Summary of BAC hybridization results
|
|
|
CHORI-253 |
RPCI-41 |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Duplicon location |
Duplicon name |
Orangutan clone no. |
Estimated copy no. |
No. of Seq variants |
Baboon clone no. |
Estimated copy no. |
No. of Seq variants |
||||
| 7p12 | PIR4 | 25 | 3.9 | 4 | 0 | 0.0 | 0 | ||||
| 11q14 | 11q | 8 | 1.3 | 1+ | 6 | 1.2 | 1 | ||||
| 12p11 | 12p | 10 | 1.9 | 2 | 5 | 1.0 | 1+ | ||||
| 22q11 | Igλ | 275 | 43.0 | nd | 230 | 44.2 | nd | ||||
| 22q12 | CHK2 | 6 | 0.9 | 1+ | 5 | 1.0 | 1 | ||||
| 4q24 | 4q24 | 11 | 1.7 | 1+ | 7 | 1.3 | 1+ | ||||
| Xq28 | ALD | 5 | 0.8 | 1 | 8 | 0.8 | 1 | ||||
| 22q11 | GGT1 | 6 | 0.9 | 1 | 12 | 2.3 | 1 | ||||
| 1p13 | IGSF3 | 2 | 0.3 | 1+ | 3 | 0.6 | 1 | ||||
| 10q26 | 10q26 | 9 | 1.4 | 1+ | 4 | 0.8 | 1 | ||||
| 7q36 | MLL3 | 5 | 0.8 | 2+ | 3 | 0.6 | 1+ | ||||
| 4p16.1 | 4p16.1 | 6 | 0.9 | 1 | 7 | 1.3 | 1+ | ||||
| 11p15 | LSP1 | 19 | 1.6 | 3+ | 26 | 5.0 | 3 | ||||
| 4p16.3
|
4p16.3
|
7
|
1.1
|
1+
|
7
|
1.3
|
1+
|
||||
-
A “+” after sequence variant number denotes another copy exists with one to four differences out of 500bp (99.8%–99.2% identity). PCR-generated probes (Supplemental Table 2) corresponding to each duplication (except Igλ which was not done (nd) due to high copy number) were hybridized to orangutan (CHORI-253) and baboon (RPCI-41) BAC libraries. The number of positives obtained and the fold coverage of the library (based on the segments screened) were used to estimate the copy number of each duplication in each species (no. positives/coverage, expected copies). Only one segment of each library was screened with the exception of the 11p15 duplicon in orangutan and Xq28 and 7p12 in baboon, where both library segments were screened. All BAC positives were PCR amplified with the hybridization primer pair, and then PCR products were directly sequenced. The PCR product sequences were compared to determine the number of different sequence variants for each duplicon within each species (Seq variants).
