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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

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

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

  1. * Defined by Nexus as being reported in public repositories as being normal polymorphic in the "normal population".
  2. Footnote:
  3. The table shows CNVs showing significant frequency differences (at P < 1x10E-10) between HNPCC cases and controls in the analysis using Nexus.
  4. 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).