Circulating tumor cells in hepatocellular carcinoma: a pilot study of detection, enumeration, and next-generation sequencing in cases and controls

Table 3 Sequencing performance by sample type

Sample type	CTC WGA DNA (n = 5)	FFPE Tumor DNA (n = 6) and PBMC DNA (n = 3) (n = 9 total^a)	pvalue (two-tailed t-test)
Mean read length	74 bp	76 bp	NS
Mean mapped reads per sample	653,878 bp	668,633 bp	NS
Mean amplicon read depth (std. dev)	2258 (4389)	2954 (1379)	p < 0.01
Proportion with coverage > 20x	50%	97%	p < 0.0002
Proportion with coverage > 100x	43%	88%	p < 0.026
Mean non-synonymous variant calls per sample	9	2^b	p < 0.03
Mean variant allele frequency	37%	61%^b	p < 0.0001

^aData from FFPE and PBMC DNA samples were combined for sequencing performance analyses (but not for genotype analyses) due to small sample size and similar observed coverage. NS = not significant. ^bPBMC samples (germline DNA) were excluded from variant analyses, n = 3.

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