Table 1.
Chromosome rearrangements of breast cancer cell lines HCC1187 (a), HCC1806 (b) and ZR-75-30 (c) as determined by array painting
| a | |||
|---|---|---|---|
| HCC1187 | |||
| Peak1 | Chromosome2 | Peak1 | Chromosome2 |
| A | der(1)(6pter->6p21.1::1p35.2->1q21.3::8p22->8pter)*3 | T | der(19)t(2;19)(p16;p13.3)* |
| B | 4 | U | del(18)(q21.2)4 |
| C | 3 | V | der(2;5) t(2;5)(p10;p10)del(2)(p16p25.1)* |
| D | der(X)(6pter->6p21.1::1p35->1p21.3::Xp11.22->Xqter) | W | 14 |
| E | der(8)(1q10->1q21.3::8p22->8q22.2::1p31.1->1pter)* | X | 15 |
| F | 5 | Y | 16 |
| G | der(20)t(2;20)(q10;q11.21)* | der(20)t(14;20)({14qter->14q24.3:}{20pter->20qter})$ | |
| H | der(8)t(1;8)(p31.1;q22.2)* | Z | 17 |
| I | 6 | a | 18 |
| J | der(1)t(1;8)(p13;q22.2)* | b | der(13)t(10;13)(p12;q21.31) * |
| K | 7 | c | i(13q)del(13)(q10q31) |
| L | X | d | 20 |
| M | del(7)(q36.1)3 | e | 19 |
| N | 8 | f | 21 |
| der(10)(13qter->13q21::10p12->10q23.1::19q13.41->19qter)*3 | g | 21 | |
| O | der(11)t(11;12)(p15.4;p11.22)del(11)(q13.5q21) | h | 22 |
| P | der(19)t(2;19)(p10;p13.3)* | i | der(19)t(1;19)(p36.22;q13.1)3 |
| Q | 9,10,11,12 | j | der(?)({20pter->20p13:}{:13q31.1->13qter})3 |
| R | der(11)t(11;16)(p15.3;q22.1)del(11)(q13.5q21)*3 | k | trc(1;X;1)(1qter->1p11::Xp21.3->Xq25::1p11->1qter) |
| S | der(16)(16pter->16q22.1::11p15.3->11p15.4::12p11.22->12pter)* | ||
| b | |||
|---|---|---|---|
| HCC1806 | |||
| Peak1 | Chromosome2 | Peak1 | Chromosome2 |
| A | der(2)(5pter->5p10::2p23.3->2q32.2::5p10->5pter)5 | S | del(11)(q23.1q23.3)3 |
| B | der(4)(1qter->1q10::6p22.3->6p21.1::4p15.33->4qter) * 3 | T | del(8)(p22p12) |
| C | der(5)t(1;5)(p10;q10) * | U | der(11)t(11;13;11;13;11;13)8 |
| D | 1 | V | der(10)t(6;10)(p22.3;p11.22)* |
| E | der(4)t(4;6)(p15.33;p21.1) * | W | der(15)(15p?->15q21.1:{:19q31.1-> 19qter}:10p12.31->10pter)3,7,9,12 |
| F | der(6)t(1;6)(q24.3;p21.1)* | X | der(17)({17pter->17qter}:3q26.32->3qter)$ |
| G | der(7)t(2;7)(q23.3;p12.3)del(7)(q36.1q36.2)* | Y | der(22)t(12;22)(q13.2;q13.2) * |
| der(14)(2qter->2q31::14p?->14qter)6+ | Z | der(14)t(6;14)(p22;p11.2)* | |
| H | 5 | a | 13 |
| I | 8 | b | 15 |
| der(3)t(3;16)(p21.1;p12.1)*3 | c | der(19)(1pter->1p36:{:19p13-> 19q13.2:}:8q22.2->8qter)#,3,9 |
|
| J | der(12)t(12;13)(p13.31;q12)del(13)(q14.11q32.3) | d | 16 |
| K | der(11)t(2;11)(p24.3;p15.4)del(11)(p12p10)3 | e | 17 |
| L | der(7)(8qter->8q23.3:{:7p15.2->7qtel}:17q23.2->17qtel)*7 | f | der(5)t(5;10)(p10;p10)* |
| der(16)(11qter->11q13.1::3pter->3p21.2::16p12->16qter)*7 | g | 18 | |
| i(10q) | h | der(21)t(3;21)(p21.31;p?)+ | |
| M | X | i | der(20)(10pter->10p12.31: {:15q14->15q21.1:}:20p12->20q11.2::7p15.2->7pter)*3,10 |
| der(20)(3qter->3q10::20p11.2->20q11.2::7p15.2->7pter)*3 | der(12)t(2;12)(p21;p10) | ||
| N | der(6)t(4;6)(p15.33;p21.1) * | j | del(6)(q10qter) |
| O | der(3;20)t(3;20)(q10;?)# | k | der(12)t(12;22)(q13.2;q13.2)*3,13 |
| P | 9 | l | der(21)t(21;22)(p?;p?)+ |
| der(2)(13qtel->13q32.3::13q14.11->13q12.13:{:11q13.5-> 11q14:}:2p11.2->2q23.3::7p12.3->7pter)* |
m | 20 | |
| Q | der(17)(3qter->3q26.32:{17pter->17q24.31:}:15q21.3->15qter)7 | n | 19 |
| R | der(9)t(9;12)(p21.1;q23) | o | der(19)t(18;19)(p10;q12?)9 |
| c | |||
|---|---|---|---|
| ZR-75-30 | |||
| Peak1 | Chromosome2 | Peak1 | Chromosome2 |
| A | dic(1;1)(1qter->1q10:{8q?;17q?}n:1q10->1qter)11 | Q | 8 |
| B | der(5)dup(5)(p)({5pter->5qter}{:13q21->13q33:}:7q11.22->7qter)* | R | der(7)t(5;7)(q21;q11.22)*3 |
| C | der(1;14)(1qter->1q10:{8q?;17q?}n:14q10->14qter)11 | S | 9 |
| D | der(14;20)(20pter->20p10::14q10->14q?:{8q?;17q?}n:14q?->14qter)11 | T | 10,11,12 |
| E | 2 | U | der(14;20)t(14;20)(q10;p10) |
| F | 1 | V | 15 |
| der(14)(8qter->8q11::8p11->8p11:{:17q25->17q21:}:14p10->14qter)11 | W | der(21?)({:21p10?->21qter}{:13q10?->13q21:})*+ | |
| G | der(1)t(1;21)(p35;q11)del(1)(p21p13)del(21)(q21q22) | X | 16 |
| H | i(13)(q10) | Y | 17 |
| I | 4 | Z | 18 |
