Statistical Genomics - Brooke L. Fridley

Publications

See Dr. Fridley's publications on PubMed

  1. Fridley BL, Jenkins G. Localizing putative markers in genetic association studies by incorporating linkage disequilibrium into Bayesian hierarchical models. Human Heredity 2010 (in press).
  2. Fridley BL, Serie D, Jenkins G, White K, Bamlet W, Potter JD, Goode EL. Incorporation of prior knowledge to inform genetic association studies. Genetic Epidemiology 2009; In Press
  3. Saito YA, Petersen GM, Larson JJ, Atkinson EJ, Fridley BL, de Andrade M, Locke GR 3rd, Zimmerman JM, Almazar-Elder AE, Talley NJ. Familial aggregation of irritable bowel syndrome: a family case-control study. Am J Gastroenterol 2010 Apr; 105(4):833-41. Epub 2010 Mar 16. PMID:20234344. DOI:10.1038/ajg.2010.116.
  4. Atkinson EJ, McDonnell SK, Witte JS, Crawford DC, Fan Y, Fridley BL, Li D, Li L, Rodin A, Sadee W, Speed T, Weiss ST, Yang J, Yerges L, Schaid DJ. Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network. Pharmacogenomics 2010 Mar; 11(3):297-303. PMID:20235785. DOI:10.2217/pgs.10.5.
  5. Goode EL, Maurer MJ, Sellers TA, Phelan CM, Kalli KR, Fridley BL, Vierkant RA, Armasu SM, White KL, Keeney GL, Cliby WA, Rider DN, Kelemen LE, Jones MB, Peethambaram PP, Lancaster JM, Olson JE, Schildkraut JM, Cunningham JM, Hartmann LC. Inherited determinants of ovarian cancer survival. Clin Cancer Res 2010 Feb 1; 16(3):995-1007. Epub 2010 Jan 26. PMID:20103664. PMCID:2818685. NIHMS:164535. DOI:10.1158/1078-0432.CCR-09-2553.
  6. White KL, Sellers TA, Fridley BL, Vierkant RA, Phelan CM, Tsai YY, Kalli KR, Berchuck A, Iversen ES, Hartmann LC, Liebow M, Armasu S, Fredericksen Z, Larson MC, Duggan D, Couch FJ, Schildkraut JM, Cunningham JM, Goode EL. Variation at 8q24 and 9p24 and risk of epithelial ovarian cancer. Twin Res Hum Genet 2010 Feb; 13(1):43-56. PMID:20158306. DOI:10.1375/twin.13.1.43.
  7. Phelan CM, Tsai YY, Goode EL, Vierkant RA, Fridley BL, Beesley J, Chen XQ, Webb PM, Chanock S, Cramer DW, Moysich K, Edwards RP, Chang-Claude J, Garcia-Closas M, Yang H, Wang-Gohrke S, Hein R, Green AC, Lissowska J, Carney ME, Lurie G, Wilkens LR, Ness RB, Pearce CL, Wu AH, Van Den Berg DJ, Stram DO, Terry KL, Whiteman DC, Whittemore AS, DiCioccio RA, McGuire V, Doherty JA, Rossing MA, Anton-Culver H, Ziogas A, Hogdall C, Hogdall E, Kruger Kjaer S, Blaakaer J, Quaye L, Ramus SJ, Jacobs I, Song H, Polymorphism in the GALNT1 gene and epithelial ovarian cancer in non-Hispanic white women: the Ovarian Cancer Association Consortium. Cancer Epidemiol Biomarkers Prev 2010 Feb; 19(2):600-4. PMID:20142253. DOI:10.1158/1055-9965.EPI-09-0861.
  8. Wang L, Ellsworth KA, Moon I, Pelleymounter LL, Eckloff BW, Martin YN, Fridley BL, Jenkins GD, Batzler A, Suman VJ, Ravi S, Dixon JM, Miller WR, Wieben ED, Buzdar A, Weinshilboum RM, Ingle JN. Functional genetic polymorphisms in the aromatase gene CYP19 vary the response of breast cancer patients to neoadjuvant therapy with aromatase inhibitors. Cancer Res 2010 Jan 1; 70(1):319-28. PMID:20048079. PMCID:2804935. NIHMS:157920. DOI:10.1158/0008-5472.CAN-09-3224.
