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Archival single-cell genomics reveals persistent subclones during DCIS progression.

Publication ,  Journal Article
Wang, K; Kumar, T; Wang, J; Minussi, DC; Sei, E; Li, J; Tran, TM; Thennavan, A; Hu, M; Casasent, AK; Xiao, Z; Bai, S; Yang, L; King, LM ...
Published in: Cell
August 31, 2023

Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.

Duke Scholars

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Published In

Cell

DOI

EISSN

1097-4172

Publication Date

August 31, 2023

Volume

186

Issue

18

Start / End Page

3968 / 3982.e15

Location

United States

Related Subject Headings

  • Single-Cell Gene Expression Analysis
  • Humans
  • Genomics
  • Female
  • Disease Progression
  • Developmental Biology
  • Cell Line, Tumor
  • Carcinoma, Intraductal, Noninfiltrating
  • Carcinoma, Ductal, Breast
  • Breast Neoplasms
 

Citation

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Wang, K., Kumar, T., Wang, J., Minussi, D. C., Sei, E., Li, J., … Navin, N. E. (2023). Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell, 186(18), 3968-3982.e15. https://doi.org/10.1016/j.cell.2023.07.024
Wang, Kaile, Tapsi Kumar, Junke Wang, Darlan Conterno Minussi, Emi Sei, Jianzhuo Li, Tuan M. Tran, et al. “Archival single-cell genomics reveals persistent subclones during DCIS progression.Cell 186, no. 18 (August 31, 2023): 3968-3982.e15. https://doi.org/10.1016/j.cell.2023.07.024.
Wang K, Kumar T, Wang J, Minussi DC, Sei E, Li J, et al. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell. 2023 Aug 31;186(18):3968-3982.e15.
Wang, Kaile, et al. “Archival single-cell genomics reveals persistent subclones during DCIS progression.Cell, vol. 186, no. 18, Aug. 2023, pp. 3968-3982.e15. Pubmed, doi:10.1016/j.cell.2023.07.024.
Wang K, Kumar T, Wang J, Minussi DC, Sei E, Li J, Tran TM, Thennavan A, Hu M, Casasent AK, Xiao Z, Bai S, Yang L, King LM, Shah V, Kristel P, van der Borden CL, Marks JR, Zhao Y, Zurita AJ, Aparicio A, Chapin B, Ye J, Zhang J, Gibbons DL, Grand Challenge PRECISION Consortium, Sawyer E, Thompson AM, Futreal A, Hwang ES, Wesseling J, Lips EH, Navin NE. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell. 2023 Aug 31;186(18):3968-3982.e15.
Journal cover image

Published In

Cell

DOI

EISSN

1097-4172

Publication Date

August 31, 2023

Volume

186

Issue

18

Start / End Page

3968 / 3982.e15

Location

United States

Related Subject Headings

  • Single-Cell Gene Expression Analysis
  • Humans
  • Genomics
  • Female
  • Disease Progression
  • Developmental Biology
  • Cell Line, Tumor
  • Carcinoma, Intraductal, Noninfiltrating
  • Carcinoma, Ductal, Breast
  • Breast Neoplasms