دورية أكاديمية
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
| العنوان: | Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. |
|---|---|
| المؤلفون: | Glusman G; Institute for Systems Biology, Seattle, WA, 98109, USA. Gustavo@SystemsBiology.org., Rose PW; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA., Prlić A; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Dougherty J; Institute for Systems Biology, Seattle, WA, 98109, USA., Duarte JM; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Hoffman AS; Human Centered Design & Engineering, University of Washington, Seattle, WA, 98195, USA., Barton GJ; Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK., Bendixen E; Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark., Bergquist T; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Bock C; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Brunk E; University of California San Diego, La Jolla, CA, 92093, USA., Buljan M; Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland., Burley SK; San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA.; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA., Cai B; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Carter H; University of California San Diego, La Jolla, CA, 92093, USA., Gao J; Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA., Godzik A; SBP Medical Discovery Institute, La Jolla, CA, 92037, USA., Heuer M; AMPLab, University of California, Berkeley, CA, 94720, USA., Hicks M; Human Longevity, Inc, San Diego, CA, 92121, USA., Hrabe T; SBP Medical Discovery Institute, La Jolla, CA, 92037, USA., Karchin R; Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.; Department of Oncology, Johns Hopkins Medicine, Baltimore, MD, 21287, USA., Leman JK; Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, 10010, USA.; Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA., Lane L; SIB Swiss Institute of Bioinformatics and University of Geneva, CH-1211, Geneva, Switzerland., Masica DL; Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA., Mooney SD; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Moult J; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA., Omenn GS; Institute for Systems Biology, Seattle, WA, 98109, USA.; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA., Pearl F; School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK., Pejaver V; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA.; The University of Washington eScience Institute, Seattle, WA, 98195, USA., Reynolds SM; Institute for Systems Biology, Seattle, WA, 98109, USA., Rokem A; The University of Washington eScience Institute, Seattle, WA, 98195, USA., Schwede T; SIB Swiss Institute of Bioinformatics and Biozentrum University of Basel, CH-4056, Basel, Switzerland., Song S; Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA., Tilgner H; Brain and Mind Research Institute, Weill Cornell Medicine, New York City, NY, 10021, USA., Valasatava Y; RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA., Zhang Y; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA., Deutsch EW; Institute for Systems Biology, Seattle, WA, 98109, USA. |
| المصدر: | Genome medicine [Genome Med] 2017 Dec 18; Vol. 9 (1), pp. 113. Date of Electronic Publication: 2017 Dec 18. |
| نوع المنشور: | Journal Article; Review |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Country of Publication: England NLM ID: 101475844 Publication Model: Electronic Cited Medium: Internet ISSN: 1756-994X (Electronic) Linking ISSN: 1756994X NLM ISO Abbreviation: Genome Med Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [London] : BioMed Central |
