SEARCH

SEARCH BY CITATION

References

  • Abraham, G., Kowalczyk, A., Zobel, J. & Inouye, M. (2013) Performance and robustness of penalized and unpenalized methods for genetic prediction of complex human disease. Genet Epidemiol 37, 184195.
  • Adrianto, I., Wang, S. F., Wiley, G. B., Lessard, C. J., Kelly, J. A., Adler, A. J., Glenn, S. B., Williams, A. H., Ziegler, J. T., Comeau, M. E., Marion, M. C., Wakeland, B. E., Liang, C. Y., Kaufman, K. M., Guthridge, J. M., Alarcon-Riquelme, M. E., Alarcon, G. S., Anaya, J. M., Bae, S. C., Kim, J. H., Joo, Y. B., Boackle, S. A., Brown, E. E., Petri, M. A., Ramsey-Goldman, R., Reveille, J. D., Vila, L. M., Criswell, L. A., Edberg, J. C., Freedman, B. I., Gilkeson, G. S., Jacob, C. O., James, J. A., Kamen, D. L., Kimberly, R. P., Martin, J., Merrill, J. T., Niewold, T. B., Pons-Estel, B. A., Scofield, R. H., Stevens, A. M., Tsao, B. P., Vyse, T. J., Langefeld, C. D., Harley, J. B., Wakeland, E. K., Moser, K. L., Montgomery, C. G., Gaffney, P. M., Network, B. & Network, G. (2012) Association of two independent functional risk haplotypes in TNIP1 with systemic lupus erythematosus. Arthritis Rheum 64, 36953705.
  • Ayers, K. L. & Cordell, H. J. (2010) SNP Selection in genome-wide and candidate gene studies via penalized logistic regression. Genet Epidemiol 34, 879891.
  • Barrett, J. H., Iles, M. M., Harland, M., Taylor, J. C., Aitken, J. F., Andresen, P. A., Akslen, L. A., Armstrong, B. K., Avril, M. F., Azizi, E., Bakker, B., Bergman, W., Bianchi-Scarra, G., Bressac-de Paillerets, B., Calista, D., Cannon-Albright, L. A., Corda, E., Cust, A. E., Debniak, T., Duffy, D., Dunning, A. M., Easton, D. F., Friedman, E., Galan, P., Ghiorzo, P., Giles, G. G., Hansson, J., Hocevar, M., Hoiom, V., Hopper, J. L., Ingvar, C., Janssen, B., Jenkins, M. A., Jonsson, G., Kefford, R. F., Landi, G., Landi, M. T., Lang, J., Lubinski, J., Mackie, R., Malvehy, J., Martin, N. G., Molven, A., Montgomery, G. W., van Nieuwpoort, F. A., Novakovic, S., Olsson, H., Pastorino, L., Puig, S., Puig-Butille, J. A., Randerson-Moor, J., Snowden, H., Tuominen, R., VanBelle, P., van der Stoep, N., Whiteman, D. C., Zelenika, D., Han, J. L., Fang, S. Y., Lee, J. E., Wei, Q. Y., Lathrop, G. M., Gillanders, E. M., Brown, K. M., Goldstein, A. M., Kanetsky, P. A., Mann, G. J., MacGregor, S., Elder, D. E., Amos, C. I., Hayward, N. K., Gruis, N. A., Demenais, F., Bishop, J. A. N., Bishop, D. T. & Geno, M. E. L. C. (2011) Genome-wide association study identifies three new melanoma susceptibility loci. Nat Genet 43, 11081113.
  • Camp, N. J., Parry, M., Knight, S., Abo, R., Elliott, G., Rigas, S. H., Balasubramanian, S. P., Reed, M. W. R., McBurney, H., Latif, A., Newman, W. G., Cannon-Albright, L. A., Evans, D. G. & Cox, A. (2012) Fine-mapping CASP8 risk variants in breast cancer. Cancer Epidemiol Biomarkers Prev 21, 176181.
