On the left we see a normal sample with the appropriate number of red blood cells and platelets.
There are serious implications in this assumption as identification of germline and rare somatic variants depend on the normal sample being the matched pair.
In contrast, in an alternate dataset that was generated on a normal multi-cell sample with the same coverage and read length, there were no uncovered regions.
Fig. 5 Topographic images of random data patterns used in the recording tests showing (a) 2 Tbit/in2 on a normal spin coated samples, and (b) 3 Tbit/in2, and (c) 4 Tbit/in2 on an ultraflat templated sample.
None showed positive reactivity, for a specificity on the normal samples of 100% (Table 2).
To secure a balanced set of tissues, the analysis focused on 17 normal samples, 18 ADCA (randomly selected from a total of 127), 21 SQCA, 20 pulmonary carcinoids and 6 small-cell lung carcinomas.
In a comparison between the low-entropy regions on the normal samples (Table S3) and the regions annotated in the CNV databases (described in Methods), 62% of the DNA probes of the low-entropy regions in normal samples are also located in known CNV regions.
6) Variant calling on >1,000 normal samples.
We examined exon 7 (with which sequencing succeeded on most normal samples but failed on the tumors) and exon 4 (with which sequencing succeeded on all tumor/normal samples and no mutation was found) of SMAD4.
The inclusion of such a normal DNA sample on each experiment also provides a reference sample for a Δ-ΔCt method of calculation, however, as the normalisation will relate to a value close to 0 for the second ΔCt, both methods essentially give the same result.
The results were validated on about 600 independent samples: experimentally by qRT-PCR on normal samples, tumors and LNM from 14 independent patients and in silico using the data from The Cancer Genome Atlas (small RNA deep-sequencing data already processed of 495 PTC, 59 normal samples and 8 LNM) [ 30].
