Low expression levels of putative HPV encoded microRNAs in cervical samples

Virtanen, Elina; Pietilä, Tuuli; Nieminen, Pekka; Qian, Kui; Auvinen, Eeva

doi:10.1186/s40064-016-3524-3

SpringerPlus

Table 2 Clinical samples and cell lines, HPV test results, histology at time of sampling, and microRNA assay results

From: Low expression levels of putative HPV encoded microRNAs in cervical samples

N:o	Sample type	HC2	Aptima	LDR	Luminex	GeneXpert	Histology	H1	H2	H3	H5	H6	RNU6B	UniSp6
1^a	Aptima	+	16				Normal	Neg	Neg	Neg	Neg	Neg	32	21
2^a	Aptima	+	16				CIN3	Neg	Neg	Neg	Neg	Neg	33	21
3^a	Aptima	+	16				CIN1	Neg	Neg	Neg	Neg	Neg	30	21
4^a	Aptima	+	16				VAIN2	38 (1)	Neg	Neg	Neg	Neg	31	22
5^a	Aptima	+	16				Normal	Neg	Neg	Neg	Neg	Neg	31	22
6^a	Aptima	+	16				CIN1	Neg	Neg	Neg	Neg	Neg	34	22
7^a	Aptima	+	16				Normal	Neg	Neg	Neg	Neg	Neg	32	21
8	Aptima	+	16				Carcinoma	Neg	Neg	Neg	Neg	Neg	32	22
9	Aptima	−	−				Normal	Neg	Neg	Neg	Neg	Neg	30	22
10	Aptima	+	16				CIN1	Neg	Neg	Neg	Neg	Neg	32	22
11	Aptima	−	−				Normal	Neg	Neg	Neg	Neg	Neg	28	21
12	HC2	+					N/A	Neg	Neg	Neg	Neg	51 (1)	24	21
13	HC2	+					Metaplasia	Neg	Neg	Neg	Neg	Neg	29	22
14	HC2	+					N/A	Neg	Neg	Neg	Neg	49 (1)	26	22
15	HC2	+					Normal	Neg	Neg	Neg	Neg	Neg	31	22
16	ThinPrep	+				hrHPV	CIN2	Neg	Neg	Neg	Neg	57 (2, var)	30	22
17	ThinPrep	+				16	CIN3	Neg	Neg	44	50 (2, var)	48 (2, var)	24	22
18	ThinPrep	+				18/45	Normal	Neg	Neg	Neg	52 (1)	Neg	28	22
19	ThinPrep	+				18/45	AIS	Neg	39 (1)	58 (1)	Neg	51 (1)	28	21
20	ThinPrep	+				hrHPV	CIN3	Neg	Neg	49 (2, var)	54 (1)	44 (2, var)	25	22
21	ThinPrep	+				hrHPV	Metaplasia	50 (1)	Neg	50 (3, var)	56 (1)	42 (3, var)	24	22
22	ThinPrep	+				16	CIN1	Neg	Neg	45 (1)	Neg	53 (1)	28	22
23	ThinPrep	+				16, hrHPV^b	CIN1	Neg	Neg	58 (2, var)	Neg	52 (2, var)	27	22
24	ThinPrep	+				hrHPV	CIN2	Neg	39 (1)	Neg	Neg	Neg	33	23
25	ThinPrep	+				hrHPV	CIN1	Neg	Neg	50 (3, var)	Neg	48 (3, var)	27	22
26	ThinPrep	+				hrHPV	Condyloma	Neg	39 (1)	Neg	49 (1)	56 (1)	32	22
27	ThinPrep	+				16	CIN2	Neg	Neg	47 (3, var)	Neg	45 (3, var)	24	22
28	ThinPrep	+				18/45	Normal	Neg	Neg	Neg	Neg	Neg	31	23
29	ThinPrep	+				hrHPV	CIN1	Neg	37 (1)	55 (1)	Neg	57 (1)	29	23
30	ThinPrep	+				16	CIN3	50 (1)	39 (1)	45 (3, var)	48 (1)	45 (3, var)	25	22
31	ThinPrep	+				16	CIN2	Neg	Neg	50 (2, var)	Neg	47 (2, var)	27	22
32	FFPE	+		16, 18	16		SCC	Neg^c	Neg	45 (2, var)	54 (1)	48 (3, var)	31	22
33	FFPE	−		6, 16			CIN3	52 (1)^c	Neg^c	47 (3, var)	48 (2, var)	39 (3, var)	33	22