  • Cox, A., Dunning, A. M., Garcia-Closas, M., Balasubramanian, S., Reed, M. W. R., Pooley, K. A., Scollen, S., Baynes, C., Ponder, B. A. J., Chanock, S., Lissowska, J., Brinton, L., Peplonska, B., Southey, M. C., Hopper, J. L., McCredie, M. R. E., Giles, G. G., Fletcher, O., Johnson, N., Silva, I. D., Gibson, L., Bojesen, S. E., Nordestgaard, B. G., Axelsson, C. K., Torres, D., Hamann, U., Justenhoven, C., Brauch, H., Chang-Claude, J., Kropp, S., Risch, A., Wang-Gohrke, S., Schurmann, P., Bogdanova, N., Dork, T., Fagerholm, R., Aaltonen, K., Blomqvist, C., Nevanlinna, H., Seal, S., Renwick, A., Stratton, M. R., Rahman, N., Sangrajrang, S., Hughes, D., Odefrey, F., Brennan, P., Spurdle, A. B., Chenevix-Trench, G., Beesley, J., Mannermaa, A., Hartikainen, J., Kataja, V., Kosma, V. M., Couch, F. J., Olson, J. E., Goode, E. L., Broeks, A., Schmidt, M. K., Hogervorst, F. B. L., Van't Veer, L. J., Kang, D., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Wedren, S., Hall, P., Low, Y. L., Liu, J. J., Milne, R. L., Ribas, G., Gonzalez-Neira, A., Benitez, J., Sigurdson, A. J., Stredrick, D. L., Alexander, B. H., Struewing, J. P., Pharoah, P. D. P., Easton, D. F. & Kathleen Cunningham Fdn Consortium, Breast Canc Assoc, Consortium. (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nat Genet 39, 352358.
  • Easton, D. F., Pooley, K. A., Dunning, A. M., Pharoah, P. D. P., Thompson, D., Ballinger, D. G., Struewing, J. P., Morrison, J., Field, H., Luben, R., Wareham, N., Ahmed, S., Healey, C. S., Bowman, R., Meyer, K. B., Haiman, C. A., Kolonel, L. K., Henderson, B. E., Le Marchand, L., Brennan, P., Sangrajrang, S., Gaborieau, V., Odefrey, F., Shen, C. Y., Wu, P. E., Wang, H. C., Eccles, D., Evans, D. G., Peto, J., Fletcher, O., Johnson, N., Seal, S., Stratton, M. R., Rahman, N., Chenevix-Trench, G., Bojesen, S. E., Nordestgaard, B. G., Axelsson, C. K., Garcia-Closas, M., Brinton, L., Chanock, S., Lissowska, J., Peplonska, B., Nevanlinna, H., Fagerholm, R., Eerola, H., Kang, D., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Hunter, D. J., Hankinson, S. E., Cox, D. G., Hall, P., Wedren, S., Liu, J. J., Low, Y. L., Bogdanova, N., Schurmann, P., Dork, T., Tollenaar, R., Jacobi, C. E., Devilee, P., Klijn, J. G. M., Sigurdson, A. J., Doody, M. M., Alexander, B. H., Zhang, J. H., Cox, A., Brock, I. W., MacPherson, G., Reed, M. W. R., Couch, F. J., Goode, E. L., Olson, J. E., Meijers-Heijboer, H., van den Ouweland, A., Uitterlinden, A., Rivadeneira, F., Milne, R. L., Ribas, G., Gonzalez-Neira, A., Benitez, J., Hopper, J. L., McCredie, M., Southey, M., Giles, G. G., Schroen, C., Justenhoven, C., Brauch, H., Hamann, U., Ko, Y. D., Spurdle, A. B., Beesley, J., Chen, X. Q., Mannermaa, A., Kosma, V. M., Kataja, V., Hartikainen, J., Day, N. E., Cox, D. A. & Ponder, B. A. J. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 10871093.
  • Encode Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9, e1001046.
  • Fawcett, T. (2006) An introduction to ROC analysis. Pattern Recognit Lett 27, 861874.
