Kenneth Kinzler and colleagues report exome sequencing of ten hepatocellular carcinoma tumors and matched normal tissue.
Andrew Feinberg and colleagues report whole-genome bisulfite sequencing of three colon cancers and matched normal tissue and two adenomatous polyps.
Additionally, according to the same database, SMO is overexpressed in 93% of the patients (at least twofold overexpression in comparison with matched normal tissue).
This mutation was not present in the matched normal tissue, nor was it seen in the other cases of pediatric-type follicular lymphoma or pediatric nodal marginal zone lymphoma.
Zhiming Cai and colleagues report the exome sequencing of tumor and matched normal tissue from nine transitional cell carcinomas (TCCs) of the bladder, with further screening in 88 additional subjects.
Five genes were identified as core fitness genes in a single cancer type and are not expressed at the basal level (<5% quantile) in matched normal tissue (red points).
Analysis of pleural mesothelioma compared to matched normal tissue data revealed that expression of these genes is also increased in human tumors compared to normal tissue, indicating that activation of these developmental pathways is not species specific.
Finally, the analysis of additional data sets also showed that PARP14 expression was higher in glioblastoma, breast, gastric and lung cancers compared with that in their matched normal tissue (Supplementary Fig. 1b).
The method does not require matched normal tissue, requires little DNA (the equivalent of ∼150 cells) and uses commercially available reagents, instrumentation, and analysis software.
The biospecimen collection also includes 431 plasma samples, 40 fine-needle aspiration samples, and a tissue microarray containing 85 pancreatic adenocarcinomas and matched normal tissue specimens.
Variants were deemed somatic if they were found to be absent in matched normal tissue.
