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Additional file 6. Effect of the qPCR filter on HPV genotype read frequencies in paired tumor samples. (A) Consistency in the percentages of HPV16, HPV18, and HPV58 reads was evaluated using three types of tumor-tumor pairs: pairs of FFPE tissue samples from the same patient, as reported in patient records (“FFPE:Both”); pairs of frozen and FFPE tissue samples from the same patient, as reported in patient records (“Mixed:Reported”); and pairs of archived DNA and frozen tissue samples, matched via QC Array data (not reported in sample records, “Mixed:QCarray”). Correlations between the read frequencies for each pair were lower for HPV58 than for HPV16 and HPV18. (B) Same as (A) but excluding samples that did not pass the qPCR filter (amplified DNA concentrations < 2 nM).

Additional file 3. Effect of varying read thresholds for detecting HPV58 and HPV co-infections.

Additional file 4. Effect of varying off-target human read thresholds on HPV genotype.

Additional file 4. Effect of varying off-target human read thresholds on HPV genotype.

Additional file 1. Reference sequences used for HPV genotyping.

Additional file 6. Effect of the qPCR filter on HPV genotype read frequencies in paired tumor samples. (A) Consistency in the percentages of HPV16, HPV18, and HPV58 reads was evaluated using three types of tumor-tumor pairs: pairs of FFPE tissue samples from the same patient, as reported in patient records (“FFPE:Both”); pairs of frozen and FFPE tissue samples from the same patient, as reported in patient records (“Mixed:Reported”); and pairs of archived DNA and frozen tissue samples, matched via QC Array data (not reported in sample records, “Mixed:QCarray”). Correlations between the read frequencies for each pair were lower for HPV58 than for HPV16 and HPV18. (B) Same as (A) but excluding samples that did not pass the qPCR filter (amplified DNA concentrations < 2 nM).

Additional file 3. Effect of varying read thresholds for detecting HPV58 and HPV co-infections.