Table 6

A table of the most significant results from the repeated association test between cases and controls including details of CNV region, cytoband location, event, region length, frequency in cases and controls, p-value and % of CNV overlap from Nexus output and CNV region, number of SNPs in segment, frequency in cases and controls, and p-value for QuantiSNP results
Nexus QuantiSNP
Region Cytoband location Event Region length Freq. in cases (%) Freq. in controls (%) p-value % of CNV Overlap* Region # SNPs in segment Freq. in cases (%) Freq. in controls (%) p-value
chr1:1,082,510-1,109,835 p36.33 CN Loss 27325 14.6 0.0 7.33E-11 100 chr1:1,064,487-1,096,336 8 0.0 0.3 0.62
chr1:192,838,687-193,008,078 q31.3 CN Gain 169391 15.6 0.0 1.29E-11 8 No overlapping CNV 0.0 0.0 NA
chr3:90,524,766-90,576,572 p11.1 CN Gain 51806 14.6 0.0 7.33E-11 100 chr3:90,421,209-90,576,572 19 16.7 0.0 4.06E-16
chr5:104,661,153-104,676,508 q21.3 CN Gain 15355 14.6 0.0 7.33E-11 100 chr5:104,667,691-104,675,112 5 1.0 0.0 0.05
chr6:31,945,137-31,947,946 p21.32 CN Loss 2809 14.6 0.0 7.33E-11 0 No overlapping CNV 0.0 0.0 NA
chr6:62,208,962-62,262,670 q11.1 CN Gain 53708 17.7 0.5 4.66E-11 100 chr6:62,176,064-62,260,258 11 15.6 0.0 3.55E-15
chr7:61,644,365-62,087,478 q11.21 CN Gain 443113 28.1 0.0 4.93E-21 100 chr7:61,667,556-61,990,710 18 7.3 0.0 9.79E-08
chr8:145,462,650-145,641,721 q24.3 CN Loss 179071 17.7 0.0 3.87E-13 100 No overlapping CNV 0.0 0.0 NA
chr9:138,620,572-138,764,838 q34.3 CN Loss 144266 15.6 0.0 1.29E-11 100 No overlapping CNV 0.0 0.0 NA
chr9:9,793,206-9,814,023 p23 CN Gain 20817 15.6 0.0 1.29E-11 100 chr9:9,778,666-9,809,028 21 1.0 0.0 0.05
chr11:50,339,475-50,370,127 p11.12 CN Gain 30652 21.9 0.0 3.08E-16 100 chr11:50,654,023-50,961,054 6 5.2 0.0 6.94E-06
chr11:54,468,566-54,554,469 q11 CN Gain 85903 20.8 0.3 3.30E-14 100 chr11:54,468,566-54,533,370 19 13.5 0.3 4.62E-12
chr12:36,616,479-36,650,608 q12 CN Gain 34129 19.8 0.5 1.66E-12 100 chr12:36,301,572-36,667,312 23 9.4 0.3 2.24E-08
chr14:104,706,668-104,721,437 q32.33 CN Loss 14769 14.6 0.0 7.33E-11 100 chr14:104,688,087-104,717,224 10 1.0 0.0 0.05
chr16:32,405,679-32,504,942 p11.2 CN Gain 99263 45.8 4.2 1.98E-22 100 chr16:32,443,063-32,460,991 23 45.8 20.1 1.96E-07
chr18:15,069,391-15,093,669 p11.21 CN Loss 24278 14.6 0.0 7.33E-11 100 chr18:15,045,092-15,219,051 20 8.3 0.0 1.17E-08
chr19:32,445,280-32,903,861 q12 CN Gain 458581 24.0 0.3 1.65E-16 100 chr19:32,520,504-32,810,457 28 11.5 0.3 3.27E-10

* Defined by Nexus as being reported in public repositories as being normal polymorphic in the "normal population".

Footnote:

The table shows CNVs showing significant frequency differences (at P < 1x10E-10) between HNPCC cases and controls in the analysis using Nexus.

For QuantiSNP results, Fisher's exact test was used for simple comparisons of CNV frequencies between cases and control (different p-values from Table 3).

Talseth-Palmer et al.

Talseth-Palmer et al. BMC Medical Genomics 2013 6:10   doi:10.1186/1755-8794-6-10

Open Data