4 Statistical Methods for Assessing Biomarkers and Analyzing Biomarker Data

Handbook of Statistics

Volumn 27, Issue , 2007, Pages 109-147

  Looney, Stephen W ^a   Hagan, Joseph L ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

EID: 67649312320     PISSN: 01697161     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0169-7161(07)27004-X     Document Type: Review

References (91)

1. Agresti A. An Introduction to Categorical Data Analysis (1996), Wiley, New York
2. Agresti A. Categorical Data Analysis. 2nd ed (2002), Wiley, Hoboken, NJ
3. Agresti A., Mehta C.R., and Patel N.R. Exact inference for contingency tables with ordered categories. Journal of the American Statistical Association 85 (1990) 453-458
4. Algina J., Oshima T.C., and Lin W. Type I error rates for Welch's test and James's second-order test under nonnormality and inequality of variance when there are two groups. Journal of Educational and Behavioral Statistics 19 (1994) 275-291
5. Altman D.G., and Bland J.M. Measurement in medicine: The analysis of method comparison studies. The Statistician 32 (1983) 307-317
6. Amorim L.C.A., and Alvarez-Leite E.M. Determination of o-cresol by gas chromatography and comparison with hippuric acid levels in urine samples of individuals exposed to toluene. Journal of Toxicology and Environmental Health 50 (1997) 401-407
7. Armitage P. Test for linear trend in proportions and frequencies. Biometrics 11 (1955) 375-386
8. Atawodi S.E., Lea S., Nyberg F., Mukeria A., Constantinescu V., Ahrens W., Brueske-Hohlfeld I., Fortes C., Boffetta P., and Friesen M.D. 4-Hydroxyl-1-(3-pyridyl)-1-butanone-hemoglobin adducts as biomarkers of exposure to tobacco smoke: Validation of a method to be used in multicenter studies. Cancer Epidemiology Biomarkers & Prevention 7 (1998) 817-821
9. Atkinson A.C. Testing transformations to normality. Journal of the Royal Statistical Society Series B 35 (1973) 473-479
10. Bartczak A., Kline S.A., Yu R., Weisel C.P., Goldstein B.D., and Witz G. Evaluation of assays for the identification and quantitation of muconic acid, a benzene metabolite in human urine. Journal of Toxicology and Environmental Health 42 (1994) 245-258
11. Bartko J.J. Measurement and reliability: Statistical thinking considerations. Schizophrenia Bulletin 17 (1991) 483-489
12. Bartko J.J. General methodology II. Measures of agreement: A single procedure. Statistics in Medicine 13 (1994) 737-745
13. Benowitz L. Biomarkers of environmental tobacco smoke exposure. Environmental Health Perspectives 107 Suppl 2 (1999) 349-355
14. Bernstein C., Bernstein H., Garewal H., Dinning P., Jabi R., Sampliner R.E., McCluskey M.K., Panda M., Roe D.J., L'Heureux L.L., and Payne C. A bile acid-induced apoptosis assay for colon cancer risk and associated quality control studies. Cancer Research 59 (1999) 2353-2357
15. Bland, J.M., Altman, D.G. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. The Lancet (February 8, 1986), 307-310.
