The effect of preservative and temperature on the analysis of circulating tumor DNA

Sonya Parpart-Li, Bjarne Bartlett, Maria Popoli, Vilmos Adleff, Laura Tucker, Rebecca Steinberg, Andrew Georgiadis, Jill Phallen, Julie Brahmer, Nilofer Azad, Ilene Browner, Daniel Laheru, Victor E Velculescu, Mark Sausen, Luis A. Diaz

Research output: Contribution to journalArticle

Abstract

Purpose: Analysis of genomic alterations in cell-free DNA (cfDNA) is evolving as an approach to detect, monitor, and genotype malignancies. Methods to separate the liquid from the cellular fraction of whole blood for circulating tumor DNA (ctDNA) analyses have been largely unstudied, although these may be a critical consideration for assay performance. Experimental Design: To evaluate the influence of blood processing on cfDNA and ctDNA quality and yield, we compared the cfDNA levels in serum with those in plasma. Given the limitations of serum for ctDNA analyses, we evaluated the effects of two plasma processing approaches, K2EDTA and Cell-Free DNA BCT (BCT) tubes, on cfDNA and ctDNA recovery. A total of 45 samples from nine patients with cancer were collected in both tube types. Once collected, blood was processed into plasma immediately or kept at room temperature and processed into plasma at 1, 3, 5, or 7 days. Results: As early as 24 hours after collection, plasma isolated from blood collected in K2EDTA tubes contained an elevated level of cfDNA that increased over time compared with BCT tubes where no significant increase in cfDNA levels was observed. When samples from an additional six patients with cancer, collected in the same manner, were stored at 4°C in K2 EDTA tubes over the course of 3 days, total cfDNA and ctDNA levels were comparable between samples collected in BCT tubes. At day 3, there was a trend toward a decrease in ctDNA levels in both tubes that was more pronounced when measuring the mutant allele fraction for cases stored at 4°C in K2EDTA tubes. Conclusions: In summary, methods of blood processing have a strong influence on cfDNA and ctDNA levels and should be a consideration when evaluating ctDNA in peripheral circulation.

Original languageEnglish (US)
Pages (from-to)2471-2477
Number of pages7
JournalClinical Cancer Research
Volume23
Issue number10
DOIs
StatePublished - May 15 2017

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Temperature
DNA
Neoplasms
Serum
Edetic Acid
Research Design
Alleles
Genotype

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Parpart-Li, S., Bartlett, B., Popoli, M., Adleff, V., Tucker, L., Steinberg, R., ... Diaz, L. A. (2017). The effect of preservative and temperature on the analysis of circulating tumor DNA. Clinical Cancer Research, 23(10), 2471-2477. https://doi.org/10.1158/1078-0432.CCR-16-1691

The effect of preservative and temperature on the analysis of circulating tumor DNA. / Parpart-Li, Sonya; Bartlett, Bjarne; Popoli, Maria; Adleff, Vilmos; Tucker, Laura; Steinberg, Rebecca; Georgiadis, Andrew; Phallen, Jill; Brahmer, Julie; Azad, Nilofer; Browner, Ilene; Laheru, Daniel; Velculescu, Victor E; Sausen, Mark; Diaz, Luis A.

In: Clinical Cancer Research, Vol. 23, No. 10, 15.05.2017, p. 2471-2477.

Research output: Contribution to journalArticle

Parpart-Li, S, Bartlett, B, Popoli, M, Adleff, V, Tucker, L, Steinberg, R, Georgiadis, A, Phallen, J, Brahmer, J, Azad, N, Browner, I, Laheru, D, Velculescu, VE, Sausen, M & Diaz, LA 2017, 'The effect of preservative and temperature on the analysis of circulating tumor DNA', Clinical Cancer Research, vol. 23, no. 10, pp. 2471-2477. https://doi.org/10.1158/1078-0432.CCR-16-1691
Parpart-Li, Sonya ; Bartlett, Bjarne ; Popoli, Maria ; Adleff, Vilmos ; Tucker, Laura ; Steinberg, Rebecca ; Georgiadis, Andrew ; Phallen, Jill ; Brahmer, Julie ; Azad, Nilofer ; Browner, Ilene ; Laheru, Daniel ; Velculescu, Victor E ; Sausen, Mark ; Diaz, Luis A. / The effect of preservative and temperature on the analysis of circulating tumor DNA. In: Clinical Cancer Research. 2017 ; Vol. 23, No. 10. pp. 2471-2477.
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AU - Parpart-Li, Sonya

