Table 1.
Whole-exome sequencing data statistics.
FFPE: formalin-fixed paraffin-embedded samples.
Fig 1.
Distribution of insert sizes and frequencies of double-sequenced regions.
The distribution of insert sizes was calculated from properly mapped paired reads. The distributions of formalin-fixed paraffin-embedded (FFPE) samples were skewed to the left because of a large number of short inserts (A). The short inserts generated abundant overlapping paired ends in FFPE samples (B), and soft clipped bases (C).
Fig 2.
Distribution of nucleotide quality according to mapping status.
The nucleotide quality scores were analyzed according to mapping status. In the mapped reads, there was no significant difference between the distributions of the 2 types of sample. In the unmapped reads, the blood and frozen samples showed a higher percentage of low-quality bases (≤ 20 on the Phred scale, black arrow) compared to the FFPE samples.
Fig 3.
Frequency of base transition in formalin-fixed paraffin-embedded (FFPE) samples.
A: A strategy for estimation of rates of sequencing errors/background DNA damage and overall base alteration rates. The discrepant bases at homozygous sites in control samples are likely to be sequencing errors or background DNA mutation. Conversely, discrepant bases at homozygous sites in frozen or FFPE tissue samples could be either sequencing errors/background DNA damage or base alteration caused by preservation methods. B: The rate of base alterations caused by formalin fixation. High frequencies of C>T and G>A were observed in FFPE tissue samples only.
Fig 4.
Comparison of somatic single nucleotide variant (SNV) calls.
The overall concordance of somatic SNV calls between FFPE-frozen paired samples. A. The overlapping fraction of somatic mutation calls. B. The overlapping fraction of somatic mutation calls in FFPE samples when the matched frozen samples have at least one supporting read at the mutation.