SuRFing the genomics wave: An R package for prioritising SNPs by functionality

Genome Medicine

Volumn 6, Issue 10, 2014, Pages

  Ryan, Niamh M ^a   Morris, Stewart W ^a   Porteous, David J ^a   Taylor, Martin S ^b   Evans, Kathryn L ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE FREQUENCY; GENE FUNCTION; GENE LOCUS; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOMICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84927918771     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-014-0079-1     Document Type: Article

References (47)

1. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753. 19812666.
2. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012, 337:1190-1195. 22955828.
3. Li X, Montgomery SB. Detection and impact of rare regulatory variants in human disease. Front Genet 2013, 4:67. 23755067.
4. Cooper GM, Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat Rev Genet 2011, 12:628-640. 21850043.
5. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
6. Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. R.P. the, and Clst, A promoter-level mammalian expression atlas. Nature 2014, 507:462-470. 24670764.
7. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073. 20981092.
8. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 2010, 28:1045-1048. 20944595.
9. Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 2010, 28:817-825. 20657582.
10. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 2012, 482:390-394. 22307276.
11. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, et al. The accessible chromatin landscape of the human genome. Nature 2012, 489:75-82. 22955617.
12. Hager G. Footprints by deep sequencing. Nat Methods 2009, 6:254-255. 19333240.
13. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS, Fields S, Stamatoyannopoulos JA. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 2009, 6:283-289. 19305407.
14. Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012, 489:83-90. 22955618.
15. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 2012, 22:1798-1812. 22955990.
16. Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 2010, 6:e1001025. 21152010.
17. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49. 21441907.
18. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 12045153.
19. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Giron CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kahari AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, et al. Ensembl 2014. Nucleic Acids Res 2014, 42:D749-D755. 24316576.
20. Ritchie GR, Dunham I, Zeggini E, Flicek P. Functional annotation of noncoding sequence variants. Nat Methods 2014, 11:294-296. 24487584.
21. 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, 46:310-315. 24487276.
22. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gumus ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013, 342:1235587. 24092746.
23. SuRFR []., http://www.cgem.ed.ac.uk/resources/
24. Cooper GM, Stone EA, Asimenos G, Program NCS, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 2005, 15:901-913. 15965027.
25. Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO, McArthur M, Stamatoyannopoulos JA. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc Natl Acad Sci U S A 2004, 101:16837-16842. 15550541.
26. Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc 2010, 2010:prot5384. 20150147.
27. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A, Weaver M, Shafer A, Lee K, Neri F, Humbert R, Singer MA, Richmond TA, Dorschner MO, McArthur M, Hawrylycz M, Green RD, Navas PA, Noble WS, Stamatoyannopoulos JA. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 2006, 3:511-518. 16791208.
28. Schork AJ, Thompson WK, Pham P, Torkamani A, Roddey JC, Sullivan PF, Kelsoe JR, O'Donovan MC, Furberg H, Schork NJ, Andreassen OA, Dale AM. All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet 2013, 9:e1003449. 23637621.
29. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 2009, 106:9362-9367. 19474294.
30. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S. An atlas of active enhancers across human cell types and tissues. Nature 2014, 507:455-461. 24670763.
31. Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res 2013, 41:D171-D176. 23203885.
32. Vihinen M. How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis. BMC Genomics 2012, 13:S2. 22759650.
33. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN. The Human Gene Mutation Database: 2008 update. Genome Med 2009, 1:13. 19348700.
34. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
35. Patrinos GP, Giardine B, Riemer C, Miller W, Chui DH, Anagnou NP, Wajcman H, Hardison RC. Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Res 2004, 32:D537-D541. 14681476.
36. Andersen MC, Engstrom PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol 2008, 4:e5. 18208319.
37. ClinVar []., http://www.ncbi.nlm.nih.gov/clinvar/
38. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 2014, 42:D980-D985. 24234437.
39. GWAVA data []., ftp://ftp.sanger.ac.uk/pub/resources/software/gwava/v1.0/paper_data/
40. Musunuru K, Strong A, Frank-Kamenetsky M, Lee NE, Ahfeldt T, Sachs KV, Li X, Li H, Kuperwasser N, Ruda VM, Pirruccello JP, Muchmore B, Prokunina-Olsson L, Hall JL, Schadt EE, Morales CR, Lund-Katz S, Phillips MC, Wong J, Cantley W, Racie T, Ejebe KG, Orho-Melander M, Melander O, Koteliansky V, Fitzgerald K, Krauss RM, Cowan CA, Kathiresan S, Rader DJ. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 2010, 466:714-719. 20686566.
41. Kathiresan S, Willer CJ, Peloso GM, Demissie S, Musunuru K, Schadt EE, Kaplan L, Bennett D, Li Y, Tanaka T, Voight BF, Bonnycastle LL, Jackson AU, Crawford G, Surti A, Guiducci C, Burtt NP, Parish S, Clarke R, Zelenika D, Kubalanza KA, Morken MA, Scott LJ, Stringham HM, Galan P, Swift AJ, Kuusisto J, Bergman RN, Sundvall J, Laakso M, et al. Common variants at 30 loci contribute to polygenic dyslipidemia. Nat Genet 2009, 41:56-65. 19060906.
42. Myouzen K, Kochi Y, Shimane K, Fujio K, Okamura T, Okada Y, Suzuki A, Atsumi T, Ito S, Takada K, Mimori A, Ikegawa S, Yamada R, Nakamura Y, Yamamoto K. Regulatory polymorphisms in EGR2 are associated with susceptibility to systemic lupus erythematosus. Hum Mol Genet 2010, 19:2313-2320. 20194224.
43. Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, Berney T, Montanya E, Mohlke KL, Lieb JD, Ferrer J. A map of open chromatin in human pancreatic islets. Nat Genet 2010, 42:255-259. 20118932.
44. Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21:3940-3941. 16096348.
45. MacIsaac KD, Lo KA, Gordon W, Motola S, Mazor T, Fraenkel E. A quantitative model of transcriptional regulation reveals the influence of binding location on expression. PLoS Comput Biol 2010, 6:e1000773. 20442865.
46. Torkamani A, Schork NJ. Predicting functional regulatory polymorphisms. Bioinformatics 2008, 24:1787-1792. 18562267.
47. Meader S, Ponting CP, Lunter G. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res 2010, 20:1335-1343. 20693480.