Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing

2021 ◽  
pp. 710-725
Author(s):  
Emmalyn Chen ◽  
Clinton L. Cario ◽  
Lancelote Leong ◽  
Karen Lopez ◽  
César P. Márquez ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Tumor Tissue ◽  
Somatic Tissue ◽  
Localized Prostate Cancer ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Free Dna ◽  
Multiple Regions ◽  
Localized Disease ◽  
Tissue Alterations

PURPOSE Cell-free DNA (cfDNA) may allow for minimally invasive identification of biologically relevant genomic alterations and genetically distinct tumor subclones. Although existing biomarkers may detect localized prostate cancer, additional strategies interrogating genomic heterogeneity are necessary for identifying and monitoring aggressive disease. In this study, we aimed to evaluate whether circulating tumor DNA can detect genomic alterations present in multiple regions of localized prostate tumor tissue. METHODS Low-pass whole-genome and targeted sequencing with a machine-learning guided 2.5-Mb targeted panel were used to identify single nucleotide variants, small insertions and deletions (indels), and copy-number alterations in cfDNA. The majority of this study focuses on the subset of 21 patients with localized disease, although 45 total individuals were evaluated, including 15 healthy controls and nine men with metastatic castration-resistant prostate cancer. Plasma cfDNA was barcoded with duplex unique molecular identifiers. For localized cases, matched tumor tissue was collected from multiple regions (one to nine samples per patient) for comparison. RESULTS Somatic tumor variants present in heterogeneous tumor foci from patients with localized disease were detected in cfDNA, and cfDNA mutational burden was found to track with disease severity. Somatic tissue alterations were identified in cfDNA, including nonsynonymous variants in FOXA1, PTEN, MED12, and ATM. Detection of these overlapping variants was associated with seminal vesicle invasion ( P = .019) and with the number of variants initially found in the matched tumor tissue samples ( P = .0005). CONCLUSION Our findings demonstrate the potential of targeted cfDNA sequencing to detect somatic tissue alterations in heterogeneous, localized prostate cancer, especially in a setting where matched tumor tissue may be unavailable (ie, active surveillance or treatment monitoring).

scholarly journals Cell-free DNA as a biomarker for prostate cancer: elevated concentration and decreased fragment size

2020 ◽  
Author(s):  
Emmalyn Chen ◽  
Clinton L. Cario ◽  
Lancelote Leong ◽  
Karen Lopez ◽  
César P. Márquez ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Fragment Size ◽  
Area Under The Curve ◽  
Localized Prostate Cancer ◽  
Elevated Concentration ◽  
Castration Resistant Prostate Cancer ◽  
Cell Free Dna ◽  
Free Dna ◽  
Increased Risk ◽  
Localized Disease

AbstractPurposeProstate cancer is the most commonly diagnosed neoplasm in American men. Although existing biomarkers may detect localized prostate cancer, additional strategies are necessary for improving detection and identifying aggressive disease that may require further intervention. One promising, minimally invasive biomarker is cell-free DNA (cfDNA), which consist of short DNA fragments released into circulation by dying or lysed cells that may reflect underlying cancer. Here we investigated whether differences in cfDNA concentration and cfDNA fragment size could improve the sensitivity for detecting more advanced and aggressive prostate cancer.Materials and MethodsThis study included 268 individuals: 34 healthy controls, 112 men with localized prostate cancer who underwent radical prostatectomy (RP), and 122 men with metastatic castration-resistant prostate cancer (mCRPC). Plasma cfDNA concentration and fragment size were quantified with the Qubit 3.0 and the 2100 Bioanalyzer. The potential relationship between cfDNA concentration or fragment size and localized or mCRPC prostate cancer was evaluated with descriptive statistics, logistic regression, and area under the curve analysis with cross-validation.ResultsPlasma cfDNA concentrations were elevated in mCRPC patients in comparison to localized disease (OR5 ng/mL = 1.34, P = 0.027) or to being a control (OR5 ng/mL = 1.69, P = 0.034). Decreased average fragment size was associated with an increased risk of localized disease compared to controls (OR5bp = 0.77, P = 0.0008).ConclusionThis study suggests that cfDNA concentration and average cfDNA fragment size may provide a quick, cost-effective approach to help determine which patients will benefit most from further screening and/or disease monitoring to help improve prostate cancer outcomes.

