Erratum: The success of pharmacogenomics in moving genetic association studies from bench to bedside: Study design and implementation of precision medicine in the post-GWAS era (Hum Genet (2012) 131 (1615-1626) DOI 10.1007/s00439-012-1221-z);The success of pharmacogenomics in moving genetic association studies from bench to bedside: Study design and implementation of precision medicine in the post-GWAS era

Human Genetics

Volumn 131, Issue 10, 2012, Pages 1615-1626

  Ritchie, Marylyn D ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABACAVIR; ANTIRETROVIRUS AGENT; AZATHIOPRINE; CODEINE; HYDROXYMETHYLGLUTARYL COENZYME A REDUCTASE INHIBITOR; MERCAPTOPURINE; NEVIRAPINE; TAMOXIFEN; TIOGUANINE; WARFARIN;

BREAST CANCER; COUGHING; DIZZINESS; DROWSINESS; DRUG EXPOSURE; DYSPNEA; EFFECT SIZE; ENTERITIS; EPIDEMIOLOGICAL DATA; FATIGUE; FEVER; GASTROINTESTINAL SYMPTOM; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOME; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HYPERSENSITIVITY REACTION; IN VITRO STUDY; LYMPH NODE METASTASIS; MEDICINE; MOLECULAR GENETICS; MYELOID LEUKEMIA; OBSERVATIONAL STUDY; PAIN; PHARMACOGENOMICS; PLACEBO EFFECT; PRIORITY JOURNAL; RANDOMIZED CONTROLLED TRIAL (TOPIC); RASH; REVIEW; RHEUMATOID ARTHRITIS; SIDE EFFECT; STUDY DESIGN; SWEATING; TREATMENT RESPONSE; UNSPECIFIED SIDE EFFECT; VOMITING;

EID: 84866740789     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-013-1359-3     Document Type: Erratum

References (96)

