In this study, be cause the use of exome sequencing data is still not well proven www.selleckchem.com/products/Y-27632.html in CNV detection, we Inhibitors,Modulators,Libraries refrained from attempting to identify small structural variants and concentrated on larger segments, which we can detect with high confi dence. In order to identify large scale rearrangements, the DNAcopy outputs were smoothed by removing small CNV calls and merging adjacent segments. Some large CNVs may be represented by more than one segment be cause they span regions where exonic data are unavailable. If there is no actual change in copy number between blood and tumor, then the ratio of RPKM values between blood and tumor should follow some distribution centered on 1. In fact, it follows a standard normal distribution after Geary Hinkley Trans formation.

Therefore Inhibitors,Modulators,Libraries using t as a test statistic for each exon, a p value can be calculated that gives the probability, under the null hypothesis, of finding a particular RPKM ratio as extreme as the one being observed. A smaller p value means that it is unlikely to observe the given RPKM ra tio under the null hypothesis, i. e. this gives an indication of copy number alteration at Inhibitors,Modulators,Libraries that exon. Let �� be the cumulative probability distribution of the transformed variable t, which follows the standard Gaussian distribu tion, then p for each exon is calculated as follows In our present analysis, the identified regions contain at least 100 exons which collectively show deviation from the expected. The probability that all of these show the same deviation by random chance is negligible.

Results and discussion We obtained 100 million sequencing reads that passed quality control for each sample. The mean read coverage in the blood, the primary tumor, the omental metastasis, and the recurrence Inhibitors,Modulators,Libraries was 174X, 130X, 162X and 146X per base, respectively, allowing for confident detection of mutations across the entire frequency spectrum. We searched for de novo somatic mutations by excluding all variants present in the blood from the list of variants detected in the three tumor samples. Based on the criteria described in the Methods section, we identi fied 39 somatic mutations in the primary tumor and a greater Inhibitors,Modulators,Libraries number of somatic mutations in the metastasis primary tumor contained a mixture of different malignant clones. Thus, we hypothesize that the primary tumor sam ple we obtained for sequencing contained a relatively lar and recurrence.

However, we found that all of the primary tumormetastasisrecurrence spe cific mutations were identified from poor alignments or variant callings, and on visual inspection of the data, the remaining mutations were also detected in the primary tumor with small numbers of supporting reads. We proceeded to examine the change in frequency of the BRCA1 missense mutation and observed AZD9291 EGFR inhibitor increasing allele frequencies of this muta tion 0.