Table 2.

Rare CNV burden analysis with respect to CNV size and CNV rate.

Rare CNV burden analyzes	T2D group	Control group	Both groups	T2D/ Control ratio	Raw P-value	Corrected P-value
CNV rate 1
Deletions	0.25	0.19	0.26	1.30	0.127	0.029*
Duplications	0.51	0.48	0.49	1.04	0.437	0.475
Deletions + Duplications	0.75	0.68	0.75	1.11	0.21	0.116
CNV sample proportion 2
Deletions	0.22	0.18	0.22	1.20	0.187	0.097
Duplications	0.40	0.37	0.37	1.08	0.319	0.533
Deletions + Duplications	0.55	0.48	0.51	1.13	0.112	0.269
Total CNV size 3
Deletions	291.9	271.1	299.30	1.08	0.386	0.258
Duplications	419.2	484.0	444.90	0.87	0.816	0.85
Deletions + Duplications	420.2	466.5	449.40	0.90	0.811	0.699
Average CNV size 4
Deletions	258.70	263.90	259.10	0.98	0.499	0.574
Duplications	341.70	360.50	336.60	0.95	0.642	0.811
Deletions + Duplications	306.20	338.00	311.10	0.91	0.779	0.871
Genic CNV rate 5
Deletions	0.32	0.16	0.27	2.03	0.079	0.073
Duplications	1.25	1.20	1.14	1.04	0.467	0.641
Deletions + Duplications	1.57	1.36	1.41	1.16	0.304	0.424
Genic CNV proportion 6
Deletions	0.11	0.08	0.11	1.38	0.176	0.116
Duplications	0.34	0.26	0.30	1.32	0.065	0.107
Deletions + Duplications	0.42	0.31	0.37	1.33	0.027*	0.044*
Genic CNV enrichment 7
Deletions	0.005	0.005	0.005	0.94	0.51	0.545
Duplications	0.009	0.008	0.009	1.23	0.195	0.176
Deletions + Duplications	0.008	0.007	0.007	1.17	0.231	0.298

¹Number of rare CNVs per sample.

²Proportion of samples with one or more rare CNVs.

³Total rare CNV kb length spanned.

⁴Average rare CNV size.

⁵Number of regions/genes spanned by rare CNVs.

⁶Proportion of rare CNVs with at least one gene.

⁷Number of regions/genes per total rare CNVs kb size.

T2D: type 2 diabetes; CNVs: Copy number variations; kb kilobases.

P-values were estimated by permutation (one-sided, 10,000 permutations). Corrected P-values were adjusted by sex, body mass index, triglycerides and ancestry (MDS1). *P < 0.05.