SVI: A simple single-nucleotide human variant interpretation tool for clinical use

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 9162, Issue , 2015, Pages 180-194

  Missier, Paolo ^a   Wijaya, Eldarina ^a   Kirby, Ryan ^a   Keogh, Michael ^b  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSIS; NUCLEOTIDES; QUALITY CONTROL;

CLINICAL SETTINGS; DIAGNOSTIC PROCESS; EXTERNAL KNOWLEDGE; GENETIC DISORDERS; INTERPRETATION TOOLS; MAPPING RESOURCES; NEXT-GENERATION SEQUENCING; SINGLE NUCLEOTIDES;

DATA INTEGRATION;

EID: 84947222502     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-21843-4_14     Document Type: Conference Paper

References (23)

1. Wetterstrand, K.: DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP) (2015)
2. Stein, L.D.: The case for cloud computing in genome informatics. Genome Biol. 11, 207 (2010)
3. Xuan, J., Yu, Y., Qing, T., Guo, L., Shi, L.: Next-generation sequencing in the clinic: promises and challenges. Cancer Lett. 340, 284-295 (2013)
4. Worthey, E.A., Mayer, A.N., Syverson, G.D., Helbling, D., Bonacci, B.B., Decker, B., Serpe, J.M., Dasu, T., Tschannen, M.R., Veith, R.L., Basehore, M.J., Broeckel, U., Tomita-Mitchell, A., Arca, M.J., Casper, J.T., Margolis, D.A., Bick, D.P., Hessner, M.J., Routes, J.M., Verbsky, J.W., Jacob, H.J., Dimmock, D.P.: Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. Official J. Am. Coll. Med. Genet. 13, 255-262 (2011)
5. Yang, Y., Muzny, D.M., Reid, J.G., Bainbridge, M.N., Willis, A., Ward, P.A., Braxton, A., Beuten, J., Xia, F., Niu, Z., Hardison, M., Person, R., Bekheirnia, M.R., Leduc, M.S., Kirby, A., Pham, P., Scull, J., Wang, M., Ding, Y., Plon, S.E., Lupski, J.R., Beaudet, A.L., Gibbs, R.A., Eng, C.M.: Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N. Engl. J. Med. 369, 1502- 1511 (2013)
6. Pabinger, S., Dander, A., Fischer, M., Snajder, R., Sperk, M., Efremova, M., Krabichler, B., Speicher, M.R., Zschocke, J., Trajanoski, Z.: A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics (2013). doi: 10.1093/bib/bbs086
7. Cala, J., Xu, Y.X., Wijaya, E.A., Missier, P.: From scripted HPC-based NGS pipelines to workflows on the cloud. In: Proceedings of C4Bio Workshop, Colocated with the 2014 CCGrid Conference. IEEE, Chicago (2013)
8. Shashi, V., McConkie-Rosell, A., Rosell, B., Schoch, K., Vellore, K., McDonald, M., Jiang, Y.H., Xie, P., Need, A., Goldstein, D.B., Goldstein, D.G.: The utility of the traditional medical genetics diagnostic evaluation in the context of nextgeneration sequencing for undiagnosed genetic disorders. Genet. Med. Official J. Am. Coll. Med. Genet. 16, 176-182 (2014)
9. Atwal, P.S., Brennan, M.L., Cox, R., Niaki, M., Platt, J., Homeyer, M., Kwan, A., Parkin, S., Schelley, S., Slattery, L., Wilnai, Y., Bernstein, J.A., Enns, G.M., Hudgins, L.: Clinical whole-exome sequencing: are we there yet? Genet. Med. Official J. Am. Coll. Med. Genet. 16, 717-719 (2014)
