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Association of fragmentation of DNA in FFPE samples with low sequencing coverage. Coverage of each sample (number of reads) versus the copies of the <t>FTH1</t> gene as assessed by a <t>Taqman</t> PCR assay (copies per microlitre). n = 253. There was a positive correlation between the FTH1 result and coverage (Spearman correlation, r = −0.29, p < 0.0001). The 50 samples with the highest C>T/G>A levels in the 1-10% allele frequency range are shown in red.
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Association of fragmentation of DNA in FFPE samples with low sequencing coverage. Coverage of each sample (number of reads) versus the copies of the FTH1 gene as assessed by a Taqman PCR assay (copies per microlitre). n = 253. There was a positive correlation between the FTH1 result and coverage (Spearman correlation, r = −0.29, p < 0.0001). The 50 samples with the highest C>T/G>A levels in the 1-10% allele frequency range are shown in red.

Journal: BMC Medical Genomics

Article Title: Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing

doi: 10.1186/1755-8794-7-23

Figure Lengend Snippet: Association of fragmentation of DNA in FFPE samples with low sequencing coverage. Coverage of each sample (number of reads) versus the copies of the FTH1 gene as assessed by a Taqman PCR assay (copies per microlitre). n = 253. There was a positive correlation between the FTH1 result and coverage (Spearman correlation, r = −0.29, p < 0.0001). The 50 samples with the highest C>T/G>A levels in the 1-10% allele frequency range are shown in red.

Article Snippet: FFPE derived DNA was checked for quality and concentration using an 180 bp FTH1 TaqMan assay (Life Technologies).

Techniques: Sequencing