16. Bland J.M., and Altman D.G. A note on the use of the intraclass correlation coefficient in the evaluation of agreement between two methods of measurement. Computers in Biology and Medicine 20 (1990) 337-340
17. Bonett D.G., and Wright T.A. Sample size requirements for estimating Pearson, Kendall, and Spearman correlations. Psychometrica 65 (2000) 23-28
18. Box G.E.P., and Cox D.R. An analysis of transformations. Journal of the Royal Statistical Society Series B 26 (1964) 211-252
19. Buckley T.J., Waldman J.M., Dhara R., Greenberg A., Ouyang Z., and Lioy P.J. An assessment of a urinary biomarker for total human environmental exposure to benzo[a]pyrene. International Archives of Occupational and Environmental Health 67 (1995) 257-266
20. Buss I.H., Senthilmohan R., Darlow B.A., Mogridge N., Kettle A.J., and Winterbourn C.C. 3-Chlorotyrosine as a marker of protein damage by myeloperoxidase in tracheal aspirates from preterm infants: Association with adverse respiratory outcome. Pediatric Research 53 (2003) 455-462
21. Byrt T., Bishop J., and Carlin J.B. Bias, prevalence, and kappa. Journal of Clinical Epidemiology 46 (1993) 423-429
22. Cheng, N.F., Gansky, S.A. A SAS macro to compute Lin's concordance correlation with confidence intervals. UCSF CAN-DO website. Accessed December 29, 2006. http://www.ucsf.edu/cando/resources/software/linscon.doc
23. Cicchetti D.V., and Feinstein A.R. High agreement but low kappa: II. Resolving the paradoxes. Journal of Clinical Epidemiology 43 (1990) 551-558
24. 2 tests. Biometrics 10 (1954) 417-454
25. Cohen J. A coefficient of agreement for nominal scales. Educational and Psychological Measurement 20 (1960) 37-46
26. Conover W.J. Practical Nonparametric Statistics. 3rd ed (1999), Wiley, New York
27. Cook D.G., Whincup P.H., Papacosta O., Strachan D.P., Jarvis M.J., and Bryant A. Relation of passive smoking as assessed by salivary cotinine concentration and questionnaire to spirometric indices in children. Thorax 48 (1993) 14-20
28. Cox D.R., and Hinkley D.V. Theoretical Statistics (1974), Chapman & Hall, London
29. D'Agostino R.B. Graphical analysis. In: D'Agostino R.B., and Stephens M.A. (Eds). Goodness-of-Fit Techniques (1986), Marcel Dekker, New York 7-62
30. Dunnett C.W. Pairwise multiple comparisons in the homogeneous variance, unequal sample size case. Journal of the American Statistical Association 75 (1980) 789-795
31. Dunnett C.W. Pairwise multiple comparisons in the unequal variance case. Journal of the American Statistical Association 75 (1980) 796-800
32. Feinstein A.R., and Cicchetti D.V. High agreement but low kappa: I. The problems of two paradoxes. Journal of Clinical Epidemiology 43 (1990) 543-549
33. Fleiss J.L. Measuring nominal scale agreement among many raters. Psychological Bulletin 76 (1971) 378-382
34. Gerson M. The techniques and uses of probability plots. The Statistician 24 (1975) 235-257
35. Gibbons J.D., and Chakraborti S. Nonparametric Statistical Inference. 4th ed (2003), Marcel Dekker, New York
36. Goldsmith L.J. Power and sample size considerations in molecular biology. In: Looney S.W. (Ed). Methods in Molecular Biology, Vol. 184: Biostatistical Methods (2001), Humana Press, Totowa, NJ 111-130
37. Graham P., and Bull B. Approximate standard errors and confidence intervals for indices of positive and negative agreement. Journal of Clinical Epidemiology 51 (1998) 763-771
38. Granella M., Priante E., Nardini B., Bono R., and Clonfero E. Excretion of mutagens, nicotine and its metabolites in urine of cigarette smokers. Mutagenesis 11 (1996) 207-211
39. Griffith J., Aldrich T.E., and Duncan R.C. Epidemiologic research methods. In: Aldrich T., Griffithh J., and Cooke C. (Eds). Environmental Epidemiology and Risk Assessment (1993), Van Nostrand Reinhold, New York 27-60
40. Hagan, J.L., Looney, S.W. (2004). Frequency of use of statistical techniques for assessing agreement between continuous measurements. Proceedings of the American Statistical Association. American Statistical Association, Alexandria, VA, pp. 344-350.
