Association false positive

Connaghan D. G Francis C. E., Ryan D. H., Marder V. J. Prevalence and clinical implications of heparin-associated false positive tests for serum fibrin(ogen) degradation products. Am J Clin Pathol 1986 86,304-10. 

RNAz assists in the final classification by providing an overall RNA-class probability, or p-value. It is important to know that this is not a p-value in a strict statistical sense, simply because there is no underlying statistical model. Instead, RNAz uses a rather ad hoc machine learning technique to calculate this value. If p > 0.5, the alignment is classified as RNA. The false-positive rate at this cutoff was found to be 4 %, i.e., we expect four positive hits in 100 random alignments. For many applications it is useful to set a more stringent cutoff of p = 0.9 with an associated false-positive rate of 1 %. Reasons why estimations of false-positives must always be taken with caution are given in Note 6. 

The premarket notification application, 510(k), is reviewed by the FDA scientific staff. This evaluation takes into consideration tumor-associated analytes, test requirements, medical usefulness of the test system for a particular clinical claim, and its application (i.e., monitoring or treatment follow-up). The FDA determines the appropriate performance requirements for each tumor analyte category. The agency s staff considers factors, such as consequences of a false positive or false negative, and the importance or impact of an absolute versus a significant change in the results or values of the tumor marker tests. The performance criteria (parameters) of a particular tumor marker test are compared with those of previously... 

As the number of SNPs evaluated in an association study increases, a concern arises with false positives. This is true for candidate gene studies, but moreso for whole genome random SNP studies where tens to hundreds of thousands of SNPs will be evaluated. The traditional cutoff for assessing statistical significance (p<0.05] by definition can result in 5% false associations occurring simply by... 

Another approach to controlling the false positive rate in carcinogenicity studies was proposed by Haseman (1983). Under this rule, a compound would be declared a carcinogen if it produced an increase significant at the 1% level in a common tumor or an increase significant at the 5% level in a rear tumor. A rare neoplasm was defined as a neoplasm that occurred with a frequency of less than 1% in control animals. The overall false positive rate associated with this decision rule was found to be not more that 7-8%, based on control tumor incidences from NTP studies in rats and mice. This false positive rate compares favorably with the expected rate of 5%, which is the probability at which one would erroneously... 

Clayton et al. found that, in addition to population substructure, false-positive association was caused by bias in genotype scoring between case and control DNA... 

Kraft P. (2006) Efficient two-stage genome-wide association designs based on false positive report probabilities. Pac Symp Biocomput. 523-534. 

Related to CYP activity, PXR interestingly displayed a negative correlation/association with reprodnctive toxicity. In general, PXR lowered the false positive rate of the model by lowering the model score of chemicals with nonspecific and low potency nuclear receptor activity. Robust PXR activity is an indication of potent xenos-ensing and potentially rapid metabolism. 

The third compound was CNS-active (target H). The feasible dose levels in animals were limited to five or six times the anticipated human dose due to convulsions associated with mortality. In FETAX (Table 4), the majority of malformed larvae were noted at the top dose of the standard range (1-62.5 mg/L) and included microencephaly and eye defects. As with the two other false positive compounds, no solubility issues were noted. Interestingly at the dose of 62.5 mg/L, all larvae appeared anesthetized, remaining stationary and not reacting to touch, probably in relation with its pharmacological activity. 

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