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Mpindi JP, Swapnil P, Dmitrii B, Jani S, Saeed K, Wennerberg K, Aittokallio T, Östling P, Kallioniemi O. Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data. Bioinformatics 2015; 31:3815-21. [PMID: 26254433 PMCID: PMC4653387 DOI: 10.1093/bioinformatics/btv455] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/30/2015] [Indexed: 12/19/2022] Open
Abstract
Motivation: Most data analysis tools for high-throughput screening (HTS) seek to uncover interesting hits for further analysis. They typically assume a low hit rate per plate. Hit rates can be dramatically higher in secondary screening, RNAi screening and in drug sensitivity testing using biologically active drugs. In particular, drug sensitivity testing on primary cells is often based on dose–response experiments, which pose a more stringent requirement for data quality and for intra- and inter-plate variation. Here, we compared common plate normalization and noise-reduction methods, including the B-score and the Loess a local polynomial fit method under high hit-rate scenarios of drug sensitivity testing. We generated simulated 384-well plate HTS datasets, each with 71 plates having a range of 20 (5%) to 160 (42%) hits per plate, with controls placed either at the edge of the plates or in a scattered configuration. Results: We identified 20% (77/384) as the critical hit-rate after which the normalizations started to perform poorly. Results from real drug testing experiments supported this estimation. In particular, the B-score resulted in incorrect normalization of high hit-rate plates, leading to poor data quality, which could be attributed to its dependency on the median polish algorithm. We conclude that a combination of a scattered layout of controls per plate and normalization using a polynomial least squares fit method, such as Loess helps to reduce column, row and edge effects in HTS experiments with high hit-rates and is optimal for generating accurate dose–response curves. Contact:john.mpindi@helsinki.fi Availability and implementation, Supplementary information: R code and Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- John-Patrick Mpindi
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Potdar Swapnil
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Bychkov Dmitrii
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Saarela Jani
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Khalid Saeed
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Krister Wennerberg
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Tero Aittokallio
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Päivi Östling
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Olli Kallioniemi
- University of Helsinki, Institute for Molecular Medicine, Tukholmankatu 8, FI-00290, Helsinki, Finland
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Stombaugh J, Licon A, Strezoska Ž, Stahl J, Anderson SB, Banos M, van Brabant Smith A, Birmingham A, Vermeulen A. The Power Decoder Simulator for the Evaluation of Pooled shRNA Screen Performance. ACTA ACUST UNITED AC 2015; 20:965-75. [PMID: 25777298 PMCID: PMC4543901 DOI: 10.1177/1087057115576715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/17/2015] [Indexed: 12/30/2022]
Abstract
RNA interference screening using pooled, short hairpin RNA (shRNA) is a powerful, high-throughput tool for determining the biological relevance of genes for a phenotype. Assessing an shRNA pooled screen’s performance is difficult in practice; one can estimate the performance only by using reproducibility as a proxy for power or by employing a large number of validated positive and negative controls. Here, we develop an open-source software tool, the Power Decoder simulator, for generating shRNA pooled screening experiments in silico that can be used to estimate a screen’s statistical power. Using the negative binomial distribution, it models both the relative abundance of multiple shRNAs within a single screening replicate and the biological noise between replicates for each individual shRNA. We demonstrate that this simulator can successfully model the data from an actual laboratory experiment. We then use it to evaluate the effects of biological replicates and sequencing counts on the performance of a pooled screen, without the necessity of gathering additional data. The Power Decoder simulator is written in R and Python and is available for download under the GNU General Public License v3.0.
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Affiliation(s)
| | - Abel Licon
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
| | | | - Joshua Stahl
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
| | | | - Michael Banos
- Dharmacon, part of GE Healthcare, Lafayette, CO, USA
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Ogier A, Dorval T. HCS-Analyzer: open source software for high-content screening data correction and analysis. Bioinformatics 2012; 28:1945-6. [DOI: 10.1093/bioinformatics/bts288] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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