41. Hazelton M.L. A graphical tool for assessing normality. The American Statistician 57 (2003) 285-288
42. Huber P.J. Robust Statistical Procedures. 2nd ed (1996), Society for Industrial and Applied Mathematics, Philadelphia
43. Johnson N.L. Systems of frequency curves generated by methods of translation. Biometrika 36 (1949) 149-176
44. Jones M.C., and Daly F. Density probability plots. Communications in Statistics - Simulation and Computation 24 (1995) 911-927
45. Kraemer H.C. Extension of the kappa coefficient. Biometrics 36 (1980) 207-216
46. Kummel C.H. Reduction of observation equations which contain more than one observed quantity. The Analyst 6 (1879) 97-105
47. Lagorio S., Crebelli R., Ricciarello R., Conti L., Iavarone I., Zona A., Ghittori S., and Carere A. Methodological issues in biomonitoring of low level exposure to benzene. Occupational Medicine 8 (1998) 497-504
48. Landis J.R., and Koch G.G. The measurement of observer agreement for categorical data. Biometrics 33 (1977) 159-174
49. Last J.M. A Dictionary of Epidemiology. 3rd ed (1995), Oxford University Press, New York
50. Lehmann E.L. Nonparametrics: Statistical Methods Based on Ranks (1975), Holden-Day, San Francisco pp. 267-270
51. Lin L.I. A concordance correlation coefficient to evaluate reproducibility. Biometrics 45 (1989) 255-268
52. Lin L.I. A note on the concordance correlation coefficient. Biometrics 56 (2000) 324-325
53. Linnet K. Estimation of the linear relationship between the measurements of two methods with proportional errors. Statistics in Medicine 9 (1990) 1463-1473
54. Linnet K. Evaluation of regression procedures for methods comparison studies. Clinical Chemistry 39 (1993) 424-432
55. Looney, S.W. (1996). Sample size determination for correlation coefficient inference: Practical problems and practical solutions. Proceedings of the Statistical Computing Section, American Statistical Association. American Statistical Association, Alexandria, VA, pp. 240-245.
56. Looney, S.W. (Ed.) (2001). Statistical methods for assessing biomarkers. Methods in Molecular Biology, Vol. 184: Biostatistical Methods. Humana Press, Totowa, NJ, pp. 81-109.
57. Looney S.W., and Gulledge T.R. Use of the correlation coefficient with normal probability plots. The American Statistician 39 (1985) 75-79
58. Lyles R.H., Williams J.K., and Chuachoowong R. Correlating two viral load assays with known detection limits. Biometrics 57 (2001) 1238-1244
59. MacRae A.R., Gardner H.A., Allen L.C., Tokmakejian S., and Lepage N. Outcome validation of the Beckman Coulter access analyzer in a second-trimester Down syndrome serum screening application. Clinical Chemistry 49 (2003) 69-76
60. Mehrotra D.V., Chan I.S.F., and Berger R.L. A cautionary note on exact unconditional inference for a difference between two independent binomial proportions. Biometrics 59 (2003) 441-450
61. Mehta C., and Patel N. StatXact 7 (2005), CYTEL Software Corporation, Cambridge, MA
62. Morton R.F., Hebel J.R., and McCarter R.J. A Study Guide to Epidemiology and Biostatistics. 4th ed (1996), Aspen Publishers, Gaithersburg, MD pp. 92-97
63. Moser B.K., and Stevens G.R. Homogeneity of variance in the two-sample means test. The American Statistician 46 (1992) 19-21
64. Moser B.K., Stevens G.R., and Watts C.L. The two-sample t test versus Satterthwaite's approximate F test. Communications in Statistics Part A-Theory and Methods 18 (1989) 3963-3975
65. Neuhäuser M., and Hothorn L.A. An exact Cochran-Armitage test for trend when dose-response shapes are a priori unknown. Computational Statistics and Data Analysis 30 (1999) 403-412
66. Pérez-Stable E.J., Benowitz N.L., and Marín G. Is serum cotinine a better measure of cigarette smoking than self-report. Preventive Medicine 24 (1995) 171-179
67. Qiao Y.-L., Tockman M.S., Li L., Erozan Y.S., Yao S., Barrett M.J., Zhou W., Giffen C.A., Luo X., and Taylor P.R. A case-cohort study of an early biomarker of lung cancer in a screening cohort of Yunnan tin miners in China. Cancer Epidemiology, Biomarkers & Prevention 6 (1997) 893-900
