Table 1.

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

Effect	Chromosome	Odds ratio estimate	Lower CL*	Upper CL
§M CTNNB1 loss versus normal	3p22	2.682	1.394	5.162
NM CTNNB1 gain versus normal		0.323	0.147	0.71
BCL6 loss versus normal	3q27	0.55	0.27	1.12
M BCL6 gain versus normal		8.989	3.155	25.612
§M IL2 loss versus normal	4q26	3.697	1.774	7.705
NM IL2 gain versus normal		0.149	0.055	0.407
NM BAK1 loss versus normal	6p21.3	0.262	0.103	0.666
BAK1 gain versus normal		0.438	0.192	0.999
§M LTA loss versus normal	6p21.3	2.156	1.172	3.965
NM LTA gain versus normal		0.266	0.108	0.655
§NM FGFR1 loss versus normal	8p21	0.275	0.126	0.598
M FGFR1 gain versus normal		5.555	1.689	18.267
§NM PRKDC loss versus normal	8q11	0.276	0.11	0.692
M PRKDC gain versus normal		5.449	2.09	14.206
§NM MYC loss versus normal	8q24.12	0.221	0.097	0.503
M MYC gain versus normal		2.218	1.136	4.332
PTP4A3 loss versus normal	8q24.3	0.493	0.214	1.135
M PTP4A3 gain versus normal		12.158	3.461	42.71
§M CDKN2A loss versus normal	9p21	1.845	1.013	3.362
NM CDKN2A gain versus normal		0.14	0.056	0.35
M CDKN2B loss versus normal	9p21	3.256	1.676	6.325
CDKN2B gain versus normal		1.168	0.442	3.087
M LMO2 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
M FGF3 gain versus normal		7.819	3.286	18.604
NM CCND1 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
NM STCH gain versus normal		0.124	0.043	0.359
§M TFF1 loss versus normal	21q22.3	3.019	1.514	6.02
NM TFF1 gain versus normal		0.08	0.024	0.268

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