34	FFPE	+		16, 18	16		AIS	42 (1)^c	Neg^c	46 (3, var)	51 (2, var)	44 (3, var)	33	21
35	FFPE	−		16, 18	16		CIN3	55 (1)^c	57 (2, var)^c	45 (3, var)	42	41 (3, var)	31	22
36	FFPE	+		16			Adenocarcinoma	Neg^c	Neg^c	44 (3, var)	47 (2, var)	42 (3, var)	32 (2)	21
37	FFPE	+		16, 18	16		SCC	57 (1)^c	Neg^c	46 (3, var)	47 (2, var)	41	33	21
38	FFPE	−		16	16, 31, 35		CIN3	56 (1)^c	40 (1)	47 (3, var)	47 (3, var)	40 (3, var)	33	22
39	FFPE	N/A					Adenocarcinoma	Neg	Neg	44 (3, var)	45 (1)	46 (3, var)	33 (2)	22
40	FFPE	+		16, 18, 33			CIN3	Neg^c	Neg	44 (3, var)	60 (1)	46 (3, var)	29	22
41	FFPE	−		16	45		AIS	48 (1)^c	Neg	41 (3, var)	44 (2, var)	41 (3, var)	31	22
42	FFPE	+		16, 58	16, 33, 58		CIN1	Neg^c	53 (1)	46 (3, var)	58 (1)	45 (3, var)	29	22
43	FFPE	−		16, 58	16, 18, 58		AIS	50 (1)^c	Neg	56 (3, var)	Neg	58 (1)	34	23
44	FFPE	+		16, 18	33, 58		CIN1	Neg	44 (1)	45 (3, var)	52 (1)	45 (3, var)	33	22
45	FFPE	+		16, 18	16		AIS	Neg^c	Neg^c	56 (2, var)	Neg	53 (3, var)	38 (3, var)	24
46	FFPE	−		16	16		CIN2, p16+	55 (1)^c	Neg	57 (2)	Neg	50 (3, var)	37 (2)	22
47	FFPE	+		16, 52	16, 35, 52, 56		CIN2, p16+	Neg^c	Neg	45 (3, var)	Neg	47 (3, var)	32	22
48	FFPE	−		−	−		CIN2, p16+	52 (1)	Neg	59 (1)	Neg	50 (3, var)	37 (2)	25
49	FFPE	−		16, 18	16		Normal EE	Neg	Neg	Neg	Neg	Neg	37	22
50	FFPE	+		16	16		SCC	Neg^c	Neg^c	43 (1)	42 (1)	46 (3, var)	28	27
51b,c	FFPE	−		16	−		Normal SE	Neg	Neg	44 (3, var)	53 (2, var)	40 (3, var)	31	22
52	HPK IA						N/A	39	58 (1)	38	37	34	20	22
53	HPK II						N/A	43 (3, var)	Neg	38 (3, var)	39 (3, var)	34	26	21
54	CaSki						N/A	42 (3, var)	Neg	40	46 (3, var)	34 (3, var)	25	22
55	SiHa						N/A	49 (3, var)	Neg	39 (3, var)	48 (3, var)	39 (3, var)	28	21

HC2 hybrid capture 2, LDR ligase detection reaction (LDR-PCR microarray), H1–H6 HPV miRNAs, CIN1-3 cervical intraepithelial neoplasia grade 1–3, VAIN vaginal intraepithelial neoplasia, AIS adenocarcinoma in situ, SCC squamous cell carcinoma, EE endocervical epithelium, SE squamous epithelium. N/A not applicable or not available. Numbers in parentheses tell the number of replicates giving signal; var, multiple signals were not obtained within one cycle. Italicised values are interpreted as true positive findings
^aAmplification of 40 cycles was performed; for all other samples 60 cycles of amplification was used
^bPositive both for HPV 16 and another high-risk HPV type(s)
^cExpression was seen in some replicates in previous work

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