1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 4 4 4 4 4 4 4 4 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 14 14 14 14 14 14 14 14 14 14 14 17 17 Start 1 695 691 7 560 864 21 108 665 24 510 700 34 556 025 41 748 621 50 753 651 78 167 375 4 502 382 6 630 532 17 630 828 23 821 562 27 171 334 27 660 543 29 138 825 38 743 324 51 627 146 66 692 031 83 324 440 86 241 308 90 510 071 95 943 885 115 040 167 121 271 511 41 934 539 53 639 912 60 889 473 71 252 362 72 268 017 115 689 469 119 256 322 122 029 011 126 779 081 136 045 554 137 517 567 50 258 487 50 554 656 End 1 703 117 7 564 463 21 114 596 24 517 176 34 562 828 41 758 338 50 761 743 78 177 556 4 510 505 6 636 941 17 634 369 23 838 973 27 203 171 27 699 166 29 161 420 38 746 353 51 633 742 66 753 950 83 331 849 86 244 612 90 513 252 95 949 065 115 050 693 121 276 035 41 940 418 53 651 468 60 895 547 71 281 840 72 274 799 115 733 497 119 263 779 122 035 919 126 784 999 136 047 297 137 521 449 50 260 569 50 559 679 Length 7 427 3 600 5 932 6 477 6 804 9 718 8 093 10 182 8 124 6 410 3 542 17 412 31 838 38 624 22 596 3 030 6 597 61 920 7 410 3 305 3 182 5 181 10 527 4 525 5 880 11 557 6 075 29 479 6 783 44 029 7 458 6 909 5 919 1 744 3 883 2 083 5 024 Gain Loss Gain Gain Loss Gain Loss Loss Loss Loss Gain Loss Loss Loss Loss Gain Loss Gain Loss Loss Gain Loss Gain Loss Loss Gain Gain Gain Loss Gain Loss Gain Loss Gain Gain Gain Gain 2 3 2 9 3 2 4 8 2 2 2 10 4 3 2 4 2 10 2 3 2 2 3 2 2 3 6 6 2 4 2 2 7 2 2 2 3 CNVs in the Pig Genome Ssc.18508 Ssc.7991, Ssc.52309 Table 1. Distribution, length(bp), status and frequency of the 37 CNVRs detected by array CGH. CNVR ID Chr Status Animals Pig Unigenes CNVRs indicated in bold overlap segmental duplications. The genomic coordinates are relative to the Sus scrofa May 2008 assembly. doi:10.1371/journal.pone.0003916.t001 regions in other mammals [16,19,21–23]. In fact, this gene is actually overlapped by a putative human CNV, as seen in the Database of Genomic Variants [9]. Validation by RT-PCR Validation of the results was made with RT-PCR [32] on eight genomic regions (Figure 4) selected to represent a range of amplifications and deletions (CNVR IDs 2, 6, 7, 12, 23, 28, 33, and 37). The Data S1 file contains primer sequences, RT-PCR results, and the correlation between the array CGH and RT-PCR. From these eight regions, four were confirmed (CNVR IDs 2, 7, 28, and 37). For CNVR 2, an additional animal having this CNVR was found by RT-PCR which was not expected from the array data. Regarding the CNVR 7, a loss was found not only in the four animals predicted by our CNV calling pipeline but also in all the other test animals relative to the reference. For CNVR 37, the PCR was negative in the reference animal, while the test animals gave well-shaped sigmoidal curves, suggesting a loss in the reference animal (data not shown). Three regions were not confirmed (CNVR IDs 12, 33, and 23) and one gave ambiguous results (CNVR ID 6). PLoS ONE | www.plosone.org 4 December 2008 | Volume 3 | Issue 12 | e3916