Malignant and Nonmalignant Gene Signatures in Squamous Head and Neck Cancer

Table 1

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

Effect	Chromosome	Odds ratio estimate	Lower CL*	Upper CL
^§MCTNNB1 loss versus normal	3p22	2.682	1.394	5.162
^NMCTNNB1 gain versus normal		0.323	0.147	0.71
BCL6 loss versus normal	3q27	0.55	0.27	1.12
^MBCL6 gain versus normal		8.989	3.155	25.612
^§MIL2 loss versus normal	4q26	3.697	1.774	7.705
^NMIL2 gain versus normal		0.149	0.055	0.407
^NMBAK1 loss versus normal	6p21.3	0.262	0.103	0.666
BAK1 gain versus normal		0.438	0.192	0.999
^§MLTA loss versus normal	6p21.3	2.156	1.172	3.965
^NMLTA gain versus normal		0.266	0.108	0.655
^§NMFGFR1 loss versus normal	8p21	0.275	0.126	0.598
^MFGFR1 gain versus normal		5.555	1.689	18.267
^§NMPRKDC loss versus normal	8q11	0.276	0.11	0.692
^MPRKDC gain versus normal		5.449	2.09	14.206
^§NMMYC loss versus normal	8q24.12	0.221	0.097	0.503
^MMYC gain versus normal		2.218	1.136	4.332
PTP4A3 loss versus normal	8q24.3	0.493	0.214	1.135
^MPTP4A3 gain versus normal		12.158	3.461	42.71
^§MCDKN2A loss versus normal	9p21	1.845	1.013	3.362
^NMCDKN2A gain versus normal		0.14	0.056	0.35
^MCDKN2B loss versus normal	9p21	3.256	1.676	6.325
CDKN2B gain versus normal		1.168	0.442	3.087
^MLMO2 loss versus normal	11p13	4.977	2.16	11.466
LMO2 gain versus normal		0.573	0.205	1.607
FGF3 loss versus normal	11q13	0.882	0.447	1.741
^MFGF3 gain versus normal		7.819	3.286	18.604
^NMCCND1 loss versus normal	11q13	0.403	0.22	0.736
CCND1 gain versus normal		1.239	0.634	2.421
STCH loss versus normal	21q11.1	1.788	0.833	3.839
^NMSTCH gain versus normal		0.124	0.043	0.359
^§MTFF1 loss versus normal	21q22.3	3.019	1.514	6.02
^NMTFF1 gain versus normal		0.08	0.024	0.268

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