Comparative analysis of circulating tumor DNA stability In K3EDTA, Streck, and CellSave blood collection tubes

Objective: To evaluate long-term whole blood (WB) storage at room temperature (RT), plasma and peripheral blood mononuclear cell (PBMC) DNA was collected simultaneously using BD Vacutainer® CPT™ Mononuclear Cell Preparation Tubes (CPT) and Streck Cell-Free DNA Blood Collection Tubes (BCT®). Methods: Plasma DNA was isolated from both types of tubes at various time points at RT. DNA from PBMCs was extracted using CPT from WB stored in BCT. The extracted DNA was used to monitor esophageal cancer treatment. Results: BCT maintained steady levels of plasma DNA for up to nine days. After transfer of BCT-stored WB to CPT, PBMC-DNA were yielded with suitable quality for up to seven days. ctDNA from esophageal cancer patients carrying TP53 mutations reflected treatment efficacy. Conclusion: BCT/CPT combinatory procedure allows storage of blood samples for up to seven days at RT for valid clinical assays using ctDNA.

Download Full-text

A Comparative Analysis of Tumors and Plasma Circulating Tumor DNA in 145 Advanced Cancer Patients Annotated by 3 Core Cellular Processes

Cancers ◽

10.3390/cancers12030701 ◽

2020 ◽

Vol 12 (3) ◽

pp. 701

Author(s):

Kristian Larson ◽

Radhamani Kannaiyan ◽

Ritu Pandey ◽

Yuliang Chen ◽

Hani M. Babiker ◽

...

Keyword(s):

Comparative Analysis ◽

Cancer Patients ◽

Cell Fate ◽

Advanced Cancer ◽

Significant Proportion ◽

Gene Mutations ◽

Circulating Tumor Dna ◽

Advanced Cancer Patients ◽

Cellular Processes ◽

Tumor Dna

Matched-targeted and immune checkpoint therapies have improved survival in cancer patients, but tumor heterogeneity contributes to drug resistance. Our study categorized gene mutations from next generation sequencing (NGS) into three core processes. This annotation helps decipher complex biologic interactions to guide therapy. We collected NGS data on 145 patients who have failed standard therapy (2016 to 2018). One hundred and forty two patients had data for tissue (Caris MI/X) and plasma cell-free circulating tumor DNA (Guardant360) platforms. The mutated genes were categorized into cell fate (CF), cell survival (CS), and genome maintenance (GM). Comparative analysis was performed for concordance and discordance, unclassified mutations, trends in TP53 alterations, and PD-L1 expression. Two gene mutation maps were generated to compare each NGS platform. Mutated genes predominantly matched to CS with concordance between Guardant360 (64.4%) and Caris (51.5%). TP53 alterations comprised a significant proportion of the mutation pool in Caris and Guardant360, 14.7% and 13.1%, respectively. Twenty-six potentially actionable gene alterations were detected from matching ctDNA to Caris unclassified alterations. The CS core cellular process was the most prevalent in our study population. Clinical trials are warranted to investigate biomarkers for the three core cellular processes in advanced cancer patients to define the next best therapies.

Download Full-text

Detection of circulating tumor DNA in pancreas cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.4_suppl.645 ◽

2020 ◽

Vol 38 (4_suppl) ◽

pp. 645-645

Author(s):

Daniel King ◽

Ash A. Alizadeh ◽

George A. Fisher

Keyword(s):

Pancreas Cancer ◽

Residual Disease ◽

Circulating Tumor Dna ◽

Pancreatic Tumors ◽

Cancer Center ◽

Blood Collection ◽

Early Assessment ◽

Response To Chemotherapy ◽

Investigation Methods ◽

Tumor Dna

645 Background: Pancreas cancer remains a leading cause of cancer-related death. Improved detection of early relapse or early failure of chemotherapy also has the potential to further improve outcomes. Exploring circulating tumor DNA (ctDNA) in this setting is an area of active investigation. Methods: We previously developed an approach, CAPP-Seq, combining high-depth sequencing with several strategies of error-suppression to identify minute amounts of circulating tumor DNA. We then trained and validated a new capture panel for pancreas cancer from 640 tumors from three data sources (TCGA, ICGC, UTSW), targeting 265 kb of the genome. We enrolled two cohorts of patients with pancreatic cancers at Stanford Cancer Center: (1) patients with localized tumors undergoing resection with curative intent, and (2) patients with unresectable or metastatic disease undergoing systemic therapy. Results: As of August 2019, we recruited 131 patients with at least one blood collection, with 63% having resectable disease and 27% having advanced disease; 59 patients had 2 or more blood collections. Stage distribution included 34% stage I, 33% stage II, 18% III, 16% IV disease. Approximately 15% had normal CA19-9 levels. Deep sequencing (4,000x unique depth) of an initial set of resected pancreatic tumors and matched germline specimens identified 1-6 non-synonymous coding mutations per case (median=3, n=14), with the most frequently mutated genes involving KRAS (79%), TP53 (50%), SMAD4 (29%). Among newly diagnosed treatment-naïve patients with resectable adenocarcinoma (n=9), we detected ctDNA in 4 patients (44%) prior to surgery including with AFs ranging from 0.27% - 0.88%. Subsequent sequencing will compare patients with and without neoadjuvant therapy prior to resection, selection of unresectable patients across a larger range of tumor burden and across multiple timepoints, and integration of large-scale copy number variant detection using low-pass whole-genome sequencing. Conclusions: Circulating tumor DNA monitoring with CAPP-Seq shows promise for improved detection of PDAC. Two key applications include early detection of minimal residual disease after resection and early assessment of response to chemotherapy.

