The serous histiotype was further demonstrated by immunohistochemistry the neoplastic cells of all tumor samples stained strongly and diffusely for CA 125, p16, TP53, Ki 67 and WTI. selleck kinase inhibitor They failed to stain for caldesmon, fascin and only very weakly and fo cally for B cadherin. This immunohistochemical profile is consistent with serous differentiation. Exome sequencing and SNPsmall indel detection Exome sequencing was applied on the primary tumor, the omental metastasis, the tumor present at relapse, and the blood from the patient to identify somatic muta tions. Exomes were captured from a total of 3 ug of genomic DNA, using the Illumina TruSeq exome enrich ment kit, according to manufacturers protocols. Samples were sequenced using one lane of paired end, 100 bp reads on Illumina Hiseq for each sample.

We ensured that only read pairs with both mates present Inhibitors,Modulators,Libraries were subsequently used. Adaptor sequences and quality trimmed reads were removed using Fastx toolkit. Reads that passed quality control were aligned to the UCSC hg19 reference genome with BWA. Duplicate reads were marked using Picard and were excluded from down stream analyses. SAMtools was used to call SNV and indel variants. Next, we applied additional quality control measures to all identified raw variants based on the fol lowing criteria 1 The Phred like score is no less than 20 for SNPs and 50 for indels. 2 the read coverage of no less than three reads per base. 3 at least three and 10% of cov ering reads Inhibitors,Modulators,Libraries had to support the alternate base for the pri mary tumor sample.

Finally, we used Annovar to identify Inhibitors,Modulators,Libraries SNVs and indels that located in protein coding regions as well as variants affecting canonical splice sites. We further filtered the variants against dbSNP and 1000 genome project data set, as well as previously iden tified variants by our lab from 100 exome sequencing blood samples unrelated to cancer. Only variants that have not been previously Inhibitors,Modulators,Libraries observed in any of the control exomes were considered potentially functional and se lected for downstream analysis. The allele frequency of the variants was calculated as reads of alternate base total reads. Variants with increased allele frequency from the primary tumor Inhibitors,Modulators,Libraries to the metastasis and the recurrence were selected for validation by Sanger sequencing. The PeakPicker software was applied to quantitatively meas ure the allele proportion of selected SNVs.

The al lele proportion was calculated by To selleck chemicals compare the allele frequency from exome sequen cing and the allele proportion from Sanger sequencing, we converted the Sanger sequencing allele proportion to allele frequency as Copy number variant detection was done by comparing normalized read coverage or read depth be tween the blood and each of the primary, metastatic, and recurrent tumors, using an algorithm based on ExomeCNV.