Therefore, even when a matched control is available, a secondary analysis using multiple unmatched normal samples as the control can be performed (in additional to a paired analysis) to improve the detection of true positives.
Additionally, we note that the focal genomic segments with high LogRatios above noise thresholds within each chromosome were repeatedly observed across multiple unique normal sample pair comparisons in both the AA and TCGA CRC datasets, providing further evidence of their being indicative of germline CNVs as opposed to random inherent noise.
Further investigation of multiple normal and AD CSF samples comparing this modified INNOTEST® assay with other methodologies (once validated to a similarly advanced level) would provide a greater understanding of the true Aβ42 concentration range in humans and would provide an indication of the absolute accuracy of each validated method.
Rhodes et al. [ 3] have proposed methods to summarize significance levels of a gene in discriminating cancer versus normal samples across multiple gene profiling studies.
Collection of a database of normal samples from multiple tissue sites will be needed to use ISOpure; however, as shown by our deconvolution of the Director's Challenge cohort of 443 samples, deconvolution can even use existing datasets of normal samples, if the collection protocol and platform are sufficiently similar.
In order to explore the possibility of a common gene panel that can reliably detect cancer originated from multiple tissue types, we created a compendia of 5 microarray datasets from prostate, lung, ovarian, colon, and breast, respectively, each with cancer and normal samples from multiple subjects (Table 1).
To investigate the role of c-CBL in lung cancer, we analyzed its genomic DNA in tumor and paired normal samples drawn from multiple ethnicities.
Microarray data showed that 48 miRNAs were differentially expressed with significant change in tumor samples compared to normal samples (Multi-class Dif multiple comparison test RVM-F test, P < 0.05, FDR < 0.05) [ 34- 36].
We found that the 5' gene SLC45A3 is expressed specifically in prostate tumor and normal samples, whereas the 3' gene ELK4 is expressed broadly across multiple tissues.