Download Full-text

Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA

Clinical Biochemistry ◽

10.1016/j.clinbiochem.2015.07.097 ◽

2015 ◽

Vol 48 (15) ◽

pp. 993-998 ◽

Cited By ~ 59

Author(s):

Patricia Valda Toro ◽

Bracha Erlanger ◽

Julia A. Beaver ◽

Rory L. Cochran ◽

Dustin A. VanDenBerg ◽

...

Keyword(s):

Blood Collection ◽

Blood Collection Tubes ◽

Tumor Dna ◽

Plasma Tumor Dna

Download Full-text

P2.01-106 A Comparative Analysis of Genomic Alterations by Tumor Tissue and Circulating Tumor DNA in Advanced Non-Small Cell Lung Cancer

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2018.08.1161 ◽

2018 ◽

Vol 13 (10) ◽

pp. S706

Author(s):

G. Woo ◽

S.H. Kim ◽

K.J. Suh ◽

Y.J. Kim ◽

J. Chung ◽

...

Keyword(s):

Lung Cancer ◽

Comparative Analysis ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Tumor Tissue ◽

Circulating Tumor Dna ◽

Small Cell ◽

Small Cell Lung ◽

Genomic Alterations ◽

Tumor Dna

Download Full-text

Circulating tumor DNA in patients with metastatic urothelial cancer: concordance of genomic findings with matched tissue biopsies.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e16036 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e16036-e16036 ◽

Cited By ~ 1

Author(s):

Jean-Michel Lavoie ◽

Gillian Vandekerkhove ◽

Matti Annala ◽

Nora Sundahl ◽

Takeshi Sano ◽

...

Keyword(s):

Urothelial Cancer ◽

Stage Iv ◽

Circulating Tumor Dna ◽

Blood Collection ◽

Liquid Biopsies ◽

Tissue Samples ◽

Metastatic Urothelial Cancer ◽

Platinum Based Chemotherapy ◽

Matched Tissue ◽

Tumor Dna

e16036 Background: Patients (pts) with metastatic urothelial cancer (mUC) now have access to many different treatment options. This creates an incentive for molecular profiling of their tumors, with the aim of developing biomarkers. Genomic profiling may leverage the presence of circulating tumor DNA (ctDNA), but it has not been shown whether this recapitulates the findings from tissue samples. Methods: Whole blood samples were collected for next-generation sequencing of leukocyte and cell-free DNA (cfDNA). Deep targeted sequencing was performed across a UC-specific custom 50-gene panel (median depth of 986x). Matched archival tissue was profiled using the same assay for 65 pts. Results: Between 11/2011 and 12/2017, 90 pts developed mUC (87 evaluable). Baseline characteristics: median age 67, 83% male, 14% upper-tract disease, 17% stage IV at initial presentation. Treatments delivered: 76% platinum-based chemotherapy, 47% PD-1/PD-L1 inhibitor. At a median follow-up of 12.8 mo., 45% remain alive. We found ctDNA fractions above 2% in at least one blood collection in 81% of cases. For 17 pts, matched metastatic biopsies and cfDNA collection were available; in those cases 82% of coding somatic mutations identified in tissue were independently detected in cfDNA. Half of discordant findings could be attributed to low ctDNA fraction. Most (89%) mutations detected in primary tissue (cystectomy or nephrectomy) were present in later cfDNA collections. ctDNA detected mutations in TP53 and ARID1A in 64% and 29% of pts, respectively. A tumor mutation burden ≥25 mutation per Mb was observed in 27% of cases. Conclusions: There is a high concordance between genomic findings from ctDNA and matched tissue of pts with mUC. This supports the use of liquid biopsies to study potential biomarkers in this disease.

Download Full-text