The sbv IMPROVER Systems Toxicology Computational Challenge: Identification of Human and Species-Independent Blood Response Markers as Predictors of Smoking Exposure and Cessation Status

Computational Toxicology
Vincenzo BelcastroSandeep Kumar Dhanda

Abstract

Cigarette smoking entails chronic exposure to a mixture of harmful chemicals that trigger molecular changes over time, and is known to increase the risk of developing diseases. Risk assessment in the context of 21st century toxicology relies on the elucidation of mechanisms of toxicity and the identification of exposure response markers, usually from high-throughput data, using advanced computational methodologies. The sbv IMPROVER Systems Toxicology computational challenge (Fall 2015-Spring 2016) aimed to evaluate whether robust and sparse (≤40 genes) human (sub-challenge 1, SC1) and species-independent (sub-challenge 2, SC2) exposure response markers (so called gene signatures) could be extracted from human and mouse blood transcriptomics data of current (S), former (FS) and never (NS) smoke-exposed subjects as predictors of smoking and cessation status. Best-performing computational methods were identified by scoring anonymized participants' predictions. Worldwide participation resulted in 12 (SC1) and six (SC2) final submissions qualified for scoring. The results showed that blood gene expression data were informative to predict smoking exposure (i.e. discriminating smoker versus never or former smokers) status in human and...Continue Reading

References

Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Sep 5, 2006·Briefings in Bioinformatics·Tina A EyreElspeth A Bruford
Jan 26, 2010·Biostatistics·Matthew N McCallRafael A Irizarry
Jun 4, 2010·The Journal of Immunology : Official Journal of the American Association of Immunologists·Sanja CickoMarco Idzko
Aug 11, 2011·PloS One·Heather G LaBrecheJohn P Chute
Dec 6, 2012·BMC Medical Genomics·Philip BeinekeUNKNOWN PREDICT Investigators
Jan 25, 2013·Scientific Reports·Shahar Barbash, Hermona Soreq
Aug 21, 2013·Toxicological Sciences : an Official Journal of the Society of Toxicology·Russell S ThomasAndy Nong
Feb 21, 2014·Arteriosclerosis, Thrombosis, and Vascular Biology·Barbara Messner, David Bernhard
Oct 9, 2014·Bioinformatics·Erhan BilalLeonidas G Alexopoulos
Nov 27, 2014·Epigenetics : Official Journal of the DNA Methylation Society·Loukia G TsaprouniPanos Deloukas
Dec 3, 2014·Toxicology Letters·Hyun-Kyung NaMihi Yang
Jan 4, 2015·Human Molecular Genetics·Florence GuidaMarc Chadeau-Hyam
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Apr 7, 2015·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Blaine PhillipsManuel C Peitsch
Aug 27, 2015·Journal of Proteomics·Bjoern TitzManuel C Peitsch
Sep 1, 2015·Atherosclerosis·Henri WeidmannEwa Ninio
Sep 12, 2015·Arteriosclerosis, Thrombosis, and Vascular Biology·Béatrice Hechler, Christian Gachet
Feb 2, 2016·Environmental Research·Yan ZhangHermann Brenner
Jul 19, 2016·Gene Regulation and Systems Biology·UNKNOWN sbv IMPROVER project team and challenge best performersYang Xiang
Jul 28, 2016·Regulatory Toxicology and Pharmacology : RTP·Maurice R SmithManuel C Peitsch
Oct 21, 2016·Circulation. Cardiovascular Genetics·Roby JoehanesStephanie J London
Nov 7, 2016·Regulatory Toxicology and Pharmacology : RTP·Christelle HazizaFrank Lüdicke

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