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. Author manuscript; available in PMC: 2007 May 10.
Published in final edited form as: Mutat Res. 2007 Jan 2;615(1-2):1–11. doi: 10.1016/j.mrfmmm.2006.09.006

Table 2.

Individual BAC clones whose loss or gain are significantly correlated to genome-wide amplification, deletion, or the patient's smoking history*

RP11- clone chromosome F statistic Adjusted p-values Interaction p-values Smoking main p-values Gain/Loss/Either Chromosome Region (bp) candidate genes in region
422P24 1q21.3 7.806 0.060 0.400 0.373 Either 148,810,010–150,938,155 S100 protein family
525G13 1q23.3 12.997 0.008 0.998 0.115 Gain 162,588,522–162,784,903 UCK2
544B14 1q32.1 13.209 0.007 0.105 0.199 Gain/Either 203,329,259–203,409,712 IL10, IL19
115P16 8.086 0.084 0.651 0.231
520H14 1q42.1-q43 7.404 0.122 0.698 0.280 Gain 222,516,739–228,034,708 RHOU, ADPRT, TSNAX, CAPN9, WNT3A, WNT9A
12H2 8.086 0.084 0.651 0.231
375H24 1q42.13 7.608 0.109 0.619 0.253 Gain/Either 223,281,925–224,613,365 WNT3A, WNT9A
334N15 2q24.3 8.741 0.059 0.450 0.757 Gain 167,814,597–169,454,975 STK39
204J18 3p14.2 7.920 0.091 0.124 0.404 Gain 60,927,060–62,456,006 FHIT, PTPRG, ID2B
90K6 3q13.2 8.520 0.066 0.322 0.234 Gain 113,221,207–114,199,281 CD200
240H8 10.016 0.029 0.064 0.029
160L16 10.016 0.029 0.064 0.029
66O14 10.144 0.028 0.049 0.041
627P22 10.016 0.029 0.064 0.029
600K23 10.016 0.029 0.064 0.029
54N19 10.016 0.029 0.064 0.029
16G1 9.033 0.051 0.040 0.060
95N10 9.033 0.051 0.040 0.060
115G23 9.033 0.051 0.040 0.060
609L3 8.742 0.059 0.040 0.068
138E20 8.398 0.071 0.043 0.064
87M15 7p21.1–p11.2 9.033 0.051 0.040 0.060 Gain/Either 19,394,202–55,274,090 EGFR, IL6, HUS1, INHBA, GLI3, VRAL, MYCLK1, IGFBP3
85E16 9.033 0.051 0.040 0.060
75O22 7.523 0.114 0.044 0.082
121A8 9.033 0.051 0.040 0.060
462D19 8.457 0.069 0.133 0.050
100C21 9.146 0.048 0.031 0.078
111K18 9.033 0.051 0.040 0.060
137P13 9.146 0.048 0.031 0.078
84O18 9.033 0.051 0.040 0.060
832D10 9.033 0.051 0.040 0.060
81B20 9.033 0.051 0.040 0.060
339F13 9.033 0.051 0.040 0.060
97P11 7.167 0.138 0.071 0.030
251I15 7p11.2 10.772 0.011 0.036 0.047 Either 55,274,090–55,781,496
86P18 7.957 0.090 0.203 0.048
92J13 7.957 0.090 0.203 0.048
78C11 7q31.1-q31.32 7.957 0.090 0.203 0.048 Gain 106,955,503–121,128,048 MET, WNT2, CYR61, ING3, DOCK4, CBLL1
110C11 7.957 0.090 0.203 0.048
95L16 7.957 0.090 0.203 0.048
140O21 7.957 0.090 0.203 0.048
247A12 8.307 0.049 0.660 0.129
409K20 9q34.11-q34.13 8.307 0.049 0.660 0.129 Loss 128,543,247–130,681,562 ABL1
618A20 8.307 0.049 0.660 0.129
173B14 7.316 0.082 0.440 0.006
318G21 13q21.1-q31.3 7.316 0.082 0.440 0.006 Either 73,769,921–81,136,723 MYCBP2
600P1 8.348 0.043 0.548 0.002
238I24 14q24.3-qter 10.815 0.012 0.708 0.052 Loss 101,461,362–106,368,585 XRCC3, MARK3, ASPP1, AKT1, HSPCA
815P21 10.815 0.012 0.708 0.052
1057H19 11.557 0.008 0.376 0.085
22M5 11.680 0.007 0.291 0.150
297B9 11.680 0.007 0.291 0.150
389H23 11.680 0.007 0.291 0.150
540P6 chr22 11.680 0.007 0.291 0.150 Loss CHK2, BCR, TOP3B, p300, NF2, ST13, TIMP3
1078O11 13.257 0.003 0.266 0.063
395B24 13.257 0.003 0.266 0.063
1021O19 13.211 0.003 0.266 0.063
1113I2 9.728 0.021 0.402 0.034

Gain = associated with genome-wide copy number amplification

Loss = associated with genome-wide copy number deletion

Either = associated with genome-wide copy number aberration

*

BACs correlated with overall genomic instability (estimated proportions of copy number aberrations) at an adjusted p-value <0.10. F-statistics correspond to the full model fit described in the methods section. The adjusted p-values are calculated with respect to the adjusted distribution (obtained via permutation) of the maximum F statistic. The p-values listed for smoking status by BAC interactions and smoking status main effects are marginal. Values significant at p<0.05 are in bold. The adjusted p-values are calculated with respect to the permutation distribution discussed in the methods section. Interaction and smoking main effect p-values correspond to the un-adjusted p-values associated with the f-tests for the comparison of the full model to reduced model 1 and the comparison of reduced model 1 to reduced model 2, respectively.