1. Armitage P (1955) Tests for linear trends in proportions and frequencies. Biometrics 11:375-386
2. Arteaga CL et al (2012) Treatment of HER2-positive breast cancer: current status and future perspectives. Nat Rev Clin Oncol 9:16-32
3. Ayers KL, Cordell HJ (2010) SNP selection in genome-wide and candidate gene studies via penalized logistic regression. Genet Epidemiol 34:879-891
4. Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7:781-791
5. Birdwell KA et al (2012) The use of a DNA biobank linked to electronic medical records to characterize pharmacogenomic predictors of tacrolimus dose requirement in kidney transplant recipients. Pharmacogenet Genomics 22:32-42
6. Breiman L (2001) Random forests. Mach Learn 45:5-32
7. Breiman L, Friedman J, Olshen RA (1984) Classification and regression trees. Chapman & Hall, New York
8. Brown C, Havener TM, Everitt L, McLeod H, Motsinger-Reif AA (2011) A comparison of association methods for cytotoxicity mapping in pharmacogenomics. Front Genet 2:86
9. Cantor RM, Lange K, Sinsheimer JS (2010) Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Am J Hum Genet 86:6-22
10. Chalise P, Batzler A, Abo R, Wang L, Fridley BL (2012) Simultaneous analysis of multiple data types in pharmacogenomic studies using weighted sparse canonical correlation analysis. OMICS 16:363-373
11. Chen W et al (2010) Genetic variants near TIMP3 and high-density lipoprotein-Associated loci influence susceptibility to age-related macular degeneration. Proc Natl Acad Sci USA 107:7401-7406
12. Coassin S, Brandstätter A, Kronenberg F (2010) Lost in the space of bioinformatic tools: a constantly updated survival guide for genetic epidemiology. The GenEpi Toolbox. Atherosclerosis 209:321-335
13. Cordell HJ (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10:392-404
14. Cree B A C et al (2010) A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1 15:01. PLoS One 5:e11296
15. Crews KR et al (2012) Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for codeine therapy in the context of cytochrome P450 2D6 (CYP2D6) genotype. Clin Pharmacol Ther 91:321-326
16. Crosslin DR et al (2012) Genetic variants associated with the white blood cell count in 13, 923 subjects in the eMERGE Network. Hum Genet 131:639-652
17. Denny JC et al (2011) Variants near FOXE1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome-And phenome-wide studies. Am J Hum Genet 89:529-542
18. Duan S et al (2009) Expression and alternative splicing of folate pathway genes in HapMap lymphoblastoid cell lines. Pharmacogenomics 10:549-563
19. Edwards TL, Gao X (2012) Methods for detecting and correcting for population stratification. Curr Protoc Hum Genet, Chap 1, Unit1.22
20. Emilsson V et al (2008) Genetics of gene expression and its effect on disease. Nature 452:423-428
21. Flynn AA (2011) Pharmacogenetics: practices and opportunities for study design and data analysis. Drug Discov Today 16:862-866
22. Fridley BL, Lund S, Jenkins GD, Wang L (2012) A Bayesian integrative genomic model for pathway analysis of complex traits. Genet Epidemiol 36:352-359
23. Garay JP, Gray JW (2012) Omics and therapy-A basis for precision medicine. Mol Oncol 6:128-139
24. Grady BJ, Ritchie MD (2011) Statistical optimization of pharmacogenomics association studies: key considerations from study design to analysis. Curr Pharmacogenomics Pers Med 9:41-66
25. Greenwood P (1996) A guide to Chi-squared testing. Wiley, New York
26. Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19:376-382
27. Hamilton CM et al (2011) The PhenX Toolkit: get the most from your measures. Am J Epidemiol 174:253-260
28. Harrell FE (2001) Regression modeling strategies: with applications to linear models, logistic regression, and survival analysis. Springer, Berlin
29. Hendershot T et al (2011) Using the PhenX Toolkit to Add Standard Measures to a study. Curr Protoc Hum Genet, Chap 1, Unit1.21
30. Hindorff LA et al (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106:9362-9367
31. Holzinger ER, Ritchie MD (2012) Integrating heterogeneous highthroughput data for meta-dimensional pharmacogenomics and disease-related studies. Pharmacogenomics 13:213-222
32. Hosmer D, Lemeshow S (2000) Applied logistic regression. Wiley Interscience, New York
33. Huang RS et al (2007) A genome-wide approach to identify genetic variants that contribute to etoposide-induced cytotoxicity. Proc Natl Acad Sci USA 104:9758-9763
34. Huang S-W et al (2009) Validation of VKORC1 and CYP2C9 genotypes on interindividual warfarin maintenance dose: a prospective study in Chinese patients. Pharmacogenet Genomics 19:226-234
