Genomic screening methodology not requiring barcoding: Single nucleotide polymorphism-based, mixed-cell screening (SMICS)

Zhuwei Zhang, Xi Chen, Wen Zhang, Jinpeng Liu, Yanqi Xie, Shulin Zhang, Arnold J. Stromberg, David S. Watt, Xifu Liu, Chi Wang, Chunming Liu

Research output: Contribution to journalArticlepeer-review

Abstract

Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous “tags” that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.

Original languageEnglish
Article number110666
JournalGenomics
Volume115
Issue number5
DOIs
StatePublished - Sep 2023

Bibliographical note

Publisher Copyright:
© 2023

Keywords

  • Cell-line screening
  • Drug screening
  • Single nucleotide polymorphisms
  • Whole exome sequencing

ASJC Scopus subject areas

  • Genetics

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