| مواضيع طبية MeSH: | Polymorphism, Genetic* , Protein Conformation*, Genome-Wide Association Study/*methods , Sequence Analysis, Protein/*methods, Algorithms ; Congresses as Topic ; Genome-Wide Association Study/standards ; Humans ; Sequence Analysis, Protein/standards |
| مستخلص: | The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods. |
| References: | Hum Mutat. 2013 Jan;34(1):42-9. (PMID: 22903802) BMC Bioinformatics. 2011;12 Suppl 4:S3. (PMID: 21992054) J Am Med Inform Assoc. 2015 May;22(3):495-506. (PMID: 25726569) Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W239-42. (PMID: 16845001) Nucleic Acids Res. 2006 Jan 1;34(Database issue):D204-6. (PMID: 16381846) Bioinformatics. 2009 May 1;25(9):1189-91. (PMID: 19151095) Database (Oxford). 2013 Apr 26;2013:bat031. (PMID: 23624946) Eur J Med Genet. 2017 Oct;60(10 ):553-558. (PMID: 28774848) Nucleic Acids Res. 2015 Jan;43(Database issue):D968-73. (PMID: 25392415) Science. 2001 Oct 5;294(5540):93-6. (PMID: 11588250) Nucleic Acids Res. 2013 Jul;41(Web Server issue):W333-9. (PMID: 23723246) Int J Mol Sci. 2016 Apr 12;17 (4):547. (PMID: 27077847) Bioinformatics. 2009 Jun 1;25(11):1431-2. (PMID: 19369493) Nat Protoc. 2015 Jun;10(6):845-58. (PMID: 25950237) Genome Biol. 2016 Jun 06;17 (1):122. (PMID: 27268795) Nucleic Acids Res. 2014 Jan;42(Database issue):D336-46. (PMID: 24271400) Nat Struct Biol. 2003 Dec;10(12):980. (PMID: 14634627) Protein Sci. 2014 Dec;23(12):1650-66. (PMID: 25234433) Bioinformatics. 2016 May 15;32(10 ):1589-91. (PMID: 26801957) J Natl Cancer Inst. 2015 Apr 11;107(7):null. (PMID: 25863335) J Am Med Inform Assoc. 2017 May 1;24(3):513-519. (PMID: 27789569) Proteins. 2011 Mar;79(3):830-8. (PMID: 21287615) Nature. 2015 Oct 15;526(7573):336-42. (PMID: 26469044) Bioinformatics. 2014 Feb 1;30(3):335-42. (PMID: 24281696) Structure. 2013 Sep 3;21(9):1531-40. (PMID: 24010712) Contemp Oncol (Pozn). 2015;19(1A):A68-77. (PMID: 25691825) PLoS Comput Biol. 2015 Oct 27;11(10):e1004494. (PMID: 26506533) Nucleic Acids Res. 2013 Jan;41(Database issue):D483-9. (PMID: 23203869) Nucleic Acids Res. 2001 Jan 1;29(1):308-11. (PMID: 11125122) Nucleic Acids Res. 2016 Apr 7;44(6):2501-13. (PMID: 26926108) Genome Biol. 2005;6(1):R9. (PMID: 15642101) Sci Data. 2016 Mar 15;3:160018. (PMID: 26978244) Nucleic Acids Res. 2013 Jan;41(Database issue):D936-41. (PMID: 23193291) Nucleic Acids Res. 2016 Jul 8;44(W1):W469-73. (PMID: 27216816) Nucleic Acids Res. 2016 Jul 8;44(W1):W463-8. (PMID: 27150811) Nucleic Acids Res. 2014 Jul;42(Web Server issue):W252-8. (PMID: 24782522) Nucleic Acids Res. 2011 Jul;39(Web Server issue):W215-22. (PMID: 21593128) Nucleic Acids Res. 2017 Jan 4;45(D1):D777-D783. (PMID: 27899578) Cancer Discov. 2017 Aug;7(8):787-788. (PMID: 28619979) Front Genet. 2014 Apr 21;5:82. (PMID: 24795746) Nucleic Acids Res. 2016 Jul 8;44(W1):W410-5. (PMID: 27131380) Hum Genet. 2017 Jun;136(6):665-677. (PMID: 28349240) Nucleic Acids Res. 2012 Jan;40(Database issue):D935-9. (PMID: 22075996) Curr Opin Struct Biol. 2009 Apr;19(2):145-55. (PMID: 19327982) Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7. (PMID: 15608251) Bioinformatics. 2007 Nov 15;23(22):3009-15. (PMID: 17921497) Genome Biol. 2013 Mar 28;14(3):303. (PMID: 23651925) Protein Eng Des Sel. 2010 Aug;23 (8):683-7. (PMID: 20573719) Proteins. 2006 Mar 1;62(4):1125-32. (PMID: 16372356) Nucleic Acids Res. 2011 Sep 1;39(17):e118. (PMID: 21727090) Nat Methods. 