35. Ingle JN et al (2010) Genome-wide associations and functional genomic studies of musculoskeletal adverse events in women receiving aromatase inhibitors. J Clin Oncol 28:4674-4682
36. Johnson JA et al (2011) Clinical Pharmacogenetics Implementation Consortium Guidelines for CYP2C9 and VKORC1 genotypes and warfarin dosing. Clin Pharmacol Ther 90:625-629
37. Kacevska M, Ivanov M, Ingelman-Sundberg M (2011) Perspectives on epigenetics and its relevance to adverse drug reactions. Clin Pharmacol Ther 89:902-907
38. Kaplan E, Meier P (1958) Nonparametric estimation from incomplete observations. J Am Stat Assoc 53:457-481
39. Kho AN et al (2011) Electronic medical records for genetic research: results of the eMERGE consortium. Sci Transl Med 3:79re1
40. Kho AN et al (2012) Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study. J Am Med Inform Assoc 19:212-218
41. Khoury MJ, Gwinn ML, Glasgow RE, Kramer BS (2012) A population approach to precision medicine. Am J Prev Med 42:639-645
42. Kiyotani K et al (2008) Association of genetic polymorphisms in SLCO1B3 and ABCC2 with docetaxel-induced leukopenia. Cancer Sci 99:967-972
43. Kiyotani K et al (2012) A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese. Hum Mol Genet 21:1665-1672
44. Kooperberg C, Ruczinski I (2005) Identifying interacting SNPs using Monte Carlo logic regression. Genet Epidemiol 28:157-170
45. Kooperberg C, Ruczinski I, LeBlanc ML, Hsu L (2001) Sequence analysis using logic regression. Genet Epidemiol 21(Suppl 1):S626-S631
46. Kraft P, Cox DG (2008) Study designs for genome-wide association studies. Adv Genet 60:465-504
47. Krueger F, Kreck B, Franke A, Andrews SR (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9:145-151
48. Ku CS, Naidoo N, Wu M, Soong R (2011) Studying the epigenome using next generation sequencing. J Med Genet 48:721-730
49. Kullo IJ et al (2011) Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. Am J Hum Genet 89:131-138
50. Lash TL, Ahern TP (2012) Bias analysis to guide new data collection. Int J Biostat 8 (2)
51. Link E et al (2008) SLCO1B1 variants and statin-induced myopathy-A genomewide study. N Engl J Med 359:789-799
52. Little J, Sharp L, Khoury MJ, Bradley L, Gwinn M (2005) The epidemiologic approach to pharmacogenomics. Am J Pharmacogenomics 5:1-20
53. Locharernkul C, Shotelersuk V, Hirankarn N (2011) Pharmacogenetic screening of carbamazepine-induced severe cutaneous allergic reactions. J Clin Neurosci 18:1289-1294
54. Lucena MI et al (2011) Susceptibility to amoxicillin-clavulanateinduced liver injury is influenced by multiple HLA class I and II alleles. Gastroenterology 141:338-347
55. Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456:18-21
56. Mallal S et al (2008) HLA-B5701 screening for hypersensitivity to abacavir. N Engl J Med 358:568-579
57. Manolio TA, Bailey-Wilson JE, Collins FS (2006) Genes, environment and the value of prospective cohort studies. Nat Rev Genet 7:812-820
58. Manolopoulos VG, Ragia G, Tavridou A (2011) Pharmacogenomics of oral antidiabetic medications: current data and pharmacoepigenomic perspective. Pharmacogenomics 12:1161-1191
59. Martin MA et al (2012) Clinical pharmacogenetics implementation consortium guidelines for hla-B genotype and abacavir dosing. Clin Pharmacol Ther 91:734-738
60. Matimba A et al (2008) Establishment of a biobank and pharmacogenetics database of African populations. Eur J Hum Genet 16:780-783
61. Matsson P et al (2012) Discovery of regulatory elements in human ATP-binding cassette transporters through expression quantitative trait mapping. Pharmacogenomics J 12:214-226
62. McCarty CA et al (2011) The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genomics 4:13
63. Meyre D et al (2009) Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations. Nat Genet 41:157-159
64. Midorikawa Y, Tsuji S, Takayama T, Aburatani H (2012) Genomic approach towards personalized anticancer drug therapy. Pharmacogenomics 13:191-199
65. Mirnezami R, Nicholson J, Darzi A (2012) Preparing for precision medicine. N Engl J Med 366:489-491
66. Motsinger AA, Ritchie MD (2006) Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Hum Genomics 2:318-328
67. Motsinger AA, Ritchie MD, Dobrin SE (2006a) Clinical applications of whole-genome association studies: future applications at the bedside. Expert Rev Mol Diagn 6:551-565
68. Motsinger AA, Lee SL, Mellick G, Ritchie MD (2006b) GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. BMC Bioinforma 7:39