  • French, J. D., Ghoussaini, M., Edwards, S. L., Meyer, K. B., Michailidou, K., Ahmed, S., Khan, S., Maranian, M. J., O'Reilly, M., Hillman, K. M., Betts, J. A., Carroll, T., Bailey, P. J., Dicks, E., Beesley, J., Tyrer, J., Maia, A.-T., Beck, A., Knoblauch, N. W., Chen, C., Kraft, P., Barnes, D., Gonzalez-Neira, A., Alonso, M. R., Herrero, D., Tessier, D. C., Vincent, D., Bacot, F., Luccarini, C., Baynes, C., Conroy, D., Dennis, J., Bolla, M. K., Wang, Q., Hopper, J. L., Southey, M. C., Schmidt, M. K., Broeks, A., Verhoef, S., Cornelissen, S., Muir, K., Lophatananon, A., Stewart-Brown, S., Siriwanarangsan, P., Fasching, P. A., Loehberg, C. R., Ekici, A. B., Beckmann, M. W., Peto, J., Dos Santos Silva, I., Johnson, N., Aitken, Z., Sawyer, E. J., Tomlinson, I., Kerin, M. J., Miller, N., Marme, F., Schneeweiss, A., Sohn, C., Burwinkel, B., Guenel, P., Truong, T., Laurent-Puig, P., Menegaux, F., Bojesen, S. E., Nordestgaard, B. G., Nielsen, S. F., Flyger, H., Milne, R. L., Zamora, M. P., Arias Perez, J. I., Benitez, J., Anton-Culver, H., Brenner, H., Muller, H., Arndt, V., Stegmaier, C., Meindl, A., Lichtner, P., Schmutzler, R. K., Engel, C., Brauch, H., Hamann, U., Justenhoven, C., Aaltonen, K., Heikkila, P., Aittomaki, K., Blomqvist, C., Matsuo, K., Ito, H., Iwata, H., Sueta, A., Bogdanova, N. V., Antonenkova, N. N., Dork, T., Lindblom, A., Margolin, S., Mannermaa, A., Kataja, V., Kosma, V.-M., Kosma, V.-M., Hartikainen, J. M. kConFab Investigators, Wu, A. H., Tseng, C. C. Van Den Berg, D., Stram, D. O. Lambrechts, D., Peeters, S., Smeets, A., Floris, G., Chang-Claude, J., Rudolph, A., Nickels, S., Flesch-Janys, D., Radice, P., Peterlongo, P., Bonanni, B., Sardella, D., Couch, F. J. Wang, X., Pankratz, V. S. Lee, A., Giles, G. G. Severi, G., Baglietto, L., Haiman, C. A. Henderson, B. E. Schumacher, F., Le Marchand, L., Simard, J., Goldberg, M. S. Labrèche, F., Dumont, M., Teo, S. H. Yip, C. H. Ng, C. H. Vithana, E. N. Kristensen, V., Zheng, W., Deming-Halverson, S., Shrubsole, M., Long, J., Winqvist, R., Pylkäs, K., Jukkola-Vuorinen, A., Grip, M., Andrulis, I. L. Knight, J. A. Glendon, G., Mulligan, A. M. Devilee, P., Seynaeve, C., García-Closas, M., Figueroa, J., Chanock, S. J. Lissowska, J., Czene, K., Klevebring, D., Schoof, N., Hooning, M. J. Martens, J. W. Collée, J. M. Tilanus-Linthorst, M., Hall, P., Li, J., Liu, J., Humphreys, K., Shu, X. O. Lu, W., Gao, Y. T. Cai, H., Cox, A., Balasubramanian, S. P. Blot, W., Signorello, L. B. Cai, Q., Pharoah, P. D. Healey, C. S. Shah, M., Pooley, K. A. Kang, D., Yoo, K. Y. Noh, D. Y. Hartman, M., Miao, H., Sng, J. H. Sim, X., Jakubowska, A., Lubinski, J., Jaworska-Bieniek, K., Durda, K., Sangrajrang, S., Gaborieau, V., McKay, J., Toland, A. E. Ambrosone, C. B. Yannoukakos, D., Godwin, A. K. Shen, C. Y. Hsiung, C. N. Wu, P. E. Chen, S. T. Swerdlow, A., Ashworth, A., Orr, N., Schoemaker, M. J. Ponder, B. A. Nevanlinna, H., Brown, M. A. Chenevix-Trench, G., Easton, D. F. & Dunning, A. M. (2013) Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. Am J Hum Genet 92, 489503.
  • Fridley, B. L., Iversen, E., Tsai, Y.-Y., Jenkins, G. D., Goode, E. L. & Sellers, T. A. (2011) A latent model for prioritization of SNPs for functional studies. PLoS One 6, e20764.
  • Guan, Y. T. & Stephens, M. (2011) Bayesian variable selection regression for genome-wide association studies and other large-scale problems. Ann Appl Stat 5, 17801815.
  • Han, S. H., Lee, K. M., Choi, J. Y., Park, S. K., Lee, J. Y., Lee, J. E., Noh, D. Y., Ahn, S. H., Han, W. S., Kim, D. H., Hong, Y. C., Ha, E., Yoo, K. Y. & Kang, D. H. (2008) CASP8 polymorphisms, estrogen and progesterone receptor status, and breast cancer risk. Breast Cancer Res Treat 110, 387393.
  • Hoggart, C. J., Whittaker, J. C., De Iorio, M. & Balding, D. J. (2008) Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies. PLoS Genet 4, e1000130.
  • Knight, J., Barnes, M. R., Breen, G. & Weale, M. E. (2011) Using functional annotation for the empirical determination of Bayes factors for genome-wide association study analysis. PLoS One 6, e14808.
  • Marchini, J. & Howie, B. (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11, 499511.
