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Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients.

Publication ,  Journal Article
Shishido, SN; Welter, L; Rodriguez-Lee, M; Kolatkar, A; Xu, L; Ruiz, C; Gerdtsson, AS; Restrepo-Vassalli, S; Carlsson, A; Larsen, J; Hwang, ES ...
Published in: J Mol Diagn
March 2020

Liquid biopsy allows assessment of multiple analytes, providing temporal information with potential for improving understanding of cancer evolution and clinical management of patients. Although liquid biopsies are intensely investigated for prediction and response monitoring, preanalytic variables are of primary concern for clinical implementation, including categories of collection method and sample storage. Herein, an integrated high-density single-cell assay workflow for morphometric and genomic analysis of the liquid biopsy is used to characterize the effects of preanalytical variation and reproducibility of data from a breast cancer cohort. Following prior work quantifying performance of commonly used blood collection tubes, this study completes the analysis of four time points to assay (24, 48, 72, and 96 hours), demonstrating precision up to 48 hours after collection for assay sensitivity, highly reproducible rare cell enumeration, morphometric characterization, and high efficiency and capacity for single-cell genomic analysis. For the cell-free analysis, both freezing and use of fresh plasma produced similar quality and quantity of cell-free DNA for sequencing. The genomic analysis (copy number variation and single-nucleotide variation) described herein is broadly applicable to liquid biopsy platforms capable of isolating cell-free and cell-based DNA. Morphometric parameters and genomic signatures of individual circulating tumor cells were evaluated in relation to patient clinical response, providing preliminary evidence of clinical validity as a potential biomarker aiding clinical diagnostics or monitoring progression.

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Published In

J Mol Diagn

DOI

EISSN

1943-7811

Publication Date

March 2020

Volume

22

Issue

3

Start / End Page

319 / 337

Location

United States

Related Subject Headings

  • Workflow
  • Single-Cell Analysis
  • Sensitivity and Specificity
  • Reproducibility of Results
  • Polymorphism, Single Nucleotide
  • Pathology
  • Neoplastic Cells, Circulating
  • Liquid Biopsy
  • Humans
  • Genomics
 

Citation

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Chicago
ICMJE
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Shishido, S. N., Welter, L., Rodriguez-Lee, M., Kolatkar, A., Xu, L., Ruiz, C., … Kuhn, P. (2020). Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn, 22(3), 319–337. https://doi.org/10.1016/j.jmoldx.2019.11.006
Shishido, Stephanie N., Lisa Welter, Mariam Rodriguez-Lee, Anand Kolatkar, Liya Xu, Carmen Ruiz, Anna S. Gerdtsson, et al. “Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients.J Mol Diagn 22, no. 3 (March 2020): 319–37. https://doi.org/10.1016/j.jmoldx.2019.11.006.
Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, et al. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn. 2020 Mar;22(3):319–37.
Shishido, Stephanie N., et al. “Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients.J Mol Diagn, vol. 22, no. 3, Mar. 2020, pp. 319–37. Pubmed, doi:10.1016/j.jmoldx.2019.11.006.
Shishido SN, Welter L, Rodriguez-Lee M, Kolatkar A, Xu L, Ruiz C, Gerdtsson AS, Restrepo-Vassalli S, Carlsson A, Larsen J, Greenspan EJ, Hwang ES, Waitman KR, Nieva J, Bethel K, Hicks J, Kuhn P. Preanalytical Variables for the Genomic Assessment of the Cellular and Acellular Fractions of the Liquid Biopsy in a Cohort of Breast Cancer Patients. J Mol Diagn. 2020 Mar;22(3):319–337.
Journal cover image

Published In

J Mol Diagn

DOI

EISSN

1943-7811

Publication Date

March 2020

Volume

22

Issue

3

Start / End Page

319 / 337

Location

United States

Related Subject Headings

  • Workflow
  • Single-Cell Analysis
  • Sensitivity and Specificity
  • Reproducibility of Results
  • Polymorphism, Single Nucleotide
  • Pathology
  • Neoplastic Cells, Circulating
  • Liquid Biopsy
  • Humans
  • Genomics