A simple method for analyzing actives in random RNAi screens: Introducing the "H score" for hit nomination & gene prioritization Journal Article
| Authors: | Bhinder, B.; Djaballah, H. |
| Article Title: | A simple method for analyzing actives in random RNAi screens: Introducing the "H score" for hit nomination & gene prioritization |
| Abstract: | Due to the numerous challenges in hit identification from random RNAi screening, we have examined current practices with a discovery of a variety of methodologies employed and published in many reports; majority of them, unfortunately, do not address the minimum associated criteria for hit nomination, as this could potentially have been the cause or may well be the explanation as to the lack of confirmation and follow up studies, currently facing the RNAi field. Overall, we find that these criteria or parameters are not well defined, in most cases arbitrary in nature, and hence rendering it extremely difficult to judge the quality of and confidence in nominated hits across published studies. For this purpose, we have developed a simple method to score actives independent of assay readout; and provide, for the first time, a homogenous platform enabling cross-comparison of active gene lists resulting from different RNAi screening technologies. Here, we report on our recently developed method dedicated to RNAi data output analysis referred to as the BDA method applicable to both arrayed and pooled RNAi technologies; wherein the concerns pertaining to inconsistent hit nomination and off-target silencing in conjugation with minimal activity criteria to identify a high value target are addressed. In this report, a combined hit rate per gene, called "H score", is introduced and defined. The H score provides a very useful tool for stringent active gene nomination, gene list comparison across multiple studies, prioritization of hits, and evaluation of the quality of the nominated gene hits. © 2012 Bentham Science Publishers. |
| Keywords: | methodology; gene; microrna; classification; small interfering rna; rna interference; gene library; publication; screening; gene identification; data analysis; 3' untranslated region; short hairpin rna; rna sequence; peer group; rnai; rna analysis; sirna; process development; mirna; shrna; hts; heteroduplex; 3'utr; bda method; esirna; h score; hcs; heptamer; off-target effect; randomness; seed sequence |
| Journal Title: | Combinatorial Chemistry and High Throughput Screening |
| Volume: | 15 |
| Issue: | 9 |
| ISSN: | 1386-2073 |
| Publisher: | Bentham Science Publishers |
| Date Published: | 2012-11-01 |
| Start Page: | 686 |
| End Page: | 704 |
| Language: | English |
| DOI: | 10.2174/138620712803519671 |
| PROVIDER: | scopus |
| PUBMED: | 22934950 |
| PMCID: | PMC3678258 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 1" - "Export Date: 2 January 2013" - "CODEN: CCHSF" - "Source: Scopus" |
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