However, the lack of matched normal specimens in this study made it difficult to make definitive determination of the somatic status of the observed mutations.
Mutations reported in this study as 'known somatic' were limited to those that have been previously confirmed to be somatic in other tumors, through sequencing of matched normal specimens.
Interestingly, all three of these regions exhibited high frequency of methylation in the tumor samples (76%, 90.5%, and 19% for ADAMTS1_Up, SCARF2_Up, and DSCR9_Down respectively) with very infrequent methylation in the matched normal specimens.
All studies assessed the entire coding region of these genes in tumors and in matched normal specimens, and they provide information regarding the somatic mutation status (single nucleotide changes, small insertions and deletions) for 662 LUAD in total.
Mean target coverage data in discovery cohort of tumor and matched normal specimen.
Hematoxylin and Eosin-stained sections from paraffin-embedded tissue blocks were reviewed by an anatomical pathologist (WAC) for tumour and matching normal tissue specimens.
Expression of SFRP5 mRNA was determined by real-time reverse-transcription PCR in 32 gastric cancer specimens and corresponding matched normal tissue specimens.
Real-time reverse-transcription PCR was performed to determine the mRNA expression of some members in MMP family, including MMP-2, MMP-7, MMP-9 and MT1-MMP in 32 gastric cancer specimens and corresponding matched normal tissue specimens.
The results showed that MMP-2, MMP-7, MMP-9 and MT1-MMP were all significantly upregulated in gastric cancer specimens compared to matched normal tissue specimens (For both MMP-2 and MMP-9, P < 0.01; for both MMP-7 and MT1-MMP, P < 0.001).
The Cancer Profiling Array (CPA) consisted of 511 dots with 494 cDNAs synthesized from various human tumors and corresponding normal tissue specimens, i.e. 241 tumor and 241 matched normal tissue specimens as well as 12 cDNAs from metastases corresponding to 12 of the tumor/normal pairs.