  • Miki, D., Kubo, M., Takahashi, A., Yoon, K. A., Kim, J., Lee, G. K., Zo, J. I., Lee, J. S., Hosono, N., Morizono, T., Tsunoda, T., Kamatani, N., Chayama, K., Takahashi, T., Inazawa, J., Nakamura, Y. & Daigo, Y. (2010) Variation in TP63 is associated with lung adenocarcinoma susceptibility in Japanese and Korean populations. Nat Genet 42, 893896.
  • Palanca Suela, S., Esteban Cardenosa, E., Barragan Gonzalez, E., de Juan Jimenez, I., Chirivella Gonzalez, I., Segura Huerta, A., Guillen Ponce, C., Martinez de Duenas, E., Montalar Salcedo, J., Castel Sanchez, V., Bolufer Gilabert, P. & Group for Assessment of Hereditary Cancer of Valencia, Community. (2010) CASP8 D302H polymorphism delays the age of onset of breast cancer in BRCA1 and BRCA2 carriers. Breast Cancer Res Treat 119, 8793.
  • R Core Team (2012) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. ISBN 3-900051-07-0.
  • Saccone, S. F., Saccone, N. L., Swan, G. E., Madden, P. A. F., Goate, A. M., Rice, J. P. & Bierut, L. J. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics 24, 18051811.
  • Schork, A. J., Thompson, W. K., Pham, P., Torkamani, A., Roddey, J. C., Sullivan, P. F., Kelsoe, J. R., O'Donovan, M. C., Furberg, H., The Tobacco and Genetics Consortium, The Bipolar Disorder Psychiatric Genomics Consortium, The Schizophrenia Psychiatric Genomics Consortium, Schork, N. J., Andreassen, O. A. & Dale, A. M. (2013) All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet 9, e1003449.
  • Smith, A. V., Thomas, D. J., Munro, H. M. & Abecasis, G. R. (2005) Sequence features in regions of weak and strong linkage disequilibrium. Genome Res 15, 15191534.
  • Spencer, C. C. A., Su, Z., Donnelly, P. & Marchini, J. (2009) Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet 5, e1000477.
  • Sun, L., Craiu, R. V., Paterson, A. D. & Bull, S. B. (2006) Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies. Genet Epidemiol 30, 519530.
  • The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467, 10611073.
  • Udler, M. S., Ahmed, S., Healey, C. S., Meyer, K., Struewing, J., Maranian, M., Kwon, E. M., Zhang, J., Tyrer, J., Karlins, E., Platte, R., Kalmyrzaev, B., Dicks, E., Field, H., Maia, A. T., Prathalingam, R., Teschendorff, A., McArthur, S., Doody, D. R., Luben, R., Caldas, C., Bernstein, L., Kolonel, L. K., Henderson, B. E., Wu, A. H., Le Marchand, L., Ursin, G., Press, M. F., Lindblom, A., Margolin, S., Shen, C. Y., Yang, S. L., Hsiung, C. N., Kang, D., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Malone, K. E., Haiman, C. A., Pharoah, P. D., Ponder, B. A. J., Ostrander, E. A., Easton, D. F. & Dunning, A. M. (2010a) Fine scale mapping of the breast cancer 16q12 locus. Hum Mol Genet 19, 25072515.
  • Udler, M. S., Meyer, K. B., Pooley, K. A., Karlins, E., Struewing, J. P., Zhang, J., Doody, D. R., MacArthur, S., Tyrer, J., Pharoah, P. D., Luben, R., Bernstein, L., Kolonel, L. N., Henderson, B. E., Le Marchand, L., Ursin, G., Press, M. F., Brennan, P., Sangrajrang, S., Gaborieau, V., Odefrey, F., Shen, C. Y., Wu, P. E., Wang, H. C., Kang, D., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Ponder, B. A. J., Haiman, C. A., Malone, K. E., Dunning, A. M., Ostrander, E. A., Easton, D. F. & SEARCH Collaborators (2009) FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum Mol Genet 18, 16921703.
  • Udler, M. S., Tyrer, J. & Easton, D. F. (2010b) Evaluating the power to discriminate between highly correlated SNPs in genetic association studies. Genet Epidemiol 34, 463468.
  • Vignal, C. M., Bansal, A. T. & Balding, D. J. (2011) Using penalised logistic regression to fine map HLA variants for rheumatoid arthritis. Ann Hum Genet 75, 655664.
  • Wakefield, J. (2007) A Bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet 81, 208227.
  • Wakefield, J. (2009) Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol 33, 7986.
  • Zhu, Q., Ge, D., Heinzen, E. L., Dickson, S. P., Urban, T. J., Zhu, M., Maia, J. M., He, M., Zhao, Q., Shianna, K. V. & Goldstein, D. B. (2012) Prioritizing genetic variants for causality on the basis of preferential linkage disequilibrium. Am J Hum Genet 91, 422434.