The aligned TCGA datasets were downloaded from the CGHub repository (website: https://cghub.ucsc.edu/) using the CGHub download client software GeneTorrent (version 3.8.5) for both tumor samples and matched normal samples (total n = 1,526).
As expected, the mean number of unstable markers per dMMR tumour was significantly reduced in non-CRC tumours (4.3 vs 5.4, P=0.001) with a lower allelic shift when compared with matched normal DNA (mean total variation, 22.5 vs 39.5 bp, P<0.0001).
Our relatively larger sample size of 99 PBA cases (n = 99 adenocarcinomas and n = 99 matched normal tissue for each case; total n = 198) provided a solid platform for investigating these diagnostic IHC biomarkers.
In our previous study, we sequenced the D-loop region (nucleotide position (np) 16024 576) of 15 pairs of ovarian tumour and matched normal samples and found a total of nine somatic mutations in three samples (20%; three out of 15) (Liu et al, 2001).
Total RNA was isolated from FFPE tissue of 34 primary tumours and matched normal tissue using the RecoverAll™ Total Nucleic Acid Isolation Kit (Applied Biosystems, Foster city, USA).
Total RNA of cancerous and matched normal tissues was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA).
Total RNA of cancerous and matched normal tissues was extracted using TRIzol (Invitrogen) and assessed by measuring absorbance at 260 nm.
We sequenced rRNA-depleted total RNA extracted from tumor and matched normal tissue from three patients with oral squamous cell carcinoma (OSCC) (Methods and Figure S1), yielding 129 256 million 50 bp long sequence reads per sample.
As a brief summary, there were 1,738 depression patients and 1,802 matched normal controls, and 424,861 markers after QC, covering a total of 16,758 genes.
Total RNA was isolated from tumor and matched normal tissues, renal cancer cell lines using RNeasy Mini Kit (Qiagen, Netherlands) according to the manufacturer's instructions.