69. Motsinger AA, Ritchie MD, Reif DM (2007) Novel methods for detecting epistasis in pharmacogenomics studies. Pharmacogenomics 8:1229-1241
70. Pan et al (2012) Using PhenX measures to identify opportunities for cross-study analysis. Hum Mutat. doi:10.1002/humu.22074
71. Pathak J et al (2011) Evaluating phenotypic data elements for genetics and epidemiological research: experiences from the eMERGE and PhenX Network Projects. AMIA Summits Transl Sci Proc 2011:41-45
72. Ramirez AH et al (2012) Predicting warfarin dosage in European-Americans and African-Americans using DNA samples linked to an electronic health record. Pharmacogenomics 13:407-418
73. Relling MV, Klein TE (2011) CPIC: Clinical Pharmacogenetics Implementation Consortium of the Pharmacogenomics Research Network. Clin Pharmacol Ther 89:464-467
74. Relling MV et al (2011) Clinical Pharmacogenetics Implementation Consortium guidelines for thiopurine methyltransferase genotype and thiopurine dosing. Clin Pharmacol Ther 89:387-391
75. Ritchie MD et al (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69:138-147
76. Rodin AS, Gogoshin G, Boerwinkle E (2011) Systems biology data analysis methodology in pharmacogenomics. Pharmacogenomics 12:1349-1360
77. Schwarz DF, König IR, Ziegler A (2010) On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data. Bioinformatics 26:1752-1758
78. Srinivasan BS et al (2009) Methods for analysis in pharmacogenomics: lessons from the Pharmacogenetics Research Network Analysis Group. Pharmacogenomics 10:243-251
79. Stephens M, Balding DJ (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10:681-690
80. Stolberg HO, Norman G, Trop I (2004) Randomized controlled trials. AJR Am J Roentgenol 183:1539-1544
81. Stover PJ, Harlan WR, Hammond JA, Hendershot T, Hamilton CM (2010) PhenX: a toolkit for interdisciplinary genetics research. Curr Opin Lipidol 21:136-140
82. Swan SH, Shaw GM, Schulman J (1992) Reporting and selection bias in case-control studies of congenital malformations. Epidemiology 3:356-363
83. Tanaka Y et al (2011) Genome-wide association study identified ITPA/DDRGK1 variants reflecting thrombocytopenia in pegylated interferon and ribavirin therapy for chronic hepatitis C. Hum Mol Genet 20:3507-3516
84. Turner S, Dudek S, Ritchie M (2010a) Grammatical evolution of neural networks for discovering epistasis among quantitative trait loci. Lect Notes Comput Sci 6023:86-97
85. Turner SD, Dudek SM, Ritchie MD (2010b) ATHENA: a knowledgebased hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. BioData Min 3:5
86. Watson VG, Hardison NE, Harris T, Motsinger-Reif A, McLeod HL (2011a) Genomic profiling in CEPH cell lines distinguishes between the camptothecins and indenoisoquinolines. Mol Cancer Ther 10:1839-1845
87. Watson VG et al (2011b) Identification and replication of loci involved in camptothecin-induced cytotoxicity using CEPH pedigrees. PLoS One 6:e17561
88. Welsh M et al (2009) Pharmacogenomic discovery using cell-based models. Pharmacol Rev 61:413-429
89. White CC et al (2011) CYP4A11 variant is associated with highdensity lipoprotein cholesterol in women. Pharmacogenomics J. doi:10.1038/tpj.2011.40
90. Wilke RA et al (2008) Characterization of low-density lipoprotein cholesterol-lowering efficacy for atorvastatin in a populationbased DNA biorepository. Basic Clin Pharmacol Toxicol 103:354-359
91. Woodahl EL et al (2008) Pharmacogenomic associations in ABCB1 and CYP3A5 with acute kidney injury and chronic kidney disease after myeloablative hematopoietic cell transplantation. Pharmacogenomics J 8:248-255
92. Yan Q (2008) The integration of personalized and systems medicine: bioinformatics support for pharmacogenomics and drug discovery. Methods Mol Biol 448:1-19
93. Yi HG et al (2009) Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are effective for leptomeningeal metastasis from non-small cell lung cancer patients with sensitive EGFR mutation or other predictive factors of good response for EGFR TKI. Lung Cancer 65:80-84
94. Zhang J, Chiodini R, Badr A, Zhang G (2011) The impact of nextgeneration sequencing on genomics. J Genet Genomics 38:95-109
95. Zheng HX et al (2004) The impact of pharmacogenomic factors on steroid dependency in pediatric heart transplant patients using logistic regression analysis. Pediatr Transplant 8:551-557
96. Zhou L, Li X, Liu Q, Zhao F, Wu J (2011) Small RNA transcriptome investigation based on next-generation sequencing technology. J Genet Genomics 38:505-513