scholarly journals Cell-free DNA concentration and fragment size as a biomarker for prostate cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Emmalyn Chen ◽  
Clinton L. Cario ◽  
Lancelote Leong ◽  
Karen Lopez ◽  
César P. Márquez ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Fragment Size ◽  
Area Under The Curve ◽  
Localized Prostate Cancer ◽  
Castration Resistant Prostate Cancer ◽  
Healthy Individuals ◽  
Cell Free Dna ◽  
Free Dna ◽  
Increased Risk ◽  
Localized Disease

AbstractProstate cancer is the most commonly diagnosed neoplasm in American men. Although existing biomarkers may detect localized prostate cancer, additional strategies are necessary for improving detection and identifying aggressive disease that may require further intervention. One promising, minimally invasive biomarker is cell-free DNA (cfDNA), which consist of short DNA fragments released into circulation by dying or lysed cells that may reflect underlying cancer. Here we investigated whether differences in cfDNA concentration and cfDNA fragment size could improve the sensitivity for detecting more advanced and aggressive prostate cancer. This study included 268 individuals: 34 healthy controls, 112 men with localized prostate cancer who underwent radical prostatectomy (RP), and 122 men with metastatic castration-resistant prostate cancer (mCRPC). Plasma cfDNA concentration and fragment size were quantified with the Qubit 3.0 and the 2100 Bioanalyzer. The potential relationship between cfDNA concentration or fragment size and localized or mCRPC prostate cancer was evaluated with descriptive statistics, logistic regression, and area under the curve analysis with cross-validation. Plasma cfDNA concentrations were elevated in mCRPC patients in comparison to localized disease (OR5ng/mL = 1.34, P = 0.027) or to being a control (OR5ng/mL = 1.69, P = 0.034). Decreased average fragment size was associated with an increased risk of localized disease compared to controls (OR5bp = 0.77, P = 0.0008). This study suggests that while cfDNA concentration can identify mCRPC patients, it is unable to distinguish between healthy individuals and patients with localized prostate cancer. In addition to PSA, average cfDNA fragment size may be an alternative that can differentiate between healthy individuals and those with localized disease, but the low sensitivity and specificity results in an imperfect diagnostic marker. While quantification of cfDNA may provide a quick, cost-effective approach to help guide treatment decisions in advanced disease, its use is limited in the setting of localized prostate cancer.

scholarly journals Cell-Free DNA Alterations in the AR Enhancer and Locus Predict Resistance to AR-Directed Therapy in Patients With Metastatic Prostate Cancer

2020 ◽  
pp. 680-713 ◽  
Author(s):  
Ha X. Dang ◽  
Pradeep S. Chauhan ◽  
Haley Ellis ◽  
Wenjia Feng ◽  
Peter K. Harris ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Metastatic Prostate Cancer ◽  
Progression Free Survival ◽  
Therapy Resistance ◽  
Cancer Resistance ◽  
Liquid Biopsies ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Free Dna