  9. Doherty JA, Rossing MA, Cushing-Haugen KL, Chen C, Van Den Berg DJ, Wu AH, Pike MC, Ness RB, Moysich K, Chenevix-Trench G, Beesley J, Webb PM, Chang-Claude J, Wang-Gohrke S, Goodman MT, Lurie G, Thompson PJ, Carney ME, Hogdall E, Kjaer SK, Hogdall C, Goode EL, Cunningham JM, Fridley BL, Vierkant RA, Berchuck A, Moorman PG, Schildkraut JM, Palmieri RT, Cramer DW, Terry KL, Yang HP, Garcia-Closas M, Chanock S, Lissowska J, Song H, Pharoah PD, Shah M, Perkins B, McGuire V, Whittemore AS, Di Cioccio RA, ESR1/SYNE1 polymorphism and invasive epithelial ovarian cancer risk: an Ovarian Cancer Association Consortium study. Cancer Epidemiol Biomarkers Prev 2010 Jan; 19(1):245-50. PMID:20056644. DOI:10.1158/1055-9965.EPI-09-0729.
  10. Peedicayil A, Vierkant RA, Hartmann LC, Fridley BL, Fredericksen ZS, White KL, Elliott EA, Phelan CM, Tsai YY, Berchuck A, Iversen ES Jr, Couch FJ, Peethamabaran P, Larson MC, Kalli KR, Kosel ML, Shridhar V, Rider DN, Liebow M, Cunningham JM, Schildkraut JM, Sellers TA, Goode EL. Risk of ovarian cancer and inherited variants in relapse-associated genes. PLoS One 2010; 5(1):e8884. Epub 2010 Jan 27. PMID:20111712. PMCID:2811736. DOI:10.1371/journal.pone.0008884.
  11. Cunningham JM, Vierkant RA, Sellers TA, Phelan C, Rider DN, Liebow M, Schildkraut J, Berchuck A, Couch FJ, Wang X, Fridley BL, Ovarian Cancer Association Consortium, Gentry-Maharaj A, Menon U, Hogdall E, Kjaer S, Whittemore A, DiCioccio R, Song H, Gayther SA, Ramus SJ, Pharaoh PD, Goode EL. Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis. Br J Cancer 2009 Oct 20; 101(8):1461-8. Epub 2009 Sep 08. PMID:19738611. PMCID:2768434. DOI:10.1038/sj.bjc.6605284.
  12. Fridley BL, Jenkins G, Schaid DJ, Wang L. A Bayesian hierarchical nonlinear model for assessing the association between genetic variation and drug cytotoxicity. Stat Med 2009 Sep 20; 28(21):2709-22. PMID:19572260. PMCID:2755562. NIHMS:146134. DOI:10.1002/sim.3649.
  13. Pei H, Li L, Fridley BL, Jenkins GD, Kalari KR, Lingle W, Petersen G, Lou Z, Wang L. FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer Cell 2009 Sep 8; 16(3):259-66. PMID:19732725. PMCID:2755578. NIHMS:136361. DOI:10.1016/j.ccr.2009.07.016.
  14. Song H, Ramus SJ, Tyrer J, Bolton KL, Gentry-Maharaj A, Wozniak E, Anton-Culver H, Chang-Claude J, Cramer DW, DiCioccio R, Dork T, Goode EL, Goodman MT, Schildkraut JM, Sellers T, Baglietto L, Beckmann MW, Beesley J, Blaakaer J, Carney ME, Chanock S, Chen Z, Cunningham JM, Dicks E, Doherty JA, Durst M, Ekici AB, Fenstermacher D, Fridley BL, Giles G, Gore ME, De Vivo I, Hillemanns P, Hogdall C, Hogdall E, Iversen ES, Jacobs IJ, Jakubowska A, Li D, Lissowska J, Lubinski J, Lurie G, McGuire V, A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. Nat Genet 2009 Sep; 41(9):996-1000. Epub 2009 Aug 02. PMID:19648919. PMCID:2844110. NIHMS:146644. DOI:10.1038/ng.424.
  15. Rule AD, Fridley BL, Hunt SC, Asmann Y, Boerwinkle E, Pankow JS, Mosley TH, Turner ST. Genome-wide linkage analysis for uric acid in families enriched for hypertension. Nephrol Dial Transplant 2009 Aug; 24(8):2414-20. Epub 2009 Mar 03. PMID:19258383. PMCID:2734170. DOI:10.1093/ndt/gfp080.
  16. Peedicayil A, Vierkant RA, Shridhar V, Schildkraut JM, Armasu S, Hartmann LC, Fridley BL, Cunningham JM, Phelan CM, Sellers TA, Goode EL. Polymorphisms in TCEAL7 and risk of epithelial ovarian cancer. Gynecol Oncol 2009 Aug; 114(2):260-4. Epub 2009 May 05. PMID:19419758. PMCID:2758312. NIHMS:146979. DOI:10.1016/j.ygyno.2009.03.038.