68. Royston J.P. An extension of Shapiro and Wilk's W test for normality to large samples. Applied Statistics - Journal of the Royal Statistical Society Series C 31 (1982) 115-124
69. Royston J.P. Correcting the Shapiro-Wilk W for ties. Journal of Statistical Computation and Simulation 31 (1989) 237-249
70. Royston J.P. Approximating the Shapiro-Wilk's W test for non-normality. Statistics and Computing 2 (1992) 117-119
71. Salmi M., Stolen C., Jousilahti P., Yegutkin G.G., Tapanainen P., Janatuinen T., Knip M., Jalkanen S., and Salomaa V. Insulin-regulated increase of soluble vascular adhesion protein-1 in diabetes. The American Journal of Pathology 161 (2002) 2255-2262
72. Scheuren F. Multiple imputation: How it began and continues. The American Statistician 59 (2005) 315-319
73. Shapiro S.S., and Wilk M.B. An analysis of variance test for normality (complete samples). Biometrika 52 (1965) 591-611
74. Shapiro S.S., Wilk M.B., and Chen H.J. A comparative study of various tests for normality. Journal of the American Statistical Association 63 (1968) 1343-1372
75. Sheskin D.J. Handbook of Parametric and Nonparametric Statistical Procedures (1997), CRC Press, Boca Raton, FL
76. Shoukri M.M. Measures of Interobserver Agreement (2004), Chapman & Hall/CRC, Boca Raton, FL
77. Siegel S., and Castellan N.J. Nonparametric Statistics for the Behavioral Sciences. 2nd ed (1988), McGraw-Hill, New York
78. Steiger J.H. Tests for comparing elements of a correlation matrix. Psychological Bulletin 87 (1980) 245-251
79. Stoline M.R., and Ury H.K. Tables of the studentized maximum modulus distribution and an application to multiple comparisons among means. Technometrics 21 (1979) 87-93
80. Strachan D.P., Jarvis M.J., and Feyerabend C. The relationship of salivary cotinine to respiratory symptoms, spirometry, and exercise-induced bronchospasm in seven-year-old children. The American Review of Respiratory Disease 142 (1990) 147-151
81. Strike P.W. Measurement in Laboratory Medicine: A Primer on Control and Interpretation (1996), Butterworth-Heinemann, Oxford pp. 147-172
82. Stuart A., and Ord J.K. Kendall's Advanced Theory of Statistics (1987), Oxford University Press, New York pp. 210-220
83. Suissa S., and Shuster J. The 2×2 matched-pairs trial: Exact unconditional design and analysis. Biometrics 47 (1991) 361-372
84. Taylor D.J., Kupper L.L., Rappaport S.M., and Lyles R.H. A mixture model for occupational exposure mean testing with a limit of detection. Biometrics 57 (2001) 681-688
85. Tockman M.S., Gupta P.K., Myers J.D., Frost J.K., Baylin S.B., Gold E.B., Chase A.M., Wilkinson P.H., and Mulshine J.L. Sensitive and specific monoclonal antibody recognition of human lung cancer antigen on preserved sputum cells: A new approach to early lung cancer detection. Journal of Clinical Oncology 6 (1988) 1685-1693
86. Tukey J.W. Exploratory Data Analysis (1977), Addison-Wesley, Reading, MA
87. Tunstall-Pedoe H., Brown C.A., Woodward M., and Tavendale R. Passive smoking by self-report and serum cotinine and the prevalence of respiratory and coronary heart disease in the Scottish heart health study. Journal of Epidemiology and Community Health 49 (1995) 139-143
88. Wang, H. (2006). Correlation analysis for left-censored biomarker data with known detection limits. Unpublished Masters thesis, Louisiana State University Health Sciences Center, Biostatistics Program, School of Public Health.
89. Westgard J.O., and Hunt M.R. Use and interpretation of common statistical tests in method-comparison studies. Clinical Chemistry 19 (1973) 49-57
90. Wilcox R.R. New Statistical Procedures for the Social Sciences (1987), Lawrence Erlbaum Associates, Hillsdale, NJ
91. Wilk M.B., and Shapiro S.S. The joint assessment of normality of several independent samples. Technometrics 10 (1968) 825-839