2010 Apr;7(4):248-9. (PMID: 20354512) Bioinformatics. 2011 Aug 1;27(15):2156-8. (PMID: 21653522) J Mol Biol. 2014 Jul 15;426(14):2692-701. (PMID: 24810707) Nat Biotechnol. 2015 Jul;33(7):736-42. (PMID: 25985263) Nat Biotechnol. 2017 Aug;35(8):747-756. (PMID: 28714965) Nat Genet. 2017 Jan 31;49(2):170-174. (PMID: 28138153) PLoS One. 2016 Mar 16;11(3):e0150965. (PMID: 26982818) Bioinformatics. 2016 Aug 15;32(16):2542-4. (PMID: 27153629) Hum Mutat. 2016 Jun;37(6):564-9. (PMID: 26931183) Nature. 2016 Aug 17;536(7616):285-91. (PMID: 27535533) Sci Rep. 2016 Jul 07;6:29575. (PMID: 27384129) Hum Mutat. 2014 Apr;35(4):413-23. (PMID: 24510514) Nucleic Acids Res. 2016 Jan 4;44(D1):D862-8. (PMID: 26582918) Bioinformatics. 2016 Oct 1;32(19):2936-46. (PMID: 27318206) Genet Med. 2015 May;17(5):405-24. (PMID: 25741868) Oncotarget. 2017 Mar 28;8(13):21290-21304. (PMID: 28423505) Nucleic Acids Res. 2012 Jul;40(Web Server issue):W71-5. (PMID: 22641855) Hum Mutat. 2015 Feb;36(2):161-6. (PMID: 25385275) Bioinformatics. 2011 Nov 15;27(22):3216-7. (PMID: 21965822) Curr Protoc Bioinformatics. 2015 Jun 19;50:1.27.1-10. (PMID: 26088053) Cancer Discov. 2012 May;2(5):401-4. (PMID: 22588877) Nucleic Acids Res. 2015 Jan;43(Database issue):D387-91. (PMID: 25324307) Int J Mol Sci. 2016 Apr 07;17 (4):512. (PMID: 27070572) Nat Methods. 2015 Jan;12(1):7-8. (PMID: 25549265) Genome Med. 2009 Jan 20;1(1):2. (PMID: 19348689) Bioinformatics. 2012 Oct 15;28(20):2600-7. (PMID: 22859501) Curr Opin Struct Biol. 2008 Jun;18(3):342-8. (PMID: 18436442) Cancer Res. 2016 Jul 1;76(13):3719-31. (PMID: 27197156) Hum Genome Var. 2016 Jan 07;3:15060. (PMID: 27081563) Genome Res. 2012 Aug;22(8):1589-98. (PMID: 22759861) Methods Enzymol. 2011;487:545-74. (PMID: 21187238) J Proteome Res. 2015 Sep 4;14(9):3461-73. (PMID: 26139527) Hum Genet. 2013 Nov;132(11):1235-43. (PMID: 23793516) Comput Struct Biotechnol J. 2015 Sep 30;13:514-9. (PMID: 26949480) Bioinformatics. 2003 Sep 22;19(14):1858-60. (PMID: 14512363) Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8. (PMID: 15980494) Structure. 2015 Jul 7;23(7):1362-9. (PMID: 26027735) Genome Med. 2017 Jan 23;9(1):4. (PMID: 28115009) Cancer Res. 2017 Nov 1;77(21):e7-e10. (PMID: 29092928) Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W306-10. (PMID: 15980478) Nucleic Acids Res. 2014 Jul;42(Web Server issue):W314-9. (PMID: 24829462) Bioinformatics. 2013 Mar 1;29(5):647-8. (PMID: 23325621) JCO Precis Oncol. 2017 Jul;2017:null. (PMID: 28890946) Genome Res. 2017 Dec 1;:null. (PMID: 29196558) J Mol Biol. 2017 Feb 3;429(3):426-434. (PMID: 27899282) Nucleic Acids Res. 2016 Jul 8;44(W1):W494-501. (PMID: 27150810) |
| معلومات مُعتمدة: | OT3 TR002026 United States TR NCATS NIH HHS; IIS-1636804 National Science Foundation; OT3TR002026 United States TR NCATS NIH HHS; BB/J019364/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; P30-CA008748 United States CA NCI NIH HHS; P30 CA008748 United States CA NCI NIH HHS; IIS-1636903 National Science Foundation; U54 HG007990 United States HG NHGRI NIH HHS; BB/G022682/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BB/L020742/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; U24 CA204817 United States CA NCI NIH HHS |
| تواريخ الأحداث: | Date Created: 20171220 Date Completed: 20180723 Latest Revision: 20210109 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC5735928 |
| DOI: | 10.1186/s13073-017-0509-y |
| PMID: | 29254494 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1756-994X |
|---|---|
| DOI: | 10.1186/s13073-017-0509-y |