associated with advanced disease, male sex, extensive nodal disease, elevated erythrocyte sedimentation rate, metabolic tumor volume, and HRS cell burden. CNAs and ctDNA rapidly diminished upon treatment initiation, and persistence of CNAs was associated with increased probability of relapse. This study endorses the development of ctDNA as gateway to the HRS genome and substrate for early disease response evaluation.

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