Table 2. Replicated CNV associations and those at replicated loci.
Only one of the several associated CNVs mapping to the HLA in the reference sequence is shown for each of RA, T1D and CD. Further details of replication assays and methods are given in the supplementary material. AC_000138.1_44 is a novel sequence insertion present in the Venter genome sequence but not in the reference sequence and hence no chromosomal location is presented. Fitted number of classes – the number of diploid copy-number classes. P-value - Combined Controls – the p value from the frequentist association test combining UKBS and 58C as controls. log10(BF) - Combined Controls – the log10 of the Bayes Factor from the Bayesian association analysis combining UKBS and 58C as controls. OR - Combined Controls – The odds ratio estimated for each additional copy of the CNV based on both UKBS and 58C as controls. Extended Reference refers to the analogous quantities calculated in comparing cases of the disease in question with UKBS, 58C, and aetiologically-unrelated cases. Control MAF – The minor allele frequency in controls (UKBS +58C). Case MAF – The minor allele frequency in cases. Minor allele frequency is only estimated for CNVs with 3 or fewer copy number classes.
| Disease | CNV | Chromosome | Start (bp) |
Length (kb) |
Locus | Fitted number ofclasses |
P-value -Combined Controls |
P-value -Extended Reference |
log10(BF) -Combined Controls |
log10(BF) -Extended Reference |
OR -Combined Controls |
OR -Extended Reference |
Control MAF |
Case MAF |
Replication: cases / controls |
Replication P value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| T2D | CNVR5583.1 | 12 | 69,818,942 | 1.0 | TSPAN8 | 3 | 3.9E-05 | 2.5E-06 | 2.8 | 4.3 | 0.85 | 0.85 | 0.40 | 0.36 | 4549 / 5579# | 3.9E-05 |
| CD | CNVR2646.1 | 5 | 150,157,836 | 3.9 | IRGM | 3 | 1.1E-07 | 5.5E-05 | 5.8 | 4.1 | 0.68 | 0.75 | 0.07 | 0.10 | 6894 / 7977# | 7.5E-11 |
| CD | CNVR2647.1 | 5 | 150,183,562 | 20.1 | IRGM | 3 | 1.0E-07 | 4.3E-05 | 6.1 | 3.8 | 0.68 | 0.76 | 0.07 | 0.10 | 6894 / 7977# | 3.9E-10 |
| CD | CNVR2841.20 | 6 | 31,416,574 | 5.1 | HLA | 3 | 1.7E-05 | 1.1E-05 | 3.6 | 3.9 | 0.80 | 0.82 | 0.19 | 0.23 | NA | NA |
| T1D | CNVR2845.46 | 6 | 32,582,950 | 6.7 | HLA | 2 | 8.0E-153 | 2.1E-196 | 125.5 | 154.4 | 0.20 | 0.26 | 0.14 | 0.01 | NA | NA |
| RA | CNVR2845.14 | 6 | 32,609,209 | 4.0 | HLA | 4 | 1.4E-39 | 8.1E-60 | 51.5 | 73.5 | 1.77 | 1.83 | NA | NA | NA | NA |
| RA | CNVR1065.1 | 2⇒6 | 179,004,449 | 0.8 | HLA | 3 | 6.8E-49 | 1.6E-69 | 51.0 | 73.7 | 1.85 | 1.94 | 0.36 | 0.49 | NA | NA |
| T1D | CNVR1065.1 | 2⇒6 | 179,004,449 | 0.8 | HLA | 3 | 1.3E-29 | 1.1E-39 | 28.0 | 38.4 | 1.62 | 1.61 | 0.36 | 0.47 | NA | NA |
| RA |
AC_000138.1 _44 |
NA | NA | 5.6 | HLA | 3 | 8.3E-04 | 1.1E-05 | 1.3 | 2.7 | 0.87 | 0.86 | 0.25 | 0.28 | 3398 / 2743 | 1.1E-03 |
| T1D |
AC_000138.1 _44 |
NA | NA | 5.6 | HLA | 3 | 2.0E-31 | 2.7E-45 | 31.0 | 45.1 | 0.59 | 0.57 | 0.25 | 0.36 | 3883 / 2649 | 7.3E-50 |
| CD | CNVR7113.6 | 17 | 40,930,407 | 33.9 | Chr17inv | 3 | 1.2E-03 | 5.8E-04 | 1.4 | 1.6 | 1.15 | 1.14 | 0.24 | 0.21 | 4978 / 6069# | 8.6E-05 |
| T1D | CNVR7113.6 | 17 | 40,930,407 | 33.9 | Chr17inv | 3 | 1.6E-03 | 7.5E-04 | 1.0 | 1.2 | 1.13 | 1.12 | 0.24 | 0.21 | 7911 / 9395# | 4.6E-06 |
Replication sample includes WTCCC samples