  17. Park KH, Fridley BL, Ryu E, Tosakulwong N, Edwards AO. Complement component 3 (C3) haplotypes and risk of advanced age-related macular degeneration. Invest Ophthalmol Vis Sci 2009 Jul; 50(7):3386-93. Epub 2009 Feb 21. PMID:19234341. DOI:10.1167/iovs.08-3231.
  18. Goode EL, Fridley BL, Vierkant RA, Cunningham JM, Phelan CM, Anderson S, Rider DN, White KL, Pankratz VS, Song H, Hogdall E, Kjaer SK, Whittemore AS, DiCioccio R, Ramus SJ, Gayther SA, Schildkraut JM, Pharaoh PP, Sellers TA. Candidate gene analysis using imputed genotypes: cell cycle single-nucleotide polymorphisms and ovarian cancer risk. Cancer Epidemiol Biomarkers Prev 2009 Mar; 18(3):935-44. Epub 2009 Mar 03. PMID:19258477. PMCID:2743184. NIHMS:105309. DOI:10.1158/1055-9965.EPI-08-0860.
  19. Srinivasan BS, Chen J, Cheng C, Conti D, Duan S, Fridley BL, Gu X, Haines JL, Jorgenson E, Kraja A, Lasky-Su J, Li L, Rodin A, Wang D, Province M, Ritchie MD. Methods for analysis in pharmacogenomics: lessons from the Pharmacogenetics Research Network Analysis Group. Pharmacogenomics 2009 Feb; 10(2):243-51. PMID:19207025. PMCID:2737060. NIHMS:110732. DOI:10.2217/14622416.10.2.243.
  20. Fridley BL. Bayesian variable and model selection methods for genetic association studies. Genet Epidemiol 2009 Jan; 33(1):27-37. PMID:18618760. DOI:10.1002/gepi.20353.
  21. White KL, Vierkant RA, Phelan CM, Fridley BL, Anderson S, Knutson KL, Schildkraut JM, Cunningham JM, Kelemen LE, Pankratz VS, Rider DN, Liebow M, Hartmann LC, Sellers TA, Goode EL. Polymorphisms in NF-kappaB inhibitors and risk of epithelial ovarian cancer. BMC Cancer 2009; 9:170. Epub 2009 Jun 06. PMID:19500386. PMCID:2706256. DOI:10.1186/1471-2407-9-170.
  22. Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Weinshilboum RM, Wang L. Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers. PLoS One 2009; 4(11):e7765. Epub 2009 Nov 09. PMID:19898621. PMCID:2770319. DOI:10.1371/journal.pone.0007765.
  23. Goode EL, Szabo C, Prokunina-Olsson L, Vierkant RA, Fredericksen ZS, Collins FS, White KL, Schmidt M, Fridley BL, Couch FJ. No association between a candidate TCF7L2 variant and risk of breast or ovarian cancer. BMC Cancer 2009; 9:312. Epub 2009 Sep 04. PMID:19732438. PMCID:2749057. DOI:10.1186/1471-2407-9-312.
  24. Fridley BL, McDonnell SK, Rabe KG, Tang R, Biernacka JM, Sinnwell JP, Rider DN, Goode EL. Single versus multiple imputation for genotypic data. BMC Proc 2009; 3 Suppl 7:S7. Epub 2009 Dec 15. PMID:20018064. PMCID:2795971.
  25. Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, Sinnwell JP, Rider DN, de Andrade M, Goode EL, Fridley BL. Assessment of genotype imputation methods. BMC Proc 2009; 3 Suppl 7:S5. Epub 2009 Dec 15. PMID:20018042. PMCID:2795949.
  26. Juran BD, Atkinson EJ, Schlicht EM, Fridley BL, Lazaridis KN. Primary biliary cirrhosis is associated with a genetic variant in the 3' flanking region of the CTLA4 gene. Gastroenterology 2008 Oct; 135(4):1200-6. Epub 2008 Jul 01. PMID:18778710. PMCID:2613835. NIHMS:73578. DOI:10.1053/j.gastro.2008.06.077.
