ShinyGAStool: A user-friendly tool for candidate gene association studies

SoftwareX - Tập 21 - Trang 101274 - 2023
Thomas J. Hoffmann1,2,3, Christine Miaskowski3,4, Kord M. Kober3,4,5
1Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, United States of America
2Institute for Human Genetics, University of California, San Francisco, CA, United States of America
3School of Nursing, University of California, San Francisco, CA, United States of America
4Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, United States of America
5Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, United States of America

Tài liệu tham khảo

Buniello, 2019, The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics, Nucleic Acids Res, 47, D1005, 10.1093/nar/gky1120 2018, GWAS to the people, Nat Med, 24, 1483, 10.1038/s41591-018-0231-3 Chen, 2009, Barriers to adopting genomics into public health education: a mixed methods study, Genet Med, 11, 104, 10.1097/GIM.0b013e31818fa2c7 Founds, 2018, Systems biology for nursing in the era of big data and precision health, Nurs Outlook, 66, 283, 10.1016/j.outlook.2017.11.006 Loscalzo, 2011, Systems biology and the future of medicine, Wiley Interdiscip Rev Syst Biol Med, 3, 619, 10.1002/wsbm.144 Dreisbach, 2020, The state of data science in genomic nursing, Biol Res Nurs, 10.1177/1099800420915991 Frohlich, 2018, From hype to reality: data science enabling personalized medicine, BMC Med, 16, 150, 10.1186/s12916-018-1122-7 Conley, 2009, Genetics and genomics in nursing research, Biol Res Nurs, 11, 5, 10.1177/1099800409336293 Khoury, 2018, From public health genomics to precision public health: a 20-year journey, Genet Med, 20, 574, 10.1038/gim.2017.211 Collins, 2015, A new initiative on precision medicine, N Engl J Med, 372, 793, 10.1056/NEJMp1500523 Genomic Nursing State of the Science Advisory, 2013, A blueprint for genomic nursing science, J Nurs Scholarsh, 45, 96, 10.1111/jnu.12007 Whitley, 2020, Genomics education in the era of personal genomics: Academic, professional, and public considerations, Int J Mol Sci, 21, 10.3390/ijms21030768 Illi, 2012, Association between pro- and anti-inflammatory cytokine genes and a symptom cluster of pain, fatigue, sleep disturbance, and depression, Cytokine, 58, 437, 10.1016/j.cyto.2012.02.015 Eshragh, 2017, Associations between neurotransmitter genes and fatigue and energy levels in women after breast cancer surgery, J Pain Symp Manag, 53, 67, 10.1016/j.jpainsymman.2016.08.004 Kober, 2016, Polymorphisms in cytokine genes are associated with higher levels of fatigue and lower levels of energy in women after breast cancer surgery, J Pain Symp Manag, 52, 695, 10.1016/j.jpainsymman.2016.04.014 Team, 2019 Church, 2011, Modernizing reference genome assemblies, PLoS Biol, 9, 10.1371/journal.pbio.1001091 Schneider, 2017, Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly, Genome Res, 27, 849, 10.1101/gr.213611.116 Turner, 2011, Quality control procedures for genome-wide association studies, Curr Protoc Hum Genet, Chapter 1, 19 Karolchik, 2011, The UCSC genome browser, Curr Protoc Hum Genet, Chapter 18, 16 Rosenbloom, 2015, The UCSC genome browser database, Nucleic Acids Res, 43, D670, 10.1093/nar/gku1177 Pujar, 2018, Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation, Nucleic Acids Res, 46, D221, 10.1093/nar/gkx1031 O’Leary, 2016, Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation, Nucleic Acids Res, 44, D733, 10.1093/nar/gkv1189 Frankish, 2019, GENCODE reference annotation for the human and mouse genomes, Nucleic Acids Res, 47, D766, 10.1093/nar/gky955 Sievert, 2020 Machiela, 2015, LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants, Bioinformatics, 31, 3555, 10.1093/bioinformatics/btv402 Kent, 2002, The human genome browser at UCSC, Genome Res, 12, 996, 10.1101/gr.229102 Watanabe, 2017, Functional mapping and annotation of genetic associations with FUMA, Nature Commun, 8, 1826, 10.1038/s41467-017-01261-5 Boughton, 2021, LocusZoom.js: Interactive and embeddable visualization of genetic association study results, Bioinformatics, 10.1093/bioinformatics/btab186 Purcell, 2007, PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet, 81, 559, 10.1086/519795 Kuznetsova, 2017, ImerTest package: Tests in linear mixed effects models, J Stat Softw, 82, 1, 10.18637/jss.v082.i13 Bates, 2015, Fitting linear mixed-effects models using lme4, J Stat Softw, 67, 1, 10.18637/jss.v067.i01