Quantitative phenotyping via deep barcode sequencing

Genome Res. 2009 Oct;19(10):1836-42. doi: 10.1101/gr.093955.109. Epub 2009 Jul 21.


Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • Cost-Benefit Analysis
  • Doxorubicin / pharmacology
  • Drug Evaluation, Preclinical / methods
  • Electronic Data Processing / economics
  • Electronic Data Processing / methods*
  • Gene Expression Profiling / methods*
  • Genomics / methods
  • Microbial Sensitivity Tests
  • Oligonucleotide Array Sequence Analysis / economics
  • Oligonucleotide Array Sequence Analysis / methods*
  • Phenotype*
  • Pyridines / pharmacology
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / economics
  • Sequence Analysis, DNA / methods*
  • Tunicamycin / pharmacology
  • Yeasts / drug effects
  • Yeasts / physiology


  • Anti-Bacterial Agents
  • Pyridines
  • Tunicamycin
  • Doxorubicin
  • cerivastatin