10. Zemojtel, T., Kohler, S., Mackenroth, L., Jager, M., Hecht, J., Krawitz, P., Graul- Neumann, L., Doelken, S., Ehmke, N., Spielmann, M., Oien, N.C., Schweiger, M.R., Kruger, U., Frommer, G., Fischer, B., Kornak, U., Flottmann, R., Ardeshirdavani, A., Moreau, Y., Lewis, S.E., Haendel, M., Smedley, D., Horn, D., Mundlos, S., Robinson, P.N.: Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci. Transl. Med. 6, 252ra123 (2014)
11. Robinson, P.N., Köhler, S., Oellrich, A., Wang, K., Mungall, C.J., Lewis, S.E., Washington, N., Bauer, S., Seelow, D., Krawitz, P., Gilissen, C., Haendel, M., Smedley, D.: Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 24, 340-348 (2014)
12. Liu, X., Jian, X., Boerwinkle, E.: dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum. Mutat. 32, 894-899 (2011)
13. Sifrim, A., Popovic, D., Tranchevent, L.C., Ardeshirdavani, A., Sakai, R., Konings, P., Vermeesch, J.R., Aerts, J., De Moor, B., Moreau, Y.: eXtasy: variant prioritization by genomic data fusion. Nat. Meth. 10, 1083-1084 (2013)
14. Sifrim, A., Van Houdt, J.K., Tranchevent, L.C., Nowakowska, B., Sakai, R., Pavlopoulos, G.A., Devriendt, K., Vermeesch, J.R., Moreau, Y., Aerts, J.: Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. Genome Med. 4, 73 (2012)
15. Swaminathan, G.J., Bragin, E., Chatzimichali, E.A., Corpas, M., Bevan, A.P., Wright, C.F., Carter, N.P., Hurles, M.E., Firth, H.V.: DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet. 21, R37-44 (2012)
16. Götz, A., Tyynismaa, H., Euro, L., Ellonen, P., Hyötyläinen, T., Ojala, T., Hämäläinen, R.H., Tommiska, J., Raivio, T., Oresic, M., Karikoski, R., Tammela, O., Simola, K.O.J., Paetau, A., Tyni, T., Suomalainen, A.: Exome sequencing identifies mitochondrial alanyl-tRNA synthetase mutations in infantile mitochondrial cardiomyopathy. Am. J. Hum. Genet. 88, 635-642 (2011)
17. Cooper, G.M., Shendure, J.: Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12, 628-640 (2011)
18. Robinson, P.N., Mundlos, S.: The human phenotype ontology. Clin. Genet. 77, 525-534 (2010)
19. Hennekam, R.C.M., Biesecker, L.G.: Next-generation sequencing demands nextgeneration phenotyping. Hum. Mutat. 33, 884-886 (2012)
20. Köhler, S., Doelken, S.C., Mungall, C.J., Bauer, S., Firth, H.V., Bailleul-Forestier, I., Black, G.C.M., Brown, D.L., Brudno, M., Campbell, J., FitzPatrick, D.R., Eppig, J.T., Jackson, A.P., Freson, K., Girdea, M., Helbig, I., Hurst, J.A., Jähn, J., Jackson, L.G., Kelly, A.M., Ledbetter, D.H., Mansour, S., Martin, C.L., Moss, C., Mumford, A., Ouwehand, W.H., Park, S.M., Riggs, E.R., Scott, R.H., Sisodiya, S., Van Vooren, S., Wapner, R.J., Wilkie, A.O.M., Wright, C.F., Vulto-van, S.A.T., de Leeuw, N., de Vries, B.B.A., Washingthon, N.L., Smith, C.L., Westerfield, M., Schofield, P., Ruef, B.J., Gkoutos, G.V., Haendel, M., Smedley, D., Lewis, S.E., Robinson, P.N.: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 42, D966-D974 (2014)
21. Wang, K., Li, M., Hakonarson, H.: ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164-e164 (2010)
22. Keogh, M.J., Daud, D., Chinnery, P.F.: Exome sequencing: how to understand it. Pract. Neurol. 1-9 (2013)
23. Thusberg, J., Olatubosun, A., Vihinen, M.: Performance of mutation pathogenicity prediction methods on missense variants. Hum. Mutat. 32, 358-368 (2011)