Table 2: RNA quality metrics and assay performance.

BenignComplex hyperplasiaHyperplasia with atypiaCancer
FF PipelleFF CurettageFFPENormalInvolvedNormalInvolvedNormalInvolved

RNA Extraction
 Number successfully extracted (over number attempted)*7/76/88/85/66/66/66/67/712/12
 Mean RNA yield ( g) (range)35.4
(20.9–62.0)
32.7
(25.1–50.4)
11.6
(2.7–26)
16.4
(5.7–24.9)
17.1
(1.6–48.5)
14.5
(6.9–21.4)
11.1
(8.0–17.8)
13.9
(6.1–43.1)
25.5
(11.1–39.7)
 Mean 260/280 ratio (range)2.05
(2.01–2.08)
2.06
(2.05–2.09)
2.00
(1.9–2.0)
2.02
(1.93–2.05)
2.05
(1.91–2.1)
2.02
(1.97–2.05)
1.98
(1.8–2.03)
2.04
(1.93–2.09)
2.00
(1.9–2.1)
DASL Pre-qualification
 Mean Ct threshold (range)15.7
(15.0–16.4)
15.7
(15–18.7)
21.0
(18.0–25.4)
20.9
(19.6–22.5)
19.5
(18.2–20.7)
20.5
(19.3–21.3)
19.9
(20.0–21.7)
21.5
(19–24.7)
21.0
(18.5–27.6)
DASL Expression Array
 Array pass rat 7/76/68/85/55/56/66/67/712/12
 Average number of probes detected (of 24,526, )18,640 (76.0%)18,165 (74.1%)17,197 (70.1%)18,455 (75.2%)18,244 (74.4%)18,239 (74.4%)18,446 (75.2%)18,177 (74.1%)17,648 (72%)
 Average number of probes detected (of 24,526, )17,064 (69.6%)16,637 (67.8%)15,640 (63.8%)16,912 (69.0%)16,846 (68.7%)16,647 (67.9%)16,823 (68.6%)16,442 (67.0%)15,874 (64.7%)
 Average number of genes detected (of 18,401, 12,917 (70.2%)12,630 (68.6%)11,931 (64.8%)12,434 (67.6%)12,580 (68.4%)12,642 (68.7%)12,645 (68.7%)12,348 (67.1%)11,930 (64.8%)
 Average Signal 7,4368,4956,6306,9066,9447,2026,9216,7036,725
191188184179184176179178192
Replicate Concordance
 Number of replicates run on array344333355
 Correlation of expression levels 0.990.990.990.990.990.980.990.990.98
 Probe concordance, 0.970.980.960.960.960.950.960.960.94
 Probe concordance, 0.980.980.970.960.970.960.960.960.94

Extractions were defined as successful if the yield was >1.2  g and the 260/280 ratio was between 1.80 and 2.20, as pure RNA has a 260/280 ratio of 2.0.
Excluding the three samples that had yields <1.2  g.
A Ct threshold of 29 or below qualifies RNA for the DASL array.
All replicates also passed.
In our high-throughput facility, the average number of genes detected is 10,000, the average p95 signal is 5,000, and the average signal-to-noise ratio is 40.