PURPOSE Cell-free DNA (cfDNA) and circulating tumor cell (CTC)–based liquid biopsies have emerged as potential tools to predict responses to androgen receptor (AR)–directed therapy in metastatic prostate cancer. However, because of complex mechanisms and incomplete understanding of genomic events involved in metastatic prostate cancer resistance, current assays (eg, CTC AR-V7) demonstrate low sensitivity and remain underutilized. The recent discovery of AR enhancer amplification in > 80% of patients with metastatic disease and its association with disease resistance presents an opportunity to improve on current assays. We hypothesized that tracking AR/enhancer genomic alterations in plasma cfDNA would detect resistance with high sensitivity and specificity. PATIENTS AND METHODS We developed a targeted sequencing and analysis method as part of a new assay called Enhancer and Neighboring Loci of Androgen Receptor Sequencing (EnhanceAR-Seq). We applied EnhanceAR-Seq to plasma collected from 40 patients with metastatic prostate cancer treated with AR-directed therapy to monitor AR/enhancer genomic alterations and correlated these events with therapy resistance, progression-free survival (PFS), and overall survival (OS). RESULTS EnhanceAR-Seq identified genomic alterations in the AR/enhancer locus in 45% of cases, including a 40% rate of AR enhancer amplification. Patients with AR/enhancer alterations had significantly worse PFS and OS than those without (6-month PFS, 30% v 71%; P = .0002; 6-month OS, 59% v 100%; P = .0015). AR/enhancer alterations in plasma cfDNA detected 18 of 23 resistant cases (78%) and outperformed the CTC AR-V7 assay, which was also run on a subset of patients. CONCLUSION cfDNA-based AR locus alterations, including of the enhancer, are strongly associated with resistance to AR-directed therapy and significantly worse survival. cfDNA analysis using EnhanceAR-Seq may enable more precise risk stratification and personalized therapeutic approaches for metastatic prostate cancer.

scholarly journals Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer

JAMA Oncology ◽  
2016 ◽  
Vol 2 (12) ◽  
pp. 1598 ◽  
Author(s):  
Alexander W. Wyatt ◽  
Arun A. Azad ◽  
Stanislav V. Volik ◽  
Matti Annala ◽  
Kevin Beja ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Castration Resistant Prostate Cancer ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Castration Resistant ◽  
Free Dna

AR enhancer and locus genomic alterations as cell-free DNA biomarkers of primary resistance to AR-directed treatment of metastatic prostate cancer.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 5529-5529
Author(s):  
Chris Maher ◽  
Ha X. Dang ◽  
Pradeep S. Chauhan ◽  
Haley Ellis ◽  
Wenjia Feng ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Metastatic Prostate Cancer ◽  
Dna Analysis ◽  
Clinical Decision Making ◽  
Cancer Center ◽  
Genomic Alterations ◽  
Primary Resistance ◽  
Cell Free Dna ◽  
Free Dna

5529 Background: Predicting primary resistance to androgen receptor (AR)-directed therapies is critical for personalizing treatment of metastatic prostate cancer (mPCa). Analyses of liquid biopsies are potential tools but remained underutilized due to limited sensitivity. We developed a cell-free DNA (cfDNA) assay (EnhanceAR-Seq) to monitor genomic alterations in mPCa including AR enhancer duplication, a resistance marker recently discovered in ~81% of mPCa patients. Here we show that applying EnhanceAR-Seq to plasma cfDNA to monitor alterations of AR gene and enhancer ( AR/enhancer) predicted primary resistance with high sensitivity and outperformed the clinically validated CTC AR-V7 assay. Methods: Forty mPCa patients were prospectively enrolled at the Washington University School of Medicine Siteman Cancer Center with plasma cfDNA analyzed by EnhanceAR-Seq. Twenty-five of them also had the Oncotype DX AR-V7 Nucleus Detect CTC assay performed at a similar timepoint at the discretion of the treating oncologist. All patients received AR-directed therapy (eg. abiraterone, enzalutamide) and underwent standard-of-care clinical and laboratory follow-up. Primary resistance was defined as PSA progression, change of treatment or death within 4 months of treatment initiation, or radiographic progression within 6 months. Results: Median clinical follow up after diagnosis was 50 months. EnhanceAR-Seq detected alterations targeting AR/enhancer in 18 patients (45%), TP53 in 8 patients (20%), and PTEN in 6 patients (15%). We found that AR/enhancer alterations (copy gain, tandem duplication, and point mutation) in cfDNA were strongly predictive of primary resistance to AR-directed therapy (PPV = 100%, Sens. = 89%). Our assay outperformed the CTC AR-V7 assay, which was positive in only two patients (PPV = 50%, Sens. = 6%). Furthermore, patients with AR/enhancer alterations had significantly worse progression-free survival (P = 0.0015; HR = 11.5) and overall survival (P = 0.0002; HR = 6.8). Finally, serial cell-free DNA analysis of 10 patients showed that AR/enhancer copy number gain was maintained or acquired in 5 of 6 AR-resistant cases, and neutrality maintained in 4 of 4 AR-sensitive cases. Conclusions: cfDNA-based AR/enhancer locus genomic alterations could potentially be used to predict primary resistance to AR-directed therapy with higher sensitivity than the clinically validated CTC AR-V7 assay, be used for serial timepoint monitoring and guiding personalized clinical decision-making.

