Quantitative phenotyping via deep barcode sequencing.
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.
Smith
Andrew M
AM
Department of Molecular Genetics, University of Toronto, Ontario, Canada.
Heisler
Lawrence E
LE
Mellor
Joseph
J
Kaper
Fiona
F
Thompson
Michael J
MJ
Chee
Mark
M
Roth
Frederick P
FP
Giaever
Guri
G
Nislow
Corey
C
D000900:Anti-Bacterial Agents / Q000494:pharmacology; D003362:Cost-Benefit Analysis; D004317:Doxorubicin / Q000494:pharmacology; D004353:Drug Evaluation, Preclinical / Q000379:methods; D001330:Electronic Data Processing / Q000191:economics / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods; D008826:Microbial Sensitivity Tests; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D010641:Phenotype; D011725:Pyridines / Q000494:pharmacology; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*; D014415:Tunicamycin / Q000494:pharmacology; D015003:Yeasts / Q000187:drug effects / Q000502:physiology
D000900:Anti-Bacterial Agents; D011725:Pyridines; D014415:Tunicamycin; D004317:Doxorubicin; C086276:cerivastatin