Summarizing performance for genome scale measurement of miRNA: reference samples and metrics

BMC Genomics

Table 1 Summary metrics derived from complete reference sample sets: five samples, three replicates each, and three rounds

Measurement		Data Source			miRNA Detected				Log2 Signals			AUC^c		Deviation
Process	Technology	by Round			Non-	TrueNeg	TruePos		Lower	Upper	Range	All	Within	Log2 Ratio		Proportion
		Pure	Mixes	Reps	Selective	1-to-1^a	Brain	Placenta	Limit^b	Limit	Range	All	Range	Median	IQR	Sum
A	NGS	3	3	3	928	56	103	104	5.8	20.0	14.3	0.959	0.996	-0.013	0.303	0.375
		4	4	3	935	72	101	105	5.7	20.2	14.5	0.977	0.990	0.007	0.309	0.384
		5	5	3	859	59	107	105	6.3	20.3	13.9	0.909	0.963	-0.053	0.373	0.355
B	NGS	3	3	3	868	56	134	47	7.3	20.2	12.8	0.905	0.953	-0.085	0.387	0.508
		4	4	3	721	38	102	58	5.7	19.0	13.2	0.922	0.951	-0.078	0.328	0.388
		5	5	3	641	43	78	44	5.8	19.2	13.4	0.906	0.928	-0.052	0.322	0.389
C	NGS	3	3	3	421	35	29	49	5.3	16.3	11.0	0.944	0.971	0.030	0.266	0.332
		4	4	3	277	22	16	30	6.3	11.8	5.6	0.831	0.829	0.088	0.557	0.359
		5	5	3	433	29	24	31	10.9	12.4	1.5	0.853	ND^d	-0.104	0.875	0.480
D	NGS	3	3	3	248	16	18	9	8.6	10.6	2.0	0.781	ND^d	-0.124	0.627	0.803
D	NGS	4	4	3	290	13	13	2	6.6	10.6	4.0	0.956	ND^d	-0.134	0.534	0.402
E	Digital Hybridization	3	3	3	693	65	8	24	7.1	13.3	6.1	0.947	1.000	-0.075	0.392	0.460
		4	4	3	633	17	8	23	5.6	14.4	8.8	0.985	0.997	-0.095	0.379	0.304
		5	5	3	586	52	16	37	13.9	15.3	1.4	0.882	1.000	-0.238	0.599	0.473

^aLiver-selective miRNA or miRNA with approximately equal signals in both brain and placenta
^bLower limits for NGS and digital hybridization were calculated with at 95% of values falling within ± 0.585 log2 difference from mean
^cROC curves were prepared with P-values using three replicates of Mix1 and Mix2
^dNot determined (ND) due to insufficient number of true negative or true positive values

ISSN: 1471-2164