  27. Li L, Fridley BL, Kalari K, Jenkins G, Batzler A, Safgren S, Hildebrandt M, Ames M, Schaid D, Wang L. Gemcitabine and cytosine arabinoside cytotoxicity: association with lymphoblastoid cell expression. Cancer Res 2008 Sep 1; 68(17):7050-8. PMID:18757419. PMCID:2562356. NIHMS:58760. DOI:10.1158/0008-5472.CAN-08-0405.
  28. Fridley BL, Turner ST, Chapman A, Rodin A, Boerwinkle E, Bailey K. Reproducibility of Genotypes as Measured by the Affymetrix GeneChip(R) 100K Human Mapping Array Set. Comput Stat Data Anal 2008 Aug 15; 52(12):5367-5374. PMID:19684844. PMCID:2597860. NIHMS:65984. DOI:10.1016/j.csda.2008.05.020.
  29. Turner ST, Bailey KR, Fridley BL, Chapman AB, Schwartz GL, Chai HS, Sicotte H, Kocher JP, Rodin AS, Boerwinkle E. Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic. Hypertension 2008 Aug; 52(2):359-65. Epub 2008 Jun 30. PMID:18591461. PMCID:2692710. NIHMS:98838. DOI:10.1161/HYPERTENSIONAHA.107.104273.
  30. Wang L, Kumar S, Fridley BL, Kalari KR, Moon I, Pelleymounter LL, Hildebrandt MA, Batzler A, Eckloff BW, Wieben ED, Greipp PR. Proteasome beta subunit pharmacogenomics: gene resequencing and functional genomics. Clin Cancer Res 2008 Jun 1; 14(11):3503-13. PMID:18519783. PMCID:2778274. NIHMS:109414. DOI:10.1158/1078-0432.CCR-07-5150.
  31. Ji Y, Snyder EM, Fridley BL, Salavaggione OE, Moon I, Batzler A, Yee VC, Schaid DJ, Joyner MJ, Johnson BD, Weinshilboum RM. Human phenylethanolamine N-methyltransferase genetic polymorphisms and exercise-induced epinephrine release. Physiol Genomics 2008 May 13; 33(3):323-32. Epub 2008 Mar 18. PMID:18349382. DOI:10.1152/physiolgenomics.00248.2007.
  32. Edwards AO, Chen D, Fridley BL, James KM, Wu Y, Abecasis G, Swaroop A, Othman M, Branham K, Iyengar SK, Sivakumaran TA, Klein R, Klein BE, Tosakulwong N. Toll-like receptor polymorphisms and age-related macular degeneration. Invest Ophthalmol Vis Sci 2008 Apr; 49(4):1652-9. PMID:18385087. DOI:10.1167/iovs.07-1378.
  33. Pardanani A, Fridley BL, Lasho TL, Gilliland DG, Tefferi A. Host genetic variation contributes to phenotypic diversity in myeloproliferative disorders. Blood 2008 Mar 1; 111(5):2785-9. Epub 2007 Nov 15. PMID:18006699. DOI:10.1182/blood-2007-06-095703.
  34. Juran BD, Atkinson EJ, Schlicht EM, Fridley BL, Petersen GM, Lazaridis KN. Interacting alleles of the coinhibitory immunoreceptor genes cytotoxic T-lymphocyte antigen 4 and programmed cell-death 1 influence risk and features of primary biliary cirrhosis. Hepatology 2008 Feb; 47(2):563-70. PMID:18041714. DOI:10.1002/hep.22048.
  35. Thomas HR, Ezzeldin HH, Guarcello V, Mattison LK, Fridley BL, Diasio RB. Genetic regulation of beta-ureidopropionase and its possible implication in altered uracil catabolism. Pharmacogenet Genomics 2008 Jan; 18(1):25-35. PMID:18216719. DOI:10.1097/FPC.0b013e3282f2f134.
  36. Fridley BL, de Andrade M. Missing phenotype data imputation in pedigree data analysis. Genet Epidemiol 2008 Jan; 32(1):52-60. PMID:17685457. DOI:10.1002/gepi.20261.
  37. Edwards AO, Lee SJ, Fridley BL, Tosakulwong N. Density of common complex ocular traits in the aging eye: analysis of secondary traits in genome-wide association studies. PLoS One 2008; 3(6):e2510. Epub 2008 Jun 25. PMID:18575587. PMCID:2424139. DOI:10.1371/journal.pone.0002510.
  38. Edwards AO, Fridley BL, James KM, Sharma AK, Cunningham JM, Tosakulwong N. Evaluation of clustering and genotype distribution for replication in genome wide association studies: the age-related eye disease study. PLoS One 2008; 3(11):e3813. Epub 2008 Nov 26. PMID:19043567. PMCID:2583911. DOI:10.1371/journal.pone.0003813.
