Table 1.
Neuroblastoma tag-array design
|
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Cytogenetic region |
Expected copy number change |
Upper microsatellite boundary 1 |
Upper flanking marker 1 |
Upper chromosome start position 1 (bp) |
Lower microsatellite boundary 2 |
Lower flanking marker 2 |
Lower chromosome end position 2 (bp) |
Region size (bp) |
Number SNPs initial |
Number SNPs final |
Final SNP density (bp) |
| 1p36.33-p36.22 | Loss | D1S243 | TSC18751 | 2,510,666 | D1S1401 | TSC43572 | 10,794,210 | 8,283,544 | 45 | 29 | 285,639 |
| 2p24 | Gain | D2S398 | TSC107089 | 10,581,928 | D2S2201 | TSC227276 | 21,962,895 | 11,380,967 | 44 | 32 | 355,655 |
| 3p14.3-p25.3 | Loss | D3S4545 | TSC675529 | 8,437,192 | D3S3128 | TSC155917 | 51,901,506 | 43,464,314 | 43 | 29 | 1,498,769 |
| 4p16 | Loss | D4S134 | TSC167093 | 419,720 | D4S1302 | TSC102843 | 9,959,135 | 9,539,415 | 39 | 32 | 298,107 |
| 7q22-q31 | Neutral | D7S2331 | TSC84355 | 93,841,952 | D7S633 | TSC318118 | 115,530,749 | 21,688,797 | 20 | 18 | 1,204,933 |
| 9p21 | Loss | D9S1778 | TSC366933 | 20,883,776 | D9S304 | TSC412535 | 32,580,085 | 11,696,309 | 48 | 33 | 354,434 |
| 11p15 | Loss | D11S4177 | TSC215570 | 262,688 | D11S4012 | TSC184258 | 20,257,814 | 19,995,126 | 21 | 18 | 1,110,840 |
| 11q23 | Loss | D11S1762 | TSC633251 | 104,213,912 | D11S1347 | TSC162036 | 114,488,878 | 10,274,966 | 39 | 30 | 342,499 |
| 12p12-p13 | Neutral | D12S994 | TSC105684 | 482,849 | D12S1822 | TSC119496 | 24,016,517 | 23,533,668 | 21 | 16 | 1,470,854 |
| 14q32 | Loss | D17S1981 | TSC135928 | 87,118,454 | D14S159 | TSC190200 | 102,985,009 | 15,866,555 | 35 | 24 | 661,106 |
| 16p13-p11.2 | Loss | D16S2596E | TSC505340 | 9,679,608 | D16S3120 | TSC124901 | 26,590,967 | 16,911,359 | 53 | 38 | 445,036 |
| 17p13-p11.2 | Loss | D15S1258 | TSC567808 | 3,866,291 | D17S2006 | TSC849352 | 15,501,271 | 11,634,980 | 19 | 16 | 727,186 |
| 17q23-q25
|
Gain
|
D17S2028
|
TSC164191
|
52,111,987
|
D9S2021
|
TSC213136
|
73,985,534
|
21,873,547
|
40
|
31
|
705,598
|
-
Cytogenetic regions (column C1) exhibiting copy number change (C2) in neuroblastoma patients are shown. Upper (C3) and lower (C6) microsatellite boundaries and flanking markers (C4 and C7, respectively) are listed with nucleotide start (C5) and end (C8) positions. Region size (C9), initial number of SNPs selected (C10), and those that were informative (C11) are also shown. Final informative SNP density is listed (C12) in base pairs.
