Table 1: Genes alterations that predict malignant (M, bolded) and nonmalignant (NM, italicized).

EffectChromosomeOdds ratio estimateLower CL*Upper CL

§MCTNNB1 loss versus normal3p222.6821.3945.162
NMCTNNB1 gain versus normal0.3230.1470.71
BCL6 loss versus normal3q270.550.271.12
MBCL6 gain versus normal8.9893.15525.612
§MIL2 loss versus normal4q263.6971.7747.705
NMIL2 gain versus normal0.1490.0550.407
NMBAK1 loss versus normal6p21.30.2620.1030.666
BAK1 gain versus normal0.4380.1920.999
§MLTA loss versus normal6p21.32.1561.1723.965
NMLTA gain versus normal0.2660.1080.655
§NMFGFR1 loss versus normal8p210.2750.1260.598
MFGFR1 gain versus normal5.5551.68918.267
§NMPRKDC loss versus normal8q110.2760.110.692
MPRKDC gain versus normal5.4492.0914.206
§NMMYC loss versus normal8q24.120.2210.0970.503
MMYC gain versus normal2.2181.1364.332
PTP4A3 loss versus normal8q24.30.4930.2141.135
MPTP4A3 gain versus normal12.1583.46142.71
§MCDKN2A loss versus normal9p211.8451.0133.362
NMCDKN2A gain versus normal0.140.0560.35
MCDKN2B loss versus normal9p213.2561.6766.325
CDKN2B gain versus normal1.1680.4423.087
MLMO2 loss versus normal11p134.9772.1611.466
LMO2 gain versus normal0.5730.2051.607
FGF3 loss versus normal11q130.8820.4471.741
MFGF3 gain versus normal7.8193.28618.604
NMCCND1 loss versus normal11q130.4030.220.736
CCND1 gain versus normal1.2390.6342.421
STCH loss versus normal21q11.11.7880.8333.839
NMSTCH gain versus normal0.1240.0430.359
§MTFF1 loss versus normal21q22.33.0191.5146.02
NMTFF1 gain versus normal0.080.0240.268

*CL: confidence limit, §: genes with loss and gain signifying aneuploidy.