Table 2

Duplications present in TKI-resistant CML samples

IDChromosomeStarting positionEnding positionLength, MbCandidate genesTreatmentDisease status
27 2p21 42500507 43164500 0.66 KCNG3, MTA3, OXER1, HAAO Imatinib Unknown 
16 2q36 227668515 227890738 0.22 RHBDD1, COL4A4, COL4A3 HU, imatinib CML 
25 2q37 231049480 231135251 0.09 SP100 HU + IFN, imatinib Unknown 
11 8p-q 180568 146263538 146.1 Trisomy 8 Imatinib CML in hematologic remission 
33-R 8p-q 180568 146263538 146.1 Trisomy 8 DA, imatinib Myeloid blast crisis 
42-R* 8p-q 180568 146263538 146.1 Trisomy 8 HU, imatinib CML in acceleration 
38-R 8q24 138371297 139210288 0.84 Hypothetical protein FLJ45872 HU, imatinib CML in hematologic remission 
45-R 8q11 53916301 146263538 92.34  Imatinib Unknown 
27 9q34 130686824 138303776 7.62 Duplication ABL1 Imatinib Unknown 
16 9q34 130686824 138303776 7.62 Duplication ABL1 HU, imatinib CML 
24 9q34 130641293 138303776 7.66 Duplication ABL1 Imatinib Unknown 
5 9q34 130737915 138303776 7.57 Duplication ABL1 Imatinib CML 
33-R* 9q34 130737915 138303776 7.57 Duplication ABL1 DA, imatinib Myeloid blast crisis 
40-R* 9q34 130659964 138303776 7.64 Duplication ABL1 Imatinib Myeloid blast crisis 
41-R 10p11 35,083,411 35,252,155 0.16 PARD3 Imatinib Unknown 
10 11q24 122000841 122217796 0.22 STS-1 / CBL interacting protein Imatinib, dasatinib, HU CML in hematologic remission 
4-R 15q21 48682473 48832856 0.15 TRPM7, SPPL2A Imatinib CML in hematologic remission 
42-R* 17q 33318471 47862514 14.54 STAT3, STAT5A/B HU, imatinib CML in acceleration 
45-R* 17q 37042201 78599918 41.55 STAT3, STAT5A/B Imatinib Unknown 
46-R* 17p-q 18857962 78599918 59.74 STAT3, STAT5A/B Unknown CML 
21-R 20p13 1658272 1861481 0.2 SIRPA Imatinib Unknown 
27 22q11 14441016 21947838 7.51 Duplication BCR Imatinib Unknown 
16 22q11 14441016 21947838 7.51 Duplication BCR HU, imatinib CML 
24 22q11 14441016 21947838 7.51 Duplication BCR Imatinib Unknown 
5 22q11 14441016 21947838 7.51 Duplication BCR Imatinib CML 
33-R* 22q11 14441016 21947838 7.51 Duplication BCR DA, imatinib Myeloid blast crisis 
40-R* 22q11 14441016 21960478 7.51 Duplication BCR Imatinib Myeloid blast crisis 
34 22q11 14441016 21947838 7.51 Duplication BCR HU, ICT, imatinib, dasatinib Lymphoid blast crisis 
33-R* X 1 154824264 154 Trisomy X DA, imatinib Myeloid blast crisis 
IDChromosomeStarting positionEnding positionLength, MbCandidate genesTreatmentDisease status
27 2p21 42500507 43164500 0.66 KCNG3, MTA3, OXER1, HAAO Imatinib Unknown 
16 2q36 227668515 227890738 0.22 RHBDD1, COL4A4, COL4A3 HU, imatinib CML 
25 2q37 231049480 231135251 0.09 SP100 HU + IFN, imatinib Unknown 
11 8p-q 180568 146263538 146.1 Trisomy 8 Imatinib CML in hematologic remission 
33-R 8p-q 180568 146263538 146.1 Trisomy 8 DA, imatinib Myeloid blast crisis 
42-R* 8p-q 180568 146263538 146.1 Trisomy 8 HU, imatinib CML in acceleration 
38-R 8q24 138371297 139210288 0.84 Hypothetical protein FLJ45872 HU, imatinib CML in hematologic remission 
45-R 8q11 53916301 146263538 92.34  Imatinib Unknown 
27 9q34 130686824 138303776 7.62 Duplication ABL1 Imatinib Unknown 
16 9q34 130686824 138303776 7.62 Duplication ABL1 HU, imatinib CML 
24 9q34 130641293 138303776 7.66 Duplication ABL1 Imatinib Unknown 
5 9q34 130737915 138303776 7.57 Duplication ABL1 Imatinib CML 
33-R* 9q34 130737915 138303776 7.57 Duplication ABL1 DA, imatinib Myeloid blast crisis 
40-R* 9q34 130659964 138303776 7.64 Duplication ABL1 Imatinib Myeloid blast crisis 
41-R 10p11 35,083,411 35,252,155 0.16 PARD3 Imatinib Unknown 
10 11q24 122000841 122217796 0.22 STS-1 / CBL interacting protein Imatinib, dasatinib, HU CML in hematologic remission 
4-R 15q21 48682473 48832856 0.15 TRPM7, SPPL2A Imatinib CML in hematologic remission 
42-R* 17q 33318471 47862514 14.54 STAT3, STAT5A/B HU, imatinib CML in acceleration 
45-R* 17q 37042201 78599918 41.55 STAT3, STAT5A/B Imatinib Unknown 
46-R* 17p-q 18857962 78599918 59.74 STAT3, STAT5A/B Unknown CML 
21-R 20p13 1658272 1861481 0.2 SIRPA Imatinib Unknown 
27 22q11 14441016 21947838 7.51 Duplication BCR Imatinib Unknown 
16 22q11 14441016 21947838 7.51 Duplication BCR HU, imatinib CML 
24 22q11 14441016 21947838 7.51 Duplication BCR Imatinib Unknown 
5 22q11 14441016 21947838 7.51 Duplication BCR Imatinib CML 
33-R* 22q11 14441016 21947838 7.51 Duplication BCR DA, imatinib Myeloid blast crisis 
40-R* 22q11 14441016 21960478 7.51 Duplication BCR Imatinib Myeloid blast crisis 
34 22q11 14441016 21947838 7.51 Duplication BCR HU, ICT, imatinib, dasatinib Lymphoid blast crisis 
33-R* X 1 154824264 154 Trisomy X DA, imatinib Myeloid blast crisis 

Copy number alterations (CNAs) in TKI-resistant samples without a matched diagnostic sample are shown with plain numbers in the column “ID.” CNAs in TKI-resistant samples with a matched diagnostic sample with the CNAs being present in both the diagnostic sample and the resistant sample are shown with numbers + “R” in the column “ID.” CNAs which were newly acquired in matched resistant samples compared to the diagnostic samples are shown with numbers + “R*” in the column “ID.”

ID indicates patient ID; Starting position, start position of genomic lesion; Ending position, end position of genomic lesion; HU, hydroxyurea; DA, daunorubicin plus cytarabine; ICT, induction chemotherapy; and IFN, interferon-α.

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