Table 2.

STAC Output for Significant regions of Copy Number Gain in RB Tumors

Chromosomal Gain Regions (based on July 2003 map of UCSC browser)
arm	aberration	fp (chr)	Start (bp)	Stop (bp)	fp_pvalue	fp_confidence (1- fp_pvalue)
chr1q	Gain	chr1q21.1	143,000,001	150,000,000	0.047952048	0.952047952
chr1q	Gain	chr1q32.1	200,000,001	203,000,000	0.053946054	0.946053946
chr1q	Gain	chr1q32.1	203,000,001	206,000,000	0.01998002	0.98001998
chr1q	Gain	chr1q32.2	206,000,001	207,000,000	0.053946054	0.946053946
chr1q	Gain	chr1q32.3	207,000,001	208,000,000	0.01998002	0.98001998
chr1q	Gain	chr1q32.3	208,000,001	212,000,000	0.053946054	0.946053946
chr1q	gain	chr1q44	240,000,001	245,000,000	0.00999001	0.99000999
chr2p	gain	chr 2p25.3	2,000,001	3,000,000	0.037	0.963
chr2p	gain	chr 2p25.3	6,000,001	16,000,000	0.005	0.995
chr2p	gain	chr 2p24.3	16,000,001	19,000,000	0.018	0.982
chr2p	gain	chr 2p25.3	41,000,001	43,000,000	0.027	0.973
chr2p	gain	chr 2p14	64,000,001	70,000,000	0.005	0.995
chr2q	gain	chr 2q12	105,000,001	106,000,000	0.051948052	0.948051948
chr2q	gain	chr 2q33	206,000,001	207,000,000	0.051948052	0.948051948
chr2q	gain	chr 2q34	214,000,001	220,000,000	0.001998002	0.998001998
chr2q	gain	chr 2q35	220,000,001	222,000,000	0.006993007	0.993006993
chr2q	gain	chr 2q36–37	221,000,001	241,000,000	0.006993007	0.993006993
chr3p	gain	chr3p25.1	4,000,001	7,000,000	0.001998002	0.998001998
chr3p	gain	chr3p25.3	9,000,001	12,000,000	0.001998002	0.998001998
chr3q	gain	chr3p25.31	157,000,001	159,000,000	0.001998002	0.998001998
chr3q	gain	chr3q25	191,000,001	200,000,000	0.01998002	0.98001998
chr4p	gain	chr4p16	1	10,000,000	0.003996004	0.996003996
chr4q	gain	chr4q13.1	65,000,001	66,000,000	0.045954046	0.954045954
chr5q	gain	chr5q23.1	115,000,001	116,000,000	0.005994006	0.994005994
chr5q	gain	chr5q35.2	168,000,001	180,000,000	0.005994006	0.994005994
chr6q	gain	chr6q21	108,000,001	109,000,000	0.007992008	0.992007992
chr6q	gain	chr6q21	109,000,001	110,000,000	0.015984016	0.984015984
chr7q	gain	chr7q34	138,000,001	142,000,000	0.006993007	0.993006993
chr7q	gain	chr7q36.2-.3	152,000,001	159,000,000	0.002997003	0.997002997
chr8p	gain	chr8p23.3	1,000,001	3,000,000	0.005994006	0.994005994
chr8p	gain	chr8p21.2	23,000,001	24,000,000	0.005994006	0.994005994
chr9p	gain	chr9p24.1-23	6,000,001	11,000,000	0.005994006	0.994005994
chr9q	gain	chr9q31.1	97,000,001	98,000,000	0.016983017	0.983016983
chr10q	gain	chr10q23.31	92,000,001	94,000,000	0.004995005	0.995004995
chr11p	gain	chr11p15	10,000,001	17,000,000	0.005994006	0.994005994
chr11p	gain	chr11p12-11	43,000,001	44,000,000	0.04995005	0.95004995
chr11q	gain	chr11q14.2	86,000,001	87,000,000	0.000999001	0.999000999
