Table 1.

Predicted regions of recurrent amplification and homozygous deletion

Cytoband *Start (Mb) *Stop (Mb) *Size (Mb) *SampleMean dCHIP copy number Binary segmentation copy numberReal-time PCR copy numberRepresentative gene within intervalTotal no. genes *
1p34.239.5140.551.04H196310.611147.8 ± 32.3MYCL123
39.5540.911.36S0173T10.7820.7 ± 4.924
2p24.3-p24.214.2016.382.18S0172T14.21256.2 ± 13.7MYCN9
15.2517.061.81H5267.0542.3 ± 6.49
2q22.1141.71142.450.73H2122000.0 ± 0.0LRP1B 1
141.79142.780.99HCC95010.0 ± 0.01
141.94142.200.26H2126000.0 ± 0.01
142.00142.200.20H157000.1 ± 0.01
3p14.260.2960.780.49HCC95000.0 ± 0.0FHIT4
60.3260.400.08H2887000.0 ± 0.01
3q25.1152.82152.950.12H2882000.0 ± 0.0 §AADAC, SUCNR12
152.82152.950.12S0177T000.0 ± 0.0 §2
3q26.31-q27.1174.86184.529.66S0465T7.8510.3 ± 1.7PIK3CA41
182.50184.471.98S0515T13.2113.9 ± 0.412
7p12.1-q11.2253.1661.4911.34HCC82711.3941.7 ± 8.6EGFR50
54.2469.629.73AD347T9.8918.3 ± 4.8123
54.3755.6313.65S0480T13.71067.1 ± 10.912
8p12-p11.2238.0539.971.93MGH1622T10.41114.9 ± 5.9FGFR122
38.7339.841.11S0449T6.456.07 ± 1.711
8q24.13-q24.21126.60128.892.3H5246.65174.5 ± 39.3MYC6
127.46128.891.43HCC8276.968.6 ± 1.46
127.59130.833.24NCI-H238.0711.1 ± 2.811
127.90129.621.72H21223.6514.5 ± 4.36
128.44129.601.16H20877.9816.0 ± 5.84
9p238.619.120.51S0177T000.0 ± 0.0PTPRD2
8.799.550.77H358000.1 ± 0.0 §2
9.419.610.20HCC1171000.2 ± 0.0 §1
9.509.750.25H2347000.0 ± 0.0 §1
9p21.320.9022.942.03H2126000.0 ± 0.0CDKN2A35
21.2022.190.98HCC1359000.0 ± 0.021
21.5825.103.52HCC1171000.0 ± 0.011
21.7023.391.69H2882010.0 ± 0.06
21.8426.834.99HCC95000.0 ± 0.011
21.9522.090.14H2122000.0 ± 0.03
24.3424.700.36H157000.0 ± 0.0 §1
10q23.3189.0389.400.37H1607000.0 ± 0.0PTEN4
89.1889.880.69S0187T000.1 ± 0.04
89.3591.161.80S0189T000.1 ± 0.0 §22
12p11.2132.1733.020.85S0515T8.8710.8 ± 5.4PKP26
32.6936.593.90H20877.8811.4 ± 5.712
12q13.3-q14.156.2657.371.10H20878.8923.4 ± 11.3CDK420
55.8256.670.85HCC827 13.01330.3 ± 11.834
19q1234.0235.551.53S0524T6.776.8 ± 1.93CCNE112
34.7937.092.30S0188T7.9710.9 ± 3.212
22q11.21-q11.2216.9920.313.32H18196.8712.6 ± 4.8CRKL92
17.5121.443.93HCC5157.4714.0 ± 3.6169
18.4720.612.14S0380T6.458.4 ± 1.268
19.4520.751.29HCC13596.578.1 ± 1.748
  • NOTE: Predicted regions of recurrent amplification contain at least four SNPs at least 5 kb in size and with an inferred copy number of ≥7, which occur in two or more samples. Amplified regions separated by <2 Mb of unamplified sequenced have been combined. Predicted regions of homozygous deletion, at least 5 kb in size, contain at least four consecutive SNPs with inferred copy number = 0, which occur in two or more samples. Deleted regions separated by <2 Mb of undeleted sequence have been combined.

  • * Based on hg16 genome assembly.

  • Mean of amplified segments include sequences with copy number <7 if regions were combined.

  • Bold indicates only gene in region.

  • § These real-time PCR values denote targets that are not in an exon of the representative gene.

  • Less than 4 SNPs, but validated with real-time PCR.