HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Table 2 Summary of HPV Genotypes and Co-Infections Among ICC Patients and Samples

		Total patients	Total samples	Archived DNA samples	Frozen tissue samples	FFPE tissue samples
Number of ICC samples^a		112	124	28	40	56
Samples passing qPCR filter		102 (91%)	110 (89%)	28 (100%)	40 (100%)	42 (75%)
HPV + patients/samples		97 (95%)	105 (95%)	25 (89%)	38 (95%)	42 (100%)
Overall “Unclear” samples		3 (3%)	3 (3%)	1 (4%)	2 (5%)	0 (0%)
HPV genotype-positive samples^b	HPV16	59 (58%)	62 (56%)	19 (68%)	21 (53%)	22 (52%)
	HPV18	19 (19%)	23 (21%)	4 (14%)	8 (20%)	11 (26%)
	HPV31	2 (2%)	2 (2%)	0 (0%)	0 (0%)	2 (5%)
	HPV33	2 (2%)	2 (2%)	0 (0%)	0 (0%)	2 (5%)
	HPV45	6 (6%)	6 (5%)	0 (0%)	2 (5%)	4 (10%)
	HPV58	8 (8%)	8 (7%)	1 (4%)	4 (10%)	3 (7%)
	HPV59	2 (2%)	3 (3%)	2 (7%)	1 (3%)	0 (0%)
	HPV67	1 (1%)	1 (1%)	0 (0%)	0 (0%)	1 (2%)
	HPV73	2 (2%)	2 (2%)	0 (0%)	0 (0%)	2 (5%)
	Unclear^c	2 (2%)	2 (2%)	0 (0%)	2 (5%)	0 (0%)
HPV genotypes per sample	1		100 (91%)	24 (86%)	38 (95%)	38 (90%)
	2		4 (4%)	1 (4%)	0 (0%)	3 (7%)
	3		1 (1%)	0 (0%)	0 (0%)	1 (2%)
	4		0 (0%)	0 (0%)	0 (0%)	0 (0%)

^aIncludes one archived DNA sample extracted from vulval cancer, as well as one FFPE sample that includes a mix of ICC and endometrial cancer; excludes negative control prostate samples, ICC-adjacent normal tissues, and non-malignant vaginal sample
^bBecause of co-infections, one sample can contribute to the counts of multiple HPV genotypes
^cSamples with an “unclear” genotype meet the read requirement for overall HPV reads but not for any particular HPV genotype. For patients, only one assignment in one sample was required to be designated positive for a given HPV genotype (i.e., “clear”)

ISSN: 1750-9378