scholarly journals Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology

2015 ◽  
Vol 8 (5) ◽  
pp. 407-416 ◽  
Author(s):  
Eser Kirkizlar ◽  
Bernhard Zimmermann ◽  
Tudor Constantin ◽  
Ryan Swenerton ◽  
Bin Hoang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number ◽  
Copy Number Variants ◽  
Cell Free Dna ◽  
Multiplexed Pcr ◽  
Free Dna

scholarly journals False positive cell free DNA screening for microdeletions due to non-pathogenic copy number variants

2016 ◽  
Vol 36 (6) ◽  
pp. 584-586 ◽  
Author(s):  
Cheryl A. Mather ◽  
Zhongxia Qi ◽  
Arun P. Wiita
Keyword(s):  
False Positive ◽  
Copy Number ◽  
Copy Number Variants ◽  
Cell Free Dna ◽  
Free Dna

Circulating cell-free DNA (ctDNA) assessments before, during, and after neoadjuvant therapy (NAC) in nonmetastatic inflammatory breast cancer (IBC).

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e12113-e12113
Author(s):  
Carolyn S. Hall ◽  
Salyna Meas ◽  
Vanessa Nicole Sarli ◽  
Anthony Lucci
Keyword(s):  
Breast Cancer ◽  
Pathologic Complete Response ◽  
Copy Number Variants ◽  
Residual Tumor ◽  
Complete Response ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

e12113 Background: : IBC is a rare and aggressive subtype of breast cancer. A significant number of IBC patients who achieve pathologic complete response (no residual tumor in breast and axillary nodes, pCR) relapse after NAC. We hypothesized that circulating cell-free DNA (ctDNA) identified in blood before, during, and after NAC would identify novel ctDNA targets. Methods: Plasma ctDNA was extracted from 43 non-metastatic IBC patients (IRB: LAB04-0698) pre, mid, and post-NAC. The Oncomine Pan Cancer ctDNA Assay (ThermoFisher) was used for library preparation, and high throughput next generation sequencing was performed on a GeneStudio S5XL System (ThermoFisher), following manufacturer’s directions. ThermoFisher Ion Reporter 5.10 Software was used to analyze single nucleotide variants (SNVs), and copy number variants (CNVs). Results: Seventeen patients had pre-NAC ctDNA assessments; 7/17 (41%) had PIK3CA SNVs; 5/7 also had MYC or FGFR2 CNVs. Five of 17 (29%) had TP53 SNVs; 2/5 also had FGFR2 CNVs. Ten patients had mid-NAC ctDNA assessments; 9/10 (90%) had PIK3CA SNVs; 5/9 also had FGFR2 CNVs, 2/9 had FGFR2 and FGFR3 CNVs, 2/9 also had TP53 SNVs, 1/9 had FGFR2 and ERB2 CNVs. Thirty-one patients had post-NAC ctDNA assessments; 5/31 (16%) had PIK3CA SNVs; 2/5 had FGFR2 CNVs, 1/5 also had a TP53 mutation and an FGFR2 CNV, 1/5 had FGFR2 CNV, and FGFR3 CNV. Six of 31 (19%) had TP53 SNVs, 1/6 had CCND1 CNVs, no CNVs were detected in 6 patients with TP53 SNVs. Six of 31 (19%) had MAP2K1 SNVs. Three of 31 (10%) had MET SNVs; 1/3 had CCND3 CNVs, no CNVs were detected in 2 patients with MET SNVs. No SNVs or CNVs were detected in 10/31 (32%) of patients post NAC. Conclusions: ctDNA assessments before, during, and after NAC identified novel targets that could be tested in future adjuvant therapies trials in IBC patients who remain at high risk for relapse.

scholarly journals Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer

2018 ◽  
Vol 36 (6) ◽  
pp. 543-553 ◽  
Author(s):  
Daniel G. Stover ◽  
Heather A. Parsons ◽  
Gavin Ha ◽  
Samuel S. Freeman ◽  
William T. Barry ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Copy Number ◽  
Triple Negative ◽  
Copy Number Alterations ◽  
Cell Free Dna ◽  
Primary Tumors ◽  
Free Dna ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.

scholarly journals Genome-wide cell-free DNA screening: a focus on copy-number variants

2021 ◽  
Author(s):  
Jill Rafalko ◽  
Erica Soster ◽  
Samantha Caldwell ◽  
Eyad Almasri ◽  
Thomas Westover ◽  
...  
Keyword(s):  
Copy Number ◽  
Chromosomal Abnormalities ◽  
Diagnostic Testing ◽  
Copy Number Variants ◽  
Cell Free Dna ◽  
Predictive Values ◽  
Free Dna ◽  
Genome Wide ◽  
Cfdna Screening ◽  
Diagnostic Outcomes

Abstract Purpose Of 86,902 prenatal genome-wide cell-free DNA (cfDNA) screening tests, 4,121 were positive for a chromosome abnormality. This study examines 490 cases screen-positive for one or more subchromosomal copy-number variants (CNV) from genome-wide cfDNA screening. Methods Cases positive for one or more subchromosomal CNV from genome-wide cfDNA screening and diagnostic outcomes were compiled. Diagnostic testing trends were analyzed, positive predictive values (PPVs) were calculated, and the type of chromosomal abnormalities ultimately confirmed by diagnostic testing were described. Results CNVs were identified in 0.56% of screened specimens. Of the 490 cases screen-positive for one or more CNV, diagnostic outcomes were available for 244 cases (50%). The overall PPV among the cases with diagnostic outcomes was 74.2% (95% CI: 68.1–79.5%) and 71.8% (95% CI: 65.5–77.4%) for “fetal-only” events. Overall, isolated CNVs showed a lower PPV of 61.0% (95% CI: 52.5–68.8%) compared to complex CNVs at 93.9% (95% CI: 86.6–97.5%). Isolated deletions/duplications and unbalanced structural rearrangements were the most common diagnostic outcomes when isolated and complex CNVs were identified by cfDNA screening, respectively. Conclusion Genome-wide cfDNA screening identifies chromosomal abnormalities beyond the scope of traditional cfDNA screening, and the overall PPV associated with subchromosomal CNVs in cases with diagnostic outcomes was >70%.

Emerging Role of Genomics and Cell-Free DNA in Breast Cancer

2019 ◽  
Vol 20 (8) ◽  
Author(s):  
Lorenzo Gerratana ◽  
Andrew A. Davis ◽  
Ami N. Shah ◽  
Chenyu Lin ◽  
Carla Corvaja ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Identification of Somatic Mutations in Thirty-year-old Serum Cell-free DNA From Patients With Breast Cancer: A Feasibility Study

2020 ◽  
Vol 20 (5) ◽  
pp. 413-421.e1
Author(s):  
Mathilde Ritter ◽  
Viola Paradiso ◽  
Patrik Widmer ◽  
Andrea Garofoli ◽  
Luca Quagliata ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Feasibility Study ◽  
Somatic Mutations ◽  
Cell Free Dna ◽  
Free Dna
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