Factors affecting reproducibility between genome-scale siRNA-based screens.

Journal of Biomolecular Screening
Nicholas J BarrowsJames L Pearson

Abstract

RNA interference-based screening is a powerful new genomic technology that addresses gene function en masse. To evaluate factors influencing hit list composition and reproducibility, the authors performed 2 identically designed small interfering RNA (siRNA)-based, whole-genome screens for host factors supporting yellow fever virus infection. These screens represent 2 separate experiments completed 5 months apart and allow the direct assessment of the reproducibility of a given siRNA technology when performed in the same environment. Candidate hit lists generated by sum rank, median absolute deviation, z-score, and strictly standardized mean difference were compared within and between whole-genome screens. Application of these analysis methodologies within a single screening data set using a fixed threshold equivalent to a p-value < or = 0.001 resulted in hit lists ranging from 82 to 1140 members and highlighted the tremendous impact analysis methodology has on hit list composition. Intra- and interscreen reproducibility was significantly influenced by the analysis methodology and ranged from 32% to 99%. This study also highlighted the power of testing at least 2 independent siRNAs for each gene product in primary screens. To fa...Continue Reading

References

Jul 1, 1982·The American Journal of Tropical Medicine and Hygiene·E A HenchalW E Brandt
Jun 6, 2000·Journal of Biomolecular Screening·J H ZhangK R Oldenburg
Aug 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·N J CaplenR A Morgan
Apr 18, 2002·Genes & Development·Patrick J PaddisonDouglas S Conklin
May 20, 2003·Nature Biotechnology·Aimee L JacksonPeter S Linsley
Apr 12, 2006·Nature Reviews. Genetics·Christophe J Echeverri, Norbert Perrimon
Sep 23, 2006·Nature Methods·Christophe J EcheverriRené Bernards
Feb 16, 2007·Journal of Virology·Manoj N KrishnanErol Fikrig
Jan 25, 2008·Journal of Biomolecular Screening·Namjin ChungBerta Strulovici
May 16, 2008·Journal of Biomolecular Screening·Xiaohua Douglas ZhangMarc Ferrer
Nov 4, 2008·Cell Host & Microbe·Honglin ZhouAmy S Espeseth
Mar 17, 2009·Cell Host & Microbe·Andrew W TaiRaymond T Chung
Apr 28, 2009·Nature·October M SessionsMariano A Garcia-Blanco
May 30, 2009·PLoS Pathogens·Frederic D BushmanSumit K Chanda
Aug 1, 2009·Nature Methods·Amanda BirminghamCaroline E Shamu
Sep 1, 2009·Proceedings of the National Academy of Sciences of the United States of America·Qisheng LiStephen J Elledge
Dec 23, 2009·Nature·Renate KönigSumit K Chanda

❮ Previous
Next ❯

Citations

Sep 6, 2011·Nature Reviews. Drug Discovery·Florian PrinzKhusru Asadullah
Nov 9, 2011·Proceedings of the National Academy of Sciences of the United States of America·Debasis PandaAsit K Pattnaik
Apr 30, 2011·Briefings in Functional Genomics·Ming JiangMichael Howell
Sep 21, 2013·Bioinformatics·Lauren A SugdenCharles E Lawrence
Oct 15, 2013·Database : the Journal of Biological Databases and Curation·Rebecca E SaundersMichael Howell
Oct 3, 2012·PLoS Neglected Tropical Diseases·Caroline Le SommerMariano A Garcia-Blanco
Jul 13, 2011·International Journal of Molecular Sciences·Andrew PrussiaRichard K Plemper
Apr 4, 2014·Methods in Molecular Biology·Nicholas J BarrowsMariano A Garcia-Blanco
Feb 13, 2014·Viruses·Manoj N Krishnan, Mariano A Garcia-Blanco
Nov 6, 2012·Current Opinion in Virology·Debasis Panda, Sara Cherry
Jun 21, 2011·Current Opinion in Chemical Biology·Priscille Brodin, Thierry Christophe
Jul 15, 2015·Methods : a Companion to Methods in Enzymology·Debasis Panda, Sara Cherry
Feb 15, 2014·Current Opinion in Virology·Samuel Kilcher, Jason Mercer
Nov 20, 2018·Brain Pathology·Daniel PeaseAdriano Aguzzi
Aug 25, 2017·Nature·Gordon J LithgowPatrick Phillips
Jul 10, 2019·Annual Review of Virology·John W Schoggins
Nov 17, 2011·Journal of Biomolecular Screening·Shane MarineEugen Buehler
Jul 6, 2019·Scientific Reports·Nicholas J BarrowsMariano A Garcia-Blanco
Dec 23, 2019·Medical Microbiology and Immunology·Sarah V Barrass, Sarah J Butcher
May 23, 2021·The Journal of General Virology·Chloe E JonesDavid J Hughes

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping

Software Mentioned

Compartmental Analysis
vHCS Scan
SSMD
vHCS View

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.