AU - Bartlett, Bjarne

AU - Popoli, Maria

AU - Adleff, Vilmos

AU - Tucker, Laura

AU - Steinberg, Rebecca

AU - Georgiadis, Andrew

AU - Phallen, Jill

AU - Brahmer, Julie

AU - Azad, Nilofer

AU - Browner, Ilene

AU - Laheru, Daniel

AU - Velculescu, Victor E

AU - Sausen, Mark

AU - Diaz, Luis A.

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N2 - Purpose: Analysis of genomic alterations in cell-free DNA (cfDNA) is evolving as an approach to detect, monitor, and genotype malignancies. Methods to separate the liquid from the cellular fraction of whole blood for circulating tumor DNA (ctDNA) analyses have been largely unstudied, although these may be a critical consideration for assay performance. Experimental Design: To evaluate the influence of blood processing on cfDNA and ctDNA quality and yield, we compared the cfDNA levels in serum with those in plasma. Given the limitations of serum for ctDNA analyses, we evaluated the effects of two plasma processing approaches, K2EDTA and Cell-Free DNA BCT (BCT) tubes, on cfDNA and ctDNA recovery. A total of 45 samples from nine patients with cancer were collected in both tube types. Once collected, blood was processed into plasma immediately or kept at room temperature and processed into plasma at 1, 3, 5, or 7 days. Results: As early as 24 hours after collection, plasma isolated from blood collected in K2EDTA tubes contained an elevated level of cfDNA that increased over time compared with BCT tubes where no significant increase in cfDNA levels was observed. When samples from an additional six patients with cancer, collected in the same manner, were stored at 4°C in K2 EDTA tubes over the course of 3 days, total cfDNA and ctDNA levels were comparable between samples collected in BCT tubes. At day 3, there was a trend toward a decrease in ctDNA levels in both tubes that was more pronounced when measuring the mutant allele fraction for cases stored at 4°C in K2EDTA tubes. Conclusions: In summary, methods of blood processing have a strong influence on cfDNA and ctDNA levels and should be a consideration when evaluating ctDNA in peripheral circulation.

AB - Purpose: Analysis of genomic alterations in cell-free DNA (cfDNA) is evolving as an approach to detect, monitor, and genotype malignancies. Methods to separate the liquid from the cellular fraction of whole blood for circulating tumor DNA (ctDNA) analyses have been largely unstudied, although these may be a critical consideration for assay performance. Experimental Design: To evaluate the influence of blood processing on cfDNA and ctDNA quality and yield, we compared the cfDNA levels in serum with those in plasma. Given the limitations of serum for ctDNA analyses, we evaluated the effects of two plasma processing approaches, K2EDTA and Cell-Free DNA BCT (BCT) tubes, on cfDNA and ctDNA recovery. A total of 45 samples from nine patients with cancer were collected in both tube types. Once collected, blood was processed into plasma immediately or kept at room temperature and processed into plasma at 1, 3, 5, or 7 days. Results: As early as 24 hours after collection, plasma isolated from blood collected in K2EDTA tubes contained an elevated level of cfDNA that increased over time compared with BCT tubes where no significant increase in cfDNA levels was observed. When samples from an additional six patients with cancer, collected in the same manner, were stored at 4°C in K2 EDTA tubes over the course of 3 days, total cfDNA and ctDNA levels were comparable between samples collected in BCT tubes. At day 3, there was a trend toward a decrease in ctDNA levels in both tubes that was more pronounced when measuring the mutant allele fraction for cases stored at 4°C in K2EDTA tubes. Conclusions: In summary, methods of blood processing have a strong influence on cfDNA and ctDNA levels and should be a consideration when evaluating ctDNA in peripheral circulation.

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