Genomic alterations associated with the progression from castration-sensitive to castration-resistant metastatic prostate cancer based on machine learning analysis of cell-free DNA genomic profile.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e17596-e17596
Author(s):  
Edwin Lin ◽  
Andrew W. Hahn ◽  
Roberto Nussenzveig ◽  
Sergiusz Wesolowski ◽  
Benjamin Louis Maughan ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Supervised Machine Learning ◽  
Pi3k Signaling ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Associated Gas ◽  
Castration Resistant ◽  
Free Dna ◽  
Pathway Level

e17596 Background: Metastatic castration-sensitive prostate cancer (mCSPC) eventually progresses to metastatic castration-resistant prostate cancer (mCRPC), which has few treatment options and carries a poor prognosis. We hypothesize that there are specific genomic alterations (GAs) associated with the progression from mCSPC to mCRPC. Methods: Patients (Pts) with mCSPC and mCRPC undergoing next-generation sequencing of cell-free DNA by a CLIA certified lab (G360, Guardant Health Inc., Redwood City, CA) as a part of routine care were retrospectively identified. Principal components analysis, an unsupervised ML algorithm, was used for data exploration and visualization. A combination of feature selection and supervised machine learning classification algorithms were used to identify genes associated with mCRPC. Gene Ontology enrichment analysis was used to identify pathways enriched for mCRPC-associated GAs. Patterns of mCRPC-associated GAs at a gene- and pathway-level were identified by Bayesian networks fitted using an exact structure learning algorithm. Results: 154 Pts with mCSPC and 187 Pts with mCRPC were included. A set of 16 GAs that robustly distinguished mCRPC from mCSPC (PPV = 94%, specificity = 91%) using supervised machine learning algorithms. These GAs, primarily amplifications, corresponded to AR, MAPK signaling, PI3K signaling, G1/S cell cycle, and receptor tyrosine kinases (RTKs). Positive statistical dependencies were observed between genes in these pathways. At a pathway-level, the presence of G1/S GAs in mCRPC samples increased the likelihood of harboring GAs in RTK, MAPK, and PI3K signaling. Limitations: The retrospective nature of our study means that unknown exposures could act as confounding variables, however this is representative of real-world clinical settings. Although the strength of this study is inclusion of clinically annotated patient samples, the limitation is that patients with mCSPC and mCRPC were unmatched. Conclusions: These results provide evidence that progression from mCSPC to mCRPC is associated with stereotyped concomitant gain-of-function in the RTK, PI3K, MAPK, and G1/S pathways in addition to AR. Upon external validation, these hypothesis generating data may warrant further investigation into combinatorial therapies that target these pathways.

scholarly journals Concordance between genomic alterations assessed by next-generation sequencing in tumor tissue or circulating cell-free DNA

Oncotarget ◽  
2016 ◽  
Vol 7 (40) ◽  
pp. 65364-65373 ◽  
Author(s):  
Young Kwang Chae ◽  
Andrew A. Davis ◽  
Benedito A. Carneiro ◽  
Sunandana Chandra ◽  
Nisha Mohindra ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tumor Tissue ◽  
Next Generation ◽  
Genomic Alterations ◽  
Cell Free Dna ◽  
Free Dna ◽  
Generation Sequencing ◽  
Circulating Cell Free Dna
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