Quantitative criteria for improving performance of buccal DNA for high-throughput genetic analysis

BMC Genomic Data

Table 2 Predictors of quality control failure among buccal samples

N	All buccal	QC passed	QC failed	P-value t-test or χ²	p-value Wilcoxon or Exact
	708	628	80
Years since sample collection	7.9 [5.3, 10.0]	8.0 [5.6, 10.0]	5.3 [4.2, 9.0]	<0.0001	<0.0001
Current cigarette smoker (%)	136 (19.2%)	116 (18.5%)	20 (25%)	0.16	0.18
Current cigar smoker (%)	21 (3%)	17 (2.7%)	4 (5%)	0.26	0.28
Average daily coffee intake (cups)	1.43 (1.28, 1.59)	1.39 (1.23, 1.54)	1.79 (1.16, 2.42)	0.23	0.25
Average daily tea intake (cups)	0.42 (0.33, 0.51)	0.42 (0.32, 0.51)	0.42 (0.19, 0.66)	0.96	0.77
Average daily sodas	0.75 (0.62, 0.87)	0.74 (0.60, 0.87)	0.85 (0.54, 1.16)	0.50	0.06
260/280 Ratio	1.81 (1.80-1.81)	1.81 (1.80-1.81)	1.82(1.80-1.84)	0.42	0.32
260/230 Ratio	1.17 (1.15- 1.20)	1.18 (1.15-1.21)	1.14 (1.06-1.21)	0.38	0.39
Total DNA (ng/μl)^a	87.4 (82.3-92.8)	85.6 (80.6-91.8)	102.5 (87.4-121.5)	0.06	0.05
ds DNA (ng/μl)^a	55.7 (52.5-59.1)	56.8 (53.5-60.3)	49.4 (41.3-59.1)	0.12	0.09
ds/total DNA ratio	0.66 (0.65-0.68)	0.68 (0.67-0.69)	0.52 (0.46-0.57)	<0.0001	<0.0001

Mean (95% confidence limits of mean) or n (%) presented; median [interquartile range] presented for years since sample collection.
^a Back-transformed from log values (geometric mean).

ISSN: 2730-6844