| der(5)dup(5)(p)( {5pter->5q14:} {:13q21->13qter})* | a | del(6)(q13) | |
| J | 3 | b | del(11)(q13.5) |
| K | der(11)t(10;11)(q11.21;q24) * | c | del(16)(q22)3 |
| L | der(7)(7pter->7q21:{8q?;17q?}n:14q32->14qter) | d | 20 |
| M | 5 | e | del(19)(p11)3,4 |
| N | 6 | f | 19 |
| O | 7 | g | der(10)t(10;11)(q11.21;q24) * |
| P | X | h | 22 |
Asterisks mark translocations that include a balanced breakpoint, which is shown in bold type.
Structural rearrangements as determined by array painting. Breaks are given by banding position for identification: bands are deduced from array painting, not cytogenetic analysis. Notation is essentially according to ISCN, using the extended notation for complex translocations. For example, der(7)t(2;7)(q23.3;p12.3)del(7)(q36.1q36.2) indicates ‘derivative of chromosome 7 which is a translocation with chromosome 2, the breakpoints being at q23.3 on chromosome 2 and p12.3 on chromosome 7, and there is also a deletion on the chromosome 7 between q36.1 and q36.2’. As the chromosome is a der(7), i.e. the centromere belongs to chromosome 7, the notation implies that the majority of chromosome 7 is present, but chromosome 2 is only present distal to the breakpoint. In extended notation this is der(7)(2qter->2q23.3::7p12.3->7q36.1::7q36.2->7qter). The order of fragments in complex translocations was deduced from SKY and in come cases FISH. The orientation of fragments was generally deduced by assuming that telomeres were provided by telomeric ends of fragments, and in complex rearrangements by comparison with similar or reciprocal junctions. Where the orientation was not known the fragment is enclosed in curly brackets {}. Mapped breakpoint intervals are provided in Table 2 and Supplementary Tables 1 and 2. A ? is given in some instances where the breakpoint position was unclear. This was either:
due to a lack of BAC clones on the p-arm of the acrocentric chromosomes;
due to no obvious break on the chromosome despite its presence in the translocation (confirmed by FISH), suggesting possible fusion at the telomere;
or due to ‘noise’ in the array data at the breakpoint.
There is one der(?) in HCC1187 where it was unclear which chromosome provided the centromere.
Part or all of rearrangement not detected in the SKY data (http://www.path.cam.ac.uk/~pawefish/) because the pieces of chromosome involved were too small to be resolved or were misclassified, but was verified by FISH. In the SKY analysis of HCC1187, a dmin classifying as chromosome 22 had also been tentatively identified but it would have been too small to appear in the flow karyotype.
Based on their position in the flow karyotype these deleted chromosomes are expected to contain a duplication in addition to the deletion.
Hybridization suggests part of 2p is duplicated.
Chromosome fraction Peak G of HCC1806 was a rare example where two chromosomes that sorted together had fragments from the same normal chromosome, chromosome 2.
There are 4 examples of 3-way translocations where only one break was detected by array painting, suggesting possible telomere fusion. The orientation of the middle fragment was not in general determined.
Breakpoint positions for the 11 and 13 breaks are given in Supplementary Table 1. Banding is not given here as the arrangement of the different pieces of 11 and 13 have not been clarified by FISH.
Chromosome 19 breaks not well resolved on array and order of fragments not confirmed.
Chromosome painting confirms order and chromosome origin of fragments. Probably the chromosome identified as der(19)t(7;19;10) in SKY.
ZR-75-30 has multiple small fragments of 17, some interspersed with fragments of 8, which were not well resolved by the 1Mb array.
SKY suggests a possible isodicentric chromosome 15. This can not be detected by array painting.
The der(12)t(12;22), which was uncertain from SKY data was confirmed to be present in all cells.