Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.
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Li Ding | Kyle Ellrott | Gad Getz | Gordon Saksena | Matthew H Bailey | Kyle R Covington | Cyriac Kandoth | Chip Stewart | Julian Hess | Singer Ma | Kami E Chiotti | Michael McLellan | Heidi J Sofia | Carolyn Hutter | David Wheeler | G. Getz | D. Wheeler | L. Ding | M. McLellan | C. Stewart | C. Kandoth | Kyle Ellrott | G. Saksena | H. Sofia | C. Hutter | K. Covington | J. Hess | Singer Ma | K. Chiotti | Matthew H. Bailey | K. Ellrott | Kami E. Chiotti
[1] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes , 2013 .
[2] Terence P. Speed,et al. Comparing somatic mutation-callers: beyond Venn diagrams , 2013, BMC Bioinformatics.
[3] J C Costello,et al. Seeking the Wisdom of Crowds Through Challenge‐Based Competitions in Biomedical Research , 2013, Clinical pharmacology and therapeutics.
[4] C. Turnbull,et al. Introducing whole-genome sequencing into routine cancer care: the Genomics England 100 000 Genomes Project. , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.
[5] P. A. Futreal,et al. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data , 2016, Genome Biology.
[6] A. Sivachenko,et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.
[7] Benjamin J. Raphael,et al. Mutational landscape and significance across 12 major cancer types , 2013, Nature.
[8] Joshua M. Stuart,et al. RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection , 2014, PloS one.
[9] Project GENIE Goes Public. , 2017, Cancer discovery.
[10] James Y. Zou. Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.
[11] Kai Ye,et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..
[12] Icgc,et al. Pan-cancer analysis of whole genomes , 2017, bioRxiv.
[13] Mingming Jia,et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..
[14] Elizabeth M. Smigielski,et al. dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..
[15] Georgina L Ryland,et al. A simple consensus approach improves somatic mutation prediction accuracy , 2013, Genome Medicine.
[16] Matthew B. Callaway,et al. MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.
[17] Trevor J Pugh,et al. Initial genome sequencing and analysis of multiple myeloma , 2011, Nature.
[18] Joshua M. Stuart,et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection , 2015, Nature Methods.
[19] F. Cunningham,et al. The Ensembl Variant Effect Predictor , 2016, Genome Biology.
[20] T. Graubert,et al. Genomics in childhood acute myeloid leukemia comes of age , 2018, Nature Medicine.
[21] Steven J. M. Jones,et al. Comprehensive genomic characterization of squamous cell lung cancers , 2012, Nature.
[22] Steven J. M. Jones,et al. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. , 2017, Cancer cell.
[23] Doron Lipson,et al. High-Throughput Genomic Profiling of Adult Solid Tumors Reveals Novel Insights into Cancer Pathogenesis. , 2017, Cancer research.
[24] Steven J. M. Jones,et al. Comprehensive Characterization of Cancer Driver Genes and Mutations , 2018, Cell.
[25] L. Stein. The case for cloud computing in genome informatics , 2010, Genome Biology.
[26] Sarah C. Ayling,et al. The Ensembl gene annotation system , 2016, Database J. Biol. Databases Curation.
[27] Michael T. Zimmermann,et al. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas , 2018, Cell reports.
[28] Steven A. Roberts,et al. Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .
[29] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[30] Steven J. M. Jones,et al. Genomic Classification of Cutaneous Melanoma , 2015, Cell.
[31] Steven J. M. Jones,et al. Comprehensive molecular profiling of lung adenocarcinoma , 2014, Nature.
[32] Adam A. Margolin,et al. The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.
[33] Alexander Lex,et al. UpSetR: an R package for the visualization of intersecting sets and their properties , 2017, bioRxiv.
[34] Ken Chen,et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data , 2012, Bioinform..
[35] Christopher A. Miller,et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.
[36] Steven J. M. Jones,et al. The Immune Landscape of Cancer , 2018, Immunity.
[37] Trevor J Pugh,et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation , 2013, Nucleic acids research.