  39. Thomas HR, Ezzeldin HH, Guarcello V, Mattison LK, Fridley BL, Diasio RB. Genetic regulation of dihydropyrimidinase and its possible implication in altered uracil catabolism. Pharmacogenet Genomics 2007 Nov; 17(11):973-87. PMID:18075467. DOI:10.1097/FPC.0b013e3282f01788.
  40. Arruda-Olson AM, Weston SA, Fridley BL, Killian JM, Koepsell EE, Roger VL. Participation bias and its impact on the assembly of a genetic specimen repository for a myocardial infarction cohort. Mayo Clin Proc 2007 Oct; 82(10):1185-91. PMID:17908525. PMCID:2630777. NIHMS:87712.
  41. Nordman D, Lahiri S, Fridley BL. Optimal block size for variance estimation by a spatial block bootstrap method. Sankhya 2007 Aug; 69(Part 3):468-93.
  42. Ye Z, Atkinson EJ, Fridley BL, de Andrade M. Comparison of variable and model selection methods for genetic association studies using the GAW15 simulated data. BMC Proc 2007; 1 Suppl 1:S34. Epub 2007 Dec 18. PMID:18466532. PMCID:2367491.
  43. Swartz MD, Thomas DC, Daw EW, Albers K, Charlesworth JC, Dyer TC, Fridley BL, Govil M, Kraft P, Kwon S, Logue MW, Oh C, Pique-Regi R, Saba L, Schumacher FR, Uh HW. Model selection and Bayesian methods in statistical genetics: summary of group 11 contributions to Genetic Analysis Workshop 15. Genet Epidemiol 2007; 31 Suppl 1:S96-102. PMID:18046760. DOI:10.1002/gepi.20285.
  44. Liu-Mares W, Sun Z, Bamlet WR, Atkinson EJ, Fridley BL, Slager SL, de Andrade M, Goode EL. Analysis of variation in NF-kappaB genes and expression levels of NF-kappaB-regulated molecules. BMC Proc 2007; 1 Suppl 1:S126. Epub 2007 Dec 18. PMID:18466468. PMCID:2367504.
  45. Goode EL, Fridley BL, Sun Z, Atkinson EJ, Nord AS, McDonnell SK, Jarvik GP, de Andrade M, Slager SL. Comparison of tagging single-nucleotide polymorphism methods in association analyses. BMC Proc 2007; 1 Suppl 1:S6 Epub 2007 Dec 18. PMID:18466560. PMCID:2367496.
  46. Fridley BL, Dixon P. Data augmentation for a Bayesian Spatial Model involving censored observations. Environmetrics 2007; 18:107-123.
  47. de Andrade M, Atkinson EJ, Fridley BL, Goode EL, McDonnell S, Liu-Mares W, Rabe KG, Sun Z, Slager SL. The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods. BMC Proc 2007; 1 Suppl 1:S151. Epub 2007 Dec 18. PMID:18466496. PMCID:2367553.
  48. Atkinson EJ, Fridley BL, Goode EL, McDonnell SK, Liu-Mares W, Rabe KG, Sun Z, Slager SL, de Andrade M. Linkage analysis using principal components of gene expression data. BMC Proc 2007; 1(Suppl 1):S79 Epub 2007 Dec 18. PMID:18466581. PMCID:2367556.
  49. de Andrade M, Fridley BL, Boerwinkle E, Turner S. Diagnostic tools in linkage analysis for quantitative traits. Genet Epidemiol 2003 May; 24(4):302-8. PMID:12687648. DOI:10.1002/gepi.10236.
  50. Sloan JA, Vargas-Chanes D, Kamath CC, Sargent DJ, Novotny P, Atherton P, Allmer C, Fridley BL, Frost M, Loprinzi CL. Detecting worms, ducks, and elephants: A simple approach for defining clinically relevant effects in quality-of-life measures. Journal of Cancer Integrative Medicine 2003; 1(1):41-7.
  51. Sloan JA, Symonds T, Vargas-Chanes D, Fridley BL. Practical guidelines for assessing the clinical significance of health-related quality of life changes within clinical trials. Drug Inf J 2003; 37(1):23-31.
  52. Fridley BL, Rabe K, de Andrade M. Imputation methods for missing data for polygenic models. BMC Genetics 2003; 4(Suppl 1):S42. PMID:14975110. PMCID:1866478. DOI:10.1186/1471-2156-4-S1-S42.

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