chr11q	gain	chr11q23.2-.3	114,000,001	119,000,000	0.000999001	0.999000999
chr11q	gain	chr11q25	132,000,001	135,000,000	0.000999001	0.999000999
chr12p	gain	chr12p13.31	5,000,001	7,000,000	0.026973027	0.973026973
chr12q	gain	chr12q24.11	109,000,001	110,000,000	0.026973027	0.973026973
chr12q	gain	chr12q24.32	127,000,001	128,000,000	0.044955045	0.955044955
chr13q	gain	chr13q14.11	39,000,001	40,000,000	0.005994006	0.994005994
chr14q	gain	chr14q23.1	52,000,001	64,000,000	0.002797202	0.997202798
chr14q	gain	chr14q23.3	64,000,001	66,000,000	0.034965035	0.965034965
chr15q	gain	chr15q15	39,000,001	40,000,000	0.013986014	0.986013986
Arm	aberration	chr	Start (bp)	Stop (bp)	fp_pvalue	fp_confidence
chr15q	gain	chr15q21.1	43,000,001	44,000,000	0.001998002	0.998001998
chr15q	gain	chr15q26.1	90,000,001	91,000,000	0.031968032	0.968031968
chr15q	gain	chr15q26.3	96,000,001	100,000,000	0.013986014	0.986013986
chr16p	gain	chr16p13	2,000,001	7,000,000	0.003996004	0.996003996
chr17p	gain	chr17p11.2	17,000,001	18,000,000	0.002997003	0.997002997
chr17q	gain	chr17q24.3-25.2	70,000,001	80,000,000	0.015984016	0.984015984
chr19q	gain	chr19q13.3	51,000,001	63,000,000	0.003996004	0.996003996
chr20p	gain	chr 20p11.21	24,000,001	26,000,000	0.015984016	0.984015984
chr20q	gain	chr 20q13.12	43,000,001	44,000,000	0.000999001	0.999000999
chr20q	gain	chr 20q13.33	60,000,001	63,000,000	0.000999001	0.999000999
chr21q	gain	chr 21q21.3	26,000,001	27,000,000	0.03996004	0.96003996
chr21q	gain	chr 21q22.3	42,000,001	43,000,000	0.003996004	0.996003996
chr22q	gain	chr 22q11.1-.22	14,000,001	22,000,000	0.008991009	0.991008991
Chromosomal Loss Regions
chr1p	loss	chr1p21.1-13.3	106,000,001	108,000,000	0.017982018	0.982017982
chr1q	loss	chr1q31.1	183,000,001	184,000,000	0.005994006	0.994005994
chr2q	loss	chr 2q32.1	185,000,001	186,000,000	0.024975025	0.975024975
chr2q	loss	chr 2q33.1	205,000,001	206,000,000	0.001998002	0.998001998
chr2q	loss	chr 2q33.3	208,000,001	209,000,000	0.001998002	0.998001998
chr3p	loss	chr3p13	70,000,001	71,000,000	0.010989011	0.989010989
chr3p	loss	chr3p12.1	86,000,001	87,000,000	0.024975025	0.975024975
chr6q	loss	chr6q22.33	128,000,001	129,000,000	0.000999001	0.999000999
chr7q	loss	chr7q21.11	80,000,001	81,000,000	0.002997003	0.997002997
chr9p	loss	chr9p22.3-22.2	16,000,001	17,000,000	0.032967033	0.967032967
chr11q	loss	chr11q13.5-14.1	77,000,001	79,000,000	0.034965035	0.965034965
chr18q	loss	chr18q22.2	68,000,001	70,000,000	0.021978022	0.978021978
chr21q	loss	chr 21q21.1	18,000,001	22,000,000	0.00999001	0.99000999
chr21q	loss	chr 21q21.1	22,000,001	24,000,000	0.047952048	0.952047952