Assessment of single-nucleotide variant discovery protocols in RNA-seq data from human cells exposed to mycotoxins

References

• Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ. 2019. Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLoS One. 14(9):e0216838.
   PubMed Web of Science ®Google Scholar
• Aguilar F, Hussain SP, Cerutti P. 1993. Aflatoxin B1 induces the transversion of G–> T in codon 249 of the p53 tumor suppressor gene in human hepatocytes. Proc Natl Acad Sci USA. 90(18):8586–8590.
   PubMed Web of Science ®Google Scholar
• Alonso-Garrido M, Manyes L, Pralea IE, Iuga CA. 2020a. Mitochondrial proteomics profile points oxidative phosphorylation as main target for beauvericin and enniatin B mixture. Food Chem Toxicol. 141:111432.
   PubMed Web of Science ®Google Scholar
• Alonso-Garrido M, Tedeschi P, Maietti A, Font G, Marchetti N, Manyes L. 2020b. Mitochondrial transcriptional study of the effect of aflatoxins, enniatins and carotenoids in vitro in a blood brain barrier model. Food Chem Toxicol. 137:111077.
   PubMed Web of Science ®Google Scholar
• Alonso-Garrido M, Escrivá L, Manyes L, Font G. 2018. Enniatin B induces expression changes in the electron transport chain pathway related genes in lymphoblastic T-cell line. Food Chem Toxicol. 121:437–443.
   PubMed Web of Science ®Google Scholar
• Andrews S, Fast QC. 2010. A Quality Control Tool for High Throughput Sequence Data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
   Google Scholar
• Brookes AJ. 1999. The essence of SNPs. Gene. 234(2):177–186.
   PubMed Web of Science ®Google Scholar
• Carballo D, Font G, Ferrer E, Berrada H. 2018. Evaluation of mycotoxin residues on ready-to-eat food by chromatographic methods coupled to mass spectrometry in tandem. Toxins. 10(6):243.
   PubMed Web of Science ®Google Scholar
• Core Team R 2017. A language and environment for statistical computing. Viena: R Foundation for Statistical Computing.
   Google Scholar
• Dellafiora D, Dall’Asta C. 2017. Forthcoming challenges in mycotoxins toxicology research for safer food-a need for multi-omics approach. Toxins (Basel). 9(1):18.
   PubMed Web of Science ®Google Scholar
• Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 29(1):15–21.
   PubMed Web of Science ®Google Scholar
• Escrivá L, Alonso-Garrido M, Font G, Manyes L. 2019. Transcriptional study after Beauvericin and Enniatin B combined exposure in Jurkat T cells. Food Chem Toxicol. 130:122–129.
   PubMed Web of Science ®Google Scholar
• Escrivá L, Jennen D, Caiment F, Manyes L. 2018. Transcriptomic study of the toxic mechanism triggered by beauvericin in Jurkat cells. Toxicol. Lett. 284:213–221.
   PubMed Web of Science ®Google Scholar
• Food and Agriculture Organization of the United Nations. Food safety and quality: Mycotoxins. 2020. Available at: http://www.fao.org/food/food-safety-quality/a-z-index/mycotoxins/en/.
   Google Scholar
• Gil L, Ruiz P, Font G, Manyes L. 2016. An overview of the applications of hazards analysis and critical control point (HACCP) system to mycotoxins. Rev Toxicol. 33:50–55.
   Google Scholar
• Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y. 2017. The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data. BMC Genomics. 18(Suppl 6):690.
   PubMedGoogle Scholar
• Hannon GJ. 2010. FASTX-Toolkit. Available at: http://hannonlab.cshl.edu/fastx_toolkit.
   Google Scholar
• Kolde R. 2019. Pheatmap: pretty heatmaps. R Package Version 1.0.10. Available at: https://CRAN.R-project.org/package=pheatmap.
   Google Scholar
• Lam S, Zeidan J, Miglior F, Suárez-Vega A, Gómez-Redondo I, Fonseca PAS, Guan LL, Waters S, Cánovas A. 2020. Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle. BMC Genomics. 21(1):703.
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 25(16):2078–2079.
   PubMed Web of Science ®Google Scholar
• Liu F, Zhang Y, Zhang L, Li Z, Fang Q, Gao R, Zhang Z. 2019. Zhang, Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biol. 20(1):242.
   PubMed Web of Science ®Google Scholar
• McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. 2016. The Ensembl Variant Effect Predictor. Genome Biol. 17(1):122.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26(1):139–140.
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. 2011. Integrative genomics viewer. Nat Biotechnol. 29(1):24–26.
   PubMed Web of Science ®Google Scholar
• Swinton J. 2013. Vennerable package [Internet]. Available at: https://github.com/js229/Vennerable.
   Google Scholar
• Tan A, Abecasis GR, Kang HM. 2015. Unified representation of genetic variants. Bioinformatics. 31(13):2202–2204.
   PubMed Web of Science ®Google Scholar
• The Broad Institute. GATK | Methods and Algorithms | Doc #3891 | Calling variants in RNAseq. GATK. Available at: http://gatk.broadinstitute.org/hc/en-us/articles/360035531192.
   Google Scholar
• Tolosa J, Rodríguez-Carrasco Y, Ferrer E, Mañes J. 2019. Identification and quantification of enniatins and beauvericin in animal feeds and their ingredients by LC-QTRAP/MS/MS. Metabolites. 9(2):33.
   PubMed Web of Science ®Google Scholar
• Tonshin AA, Teplova VV, Andersson MA, Salkinoja-Salonen MS. 2010. The Fusarium mycotoxins enniatins and beauvericin cause mitochondrial dysfunction by affecting the mitochondrial volume regulation, oxidative phosphorylation and ion homeostasis. Toxicology. 276(1):49–57.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Wang K, Wang WK, Yin TT, Dong WQ, Xu CJ. 2019. A high-throughput SNP discovery strategy for RNA-seq data. BMC Genomics. 20(1):160.
   PubMedGoogle Scholar