Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients

Table 4 CNV burden

Sample group	Total CNV length		Average CNV length of CNVs		Number of CNV’s
Software	Nexus	QuantiSNP	Nexus	QuantiSNP	Nexus	QuantiSNP
HNPCC vs. Controls	p = 0.0006	p = 0.0001	p = 0.0044	p ≤ 0.0001	p ≤ 0.0001	p = 0.8981
96 LS/HNPCC probands
Mean (95% CI)	31.2 Mb (15.4 – 46.9 Mb)	1.4 Mb (1.2-1.7 Mb)	82.5 kb (68.5-96.5 kb)	87.8 kb (75.0-100.6 kb)	233 (186–281)	16 (14–17)
384 Healthy controls
	3.1 Mb (2.7-3.6 Mb )	900 kb (847–953 Kb)	61.7 kb (59,6-63,7 kb)	56.9 kb (53.7-60.2 kb)	50 (46–54)	16 (15–16)
Mean (95% CI)
60 MMR + vs. 36 MMR-	p = 0.8630	p = 0.6355	p = 0.6302	p = 0.0069	p = 0.0509	p = 0.0021
60 MMR + LS probands
Mean (95% CI)	30.0 Mb (11.7-48.3 Mb)	1.4 Mb (1.0-1.7 Mb)	85.3 kb (68.7-101.8 kb)	72.4 kb (61.0-83.4 kb)	199 (135–264)	17 (15–19)
36 MMR- HNPCC probands
Mean (95% CI)	33.0 Mb (2.9-63.1 Mb)	1.5 Mb (1.1-1.9 Mb)	77.9 kb (51.6-104.1 kb)	11.3 kb (86.2-140.6 kb)	290 (224–356)	13 (11–14)

Nexus and QuantiSNP output analysis of overall CNV burden; total length of CNV’s, average length of CNV’s and number of CNV’s in Lynch syndrome/HNPCC patients (n = 96) vs. Controls (n = 384) and between MMR + individuals (n = 60) vs. MMR- individuals.