High-performance web services for querying gene and variant annotation

Genome Biology

Volumn 17, Issue 1, 2016, Pages

  Xin, Jiwen ^a   Mark, Adam ^a,b   Afrasiabi, Cyrus ^a   Tsueng, Ginger ^a   Juchler, Moritz ^c   Gopal, Nikhil ^c   Stupp, Gregory S ^a   Putman, Timothy E ^a   Ainscough, Benjamin J ^d   Griffith, Obi L ^d   Torkamani, Ali ^a   Whetzel, Patricia L ^e   Mungall, Christopher J ^f   Mooney, Sean D ^c   Su, Andrew I ^a   Wu, Chunlei ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b Avera Cancer Institute   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

Annotation; API; Cloud; Database; Gene; Repository; Variant

Indexed keywords

DATA BASE; HUMAN; MODEL; COMPUTER INTERFACE; DATABASE MANAGEMENT SYSTEM; DNA SEQUENCE; GENETIC DATABASE; GENETIC VARIATION; INTERNET; MOLECULAR GENETICS; SOFTWARE;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENETIC VARIATION; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84965081698     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-0953-9     Document Type: Article

References (55)

1. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014;42:D749-755.
2. UniProt C. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42:D191-198.
3. Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, et al. New and continuing developments at PROSITE. Nucleic Acids Res. 2013;41:D344-347.
4. Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42:D472-477.
5. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
6. Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, et al. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015;43:W589-598.
7. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
8. Brown GR, Hem V, Katz KS, Ovetsky M, Wallin C, Ermolaeva O, et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 2015;43:D36-42.
9. MyGene.info annotation fields. 2013. http://docs.mygene.info/en/latest/doc/data.html#available-fields. Accessed 25 Mar 2016.
10. MyGene.info metadata information. http://mygene.info/metadata. Accessed 25 Mar 2016.
11. den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15:7-12.
12. MyVariant.info annotation fields. 2015. http://docs.myvariant.info/en/latest/doc/data.html#available-fields. Accessed 25 Mar 2016.
13. MyVariant.info metadata information. http://myvariant.info/metadata. Accessed 25 Mar 2016.
14. Wu C, Macleod I, Su AI. BioGPS and MyGene.info: organizing online, gene-centric information. Nucleic Acids Res. 2013;41:D561-565.
15. Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Kohler S, et al. Use of model organism and disease databases to support matchmaking for human disease gene discovery. Hum Mutat. 2015;36:979-84. Accessed 25 Mar 2016.
16. Clinical Intepretations of Variants in Cancer. https://civic.genome.wustl.edu/.
17. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010;42:30-5.
18. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308-11.
19. Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
20. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-9.
21. A demo use case of MyVariant.info and MyGene.info services in IPython Notebook. https://github.com/sulab/myvariant.info/blob/master/docs/ipynb/myvariant_R_miller.ipynb. Accessed 25 Mar 2016.
22. Exome Aggregation Consortium, Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell T, O'Donnell-Luria A, Ware J, Hill A, et al. Analysis of protein-coding genetic variation in 60,706 humans. bioRxiv. 2015. http://dx.doi.org/10.1101/030338.
23. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5.
24. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-81.
25. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980-985.
26. MyGene.info parser code. https://bitbucket.org/sulab/mygene.hub/src/default/src/dataload/sources/. Accessed 25 Mar 2016.
27. MyVariant.info parser code. https://github.com/sulab/myvariant.info/tree/master/src/dataload/contrib/. Accessed 25 Mar 2016.
28. Cingolani P, Platts A, le Wang L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80-92.
29. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-8.
30. MyGene.info Python client. https://pypi.python.org/pypi/mygene. Accessed 25 Mar 2016.
31. Mark A, Thompson R, Wu C. MyGene.info R client. 2014. http://bioconductor.org/packages/release/bioc/html/mygene.html. Accessed 25 Mar 2016.
32. MyVariant.info Python client. https://pypi.python.org/pypi/myvariant/.
33. Mark A. MyVariant.info R client. 2015. http://bioconductor.org/packages/release/bioc/html/myvariant.html.
34. MyGene.info web frontend source code. https://bitbucket.org/sulab/mygene.info.
35. MyGene.info data backend source code. https://bitbucket.org/sulab/mygene.hub.
36. MyVariant.info source code. https://github.com/sulab/myvariant.info.
37. Xin J, et al. MyGene.info web frontend component. Zenodo. 2016. http://dx.doi.org/10.5281/zenodo.48146. Accessed 25 Mar 2016.
38. Xin J, et al. MyGene.info data backend component. Zenodo. 2016. http://dx.doi.org/10.5281/zenodo.48145.
39. Xin J, et al. MyVariant.info - build fb2a871. Zenodo. 2016. http://dx.doi.org/10.5281/zenodo.48086.
40. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2005;33:D54-58.
41. Liu G et al. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003;31:82-6.
42. Whirl-Carrillo M, McDonagh EM, Hebert JM, Gong L, Sangkuhl K, Thorn CF, et al. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther. 2012;92:414-7.
43. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12:996-1006.
44. Kamburov A, Stelzl U, Lehrach H, Herwig R. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res. 2013;41:D793-800.
45. Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014;42:D756-763.
46. Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013;34:E2393-2402.
47. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA. http://evs.gs.washington.edu/EVS/. Accessed 25 Mar 2016.
48. Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, et al. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. 2008;36:D815-819.
49. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42:D1001-1006.
50. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43:D805-811.
51. Database of Curated Mutations. http://docm.genome.wustl.edu. Accessed 25 Mar 2016.
52. Cariaso M, Lennon G. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic Acids Res. 2012;40:D1308-1312.
53. Bean LJ, Tinker SW, da Silva C, Hegde MR. Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Hum Mutat. 2013;34:1183-8.
54. STSI Variant Browser - Wellderly. http://www.stsiweb.org/wellderly. Accessed 25 Mar 2016.
55. Leslie R, O'Donnell CJ, Johnson AD. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics. 2014;30:i185-194.