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Literature DB >> 30391162

Unbiased Fitness Estimation of Pooled Barcode or Amplicon Sequencing Studies.

Fangfei Li¹, Marc L Salit², Sasha F Levy³.

Abstract

Standard practice for phenotyping complex cell pools is to measure the fold enrichment of genotype-specific amplicons after a period of competitive growth. Here, we show that fold-enrichment measures cannot be compared across genotype pools with different fitness distributions. We develop a method to calculate an unbiased estimate of relative fitness by tracking abundances over several time points and show how to optimize experimental protocols to minimize fitness measurement error.

Entities: Chemical Disease Species

Keywords: CRISPR; Fit-Seq; amplicon sequencing; barcode sequencing; deep mutational scanning; experimental bias; fitness; fold enrichment; log-linear regression; pooled growth; reproducibility

Mesh：

Year: 2018 PMID： 30391162 PMCID： PMC6265064 DOI： 10.1016/j.cels.2018.09.004

Source DB: PubMed Journal: Cell Syst ISSN： 2405-4712 Impact factor: 10.304

21 in total

1. Genome-scale CRISPR-Cas9 knockout screening in human cells.

Authors: Ophir Shalem; Neville E Sanjana; Ella Hartenian; Xi Shi; David A Scott; Tarjei Mikkelson; Dirk Heckl; Benjamin L Ebert; David E Root; John G Doench; Feng Zhang
Journal: Science Date: 2013-12-12 Impact factor: 47.728

2. Mutant phenotypes for thousands of bacterial genes of unknown function.

Authors: Morgan N Price; Kelly M Wetmore; R Jordan Waters; Mark Callaghan; Jayashree Ray; Hualan Liu; Jennifer V Kuehl; Ryan A Melnyk; Jacob S Lamson; Yumi Suh; Hans K Carlson; Zuelma Esquivel; Harini Sadeeshkumar; Romy Chakraborty; Grant M Zane; Benjamin E Rubin; Judy D Wall; Axel Visel; James Bristow; Matthew J Blow; Adam P Arkin; Adam M Deutschbauer
Journal: Nature Date: 2018-05-16 Impact factor: 49.962

3. Genetic interaction mapping in mammalian cells using CRISPR interference.

Authors: Dan Du; Assen Roguev; David E Gordon; Meng Chen; Si-Han Chen; Michael Shales; John Paul Shen; Trey Ideker; Prashant Mali; Lei S Qi; Nevan J Krogan
Journal: Nat Methods Date: 2017-05-08 Impact factor: 28.547

4. Quantitative evolutionary dynamics using high-resolution lineage tracking.

Authors: Sasha F Levy; Jamie R Blundell; Sandeep Venkataram; Dmitri A Petrov; Daniel S Fisher; Gavin Sherlock
Journal: Nature Date: 2015-02-25 Impact factor: 49.962

5. A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

Authors: Ulrich Schlecht; Zhimin Liu; Jamie R Blundell; Robert P St Onge; Sasha F Levy
Journal: Nat Commun Date: 2017-05-25 Impact factor: 14.919

6. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

Authors: Andrew M Smith; Lawrence E Heisler; Robert P St Onge; Eveline Farias-Hesson; Iain M Wallace; John Bodeau; Adam N Harris; Kathleen M Perry; Guri Giaever; Nader Pourmand; Corey Nislow
Journal: Nucleic Acids Res Date: 2010-05-11 Impact factor: 16.971

7. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.

Authors: Cheuk Hei Ho; Leslie Magtanong; Sarah L Barker; David Gresham; Shinichi Nishimura; Paramasivam Natarajan; Judice L Y Koh; Justin Porter; Christopher A Gray; Raymond J Andersen; Guri Giaever; Corey Nislow; Brenda Andrews; David Botstein; Todd R Graham; Minoru Yoshida; Charles Boone
Journal: Nat Biotechnol Date: 2009-04-06 Impact factor: 54.908

8. Deep mutational scanning: a new style of protein science.

Authors: Douglas M Fowler; Stanley Fields
Journal: Nat Methods Date: 2014-08 Impact factor: 28.547

9. Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

Authors: Nozomu Yachie; Evangelia Petsalaki; Joseph C Mellor; Jochen Weile; Yves Jacob; Marta Verby; Sedide B Ozturk; Siyang Li; Atina G Cote; Roberto Mosca; Jennifer J Knapp; Minjeong Ko; Analyn Yu; Marinella Gebbia; Nidhi Sahni; Song Yi; Tanya Tyagi; Dayag Sheykhkarimli; Jonathan F Roth; Cassandra Wong; Louai Musa; Jamie Snider; Yi-Chun Liu; Haiyuan Yu; Pascal Braun; Igor Stagljar; Tong Hao; Michael A Calderwood; Laurence Pelletier; Patrick Aloy; David E Hill; Marc Vidal; Frederick P Roth
Journal: Mol Syst Biol Date: 2016-04-22 Impact factor: 11.429

10. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

Authors: Justin D Smith; Sundari Suresh; Ulrich Schlecht; Manhong Wu; Omar Wagih; Gary Peltz; Ronald W Davis; Lars M Steinmetz; Leopold Parts; Robert P St Onge
Journal: Genome Biol Date: 2016-03-08 Impact factor: 13.583

8 in total

Unbiased Fitness Estimation of Pooled Barcode or Amplicon Sequencing Studies.

1. Genome-scale CRISPR-Cas9 knockout screening in human cells.

2. Mutant phenotypes for thousands of bacterial genes of unknown function.

3. Genetic interaction mapping in mammalian cells using CRISPR interference.

4. Quantitative evolutionary dynamics using high-resolution lineage tracking.

5. A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions.

6. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples.

7. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds.

8. Deep mutational scanning: a new style of protein science.

9. Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

10. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

1. iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.

2. Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful.

3. A large accessory protein interactome is rewired across environments.

4. Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements.

5. The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross.

6. PhenoMIP: High-Throughput Phenotyping of Diverse Caenorhabditis elegans Populations via Molecular Inversion Probes.

7. High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae.

8. The Effects of Sequence Length and Composition of Random Sequence Peptides on the Growth of E. coli Cells.