Total 49 chromosomes. No. of cases Age Median (range) < Sex Female Male 65 (0-83) 9 (13%) 32 (48%) 26 (39%)

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Stanley Bell
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1 Supplementary Information Table S1: Demographic, clinical features and outcomes for 221 patients with hyperdiploid (49-65 chromosomes) AML stratified by modal chromosome number into two subgroups: 49 chromosomes and chromosomes. Total 49 chromosomes chromosomes p values No. of cases Age Median (range) < Sex Female Male 55 (0-87) 34 (15%) 100 (45%) 87 (39%) a : Mantel-Haenszel test for trend all other tests using chi-square * data available for 217 cases (98%) 65 (0-83) 9 (13%) 32 (48%) 26 (39%) 55 (0-87) 25 (16%) 68 (44%) 61 (40%) 0.80 a 90 (41%) 29 (43%) 61 (40%) (59%) 38 (57%) 93 (60%) Secondary disease 36 (16%) 6 (9%) 30 (19%) 0.05 WBC x10 9 /L* Median (range) 6.8 ( ) 9.5 ( ) 5.6 ( ) 0.05 a < (59%) 54 (25%) 36 (17%) 32 (49%) 18 (28%) 15 (23%) 95 (63%) 36 (24%) 21 (14%) Trial AML10/12/15 AML11/14/ (62%) 85 (38%) 40 (60%) 27 (40%) 96 (62%) 58 (38%) 0.71 Treatment Non-Intensive Intensive 10 (5%) 211 (95%) 3 (4%) 64 (96%) 7 (5%) 147 (95%) Complete remission % 42 63% 97 63% 1.00 Survival at 5 years 33 15% 10 15% 23 15%

2 Table S2: Outcome data for AML patients with hyperdiploid karyotypes categorised by being (a) purely numerical changes (b) structural abnormalities and (c) adverse cytogenetic risk aberrations. Patients were stratified by age into children (up to the age of 15) and adults (aged 16 or over). Outcome Purely Numerical (NUM) Structural (STR) Adverse Cytogenetics (ACR) Unadjusted analyses Odds/Hazard Ratios vs NUM, 95% CI, Complete remission* Adult 67% 60% 51% STR: 1.33 ( ) ACR: 1.88 ( ) Complete Child 100% 93% 70% STR: 5.55 ( ) remission* ACR: 9.35 ( ) 5-year Adult 22% 6% 5% STR: 1.70 ( ) Survival** ACR: 1.96 ( ) 5-year Child 67% 50% 20% STR:1.80 ( ) Survival** ACR: 2.84 ( ) 5-year RFS Adult 25% 10% 10% STR:1.74 ( ) ACR: 2.02 ( ) 5-year RFS Child 67% 54% 29% STR: 1.58 ( ) ACR:2.02 ( ) 5-year CIR Adult 59% 86% 76% STR:2.09 ( ) ACR: 2.12 ( ) 5-year CIR Child 22% 39% 71% STR: 2.22 ( ) ACR: 3.53 ( ) p-value for het. (2 d.f.) P for interaction Adjusted analyses Odds/Hazard Ratios vs NUM, 95% CI, 0.18 Not STR: 1.07 ( ) assessable ACR: 1.97 ( ) 0.09 Not assessable STR: 1.66 ( ) ACR: 2.09 ( ) 0.2 STR: 1.90 ( ) ACR: 3.52 ( ) STR: 1.78 ( ) ACR: 1.92 ( ) 0.6 STR: 1.48 ( ) ACR: 0.60 ( ) STR: 2.28 ( ) ACR: 1.97 ( ) 0.3 STR: 2.45 ( ) ACR:1.49 ( ) p-value for het (2 d.f.) P for interaction 0.16 Not assessable * CR data available for all 211 patients (100%) ** Survival data available for all 211 patients (100%) adverse cytogenetic risks were defined as those previous shown to be associated with poor outcome 2, namely-5/del(5q), -7/del(7q), t(9;22)(q34;q11), MLL translocations (except t(9;11)(p21;q23) and t(11;19)(q23;p13)) and abnormalities of 3q or 17p. 0.5 Note: Not assessable interactions due to insufficient events for logistic regression. 2

3 Table S3 : French-American-British (FAB) Classification for 1216 AML patients with three or more abnormalities, stratified by the presence or absence of a hyperdiploid karyotype (HK, chromosomes). The analysis was repeated focusing on children aged under 16. All HK patients were then further categorised as having (a) purely numerical changes (NUM) (b) structural abnormalities (STR) and (c) adverse cytogenetic risk aberrations (ACR). Total All cases Paediatric Cases HK cases NHK HK p value NHK HK p value NUM STR ACR p value No. of cases with data FAB* M0 M1 M2 M4 M5 M6 M7 RAEBt Other (85%) 181 (15%) 111 (78%) 32 (22%) 63 (35%) 43 (24%) 75 (41%) 98 (8%) 282 (23%) 269 (22%) 154 (13%) 144 (12%) 110 (9%) 56 (5%) 60 (5%) 43 (4%) 91 (9%) 235 (23%) 245 (24%) 125 (12%) 113 (11%) 94 (9%) 44 (4%) 53 (5%) 35 (3%) 7 (4%) 47 (26%) 24 (13%) 29 (16%) 31 (17%) 16 (9%) 12 (7%) 7 (4%) 8 (4%) (12%) 10 (9%) 14 (13%) 12 (11%) 33 (30%) 3 (3%) 16 (14%) 9 (8%) 1 (1%) 1 (3%) 7 (22%) 6 (19%) 0 6 (19%) 1 (3%) 9 (28%) 2 (6%) (5%) 20 (32%) 8 (13%) 6 10% 12 (19%) 3 (5%) 3 (5%) 4 (6%) 4 (6%) 1 (2%) 11 (26%) 5 (12%) 6 (14%) 9 (21%) 4 (9%) 6 (14%) 1 (2%) 0 3 (4%) 16 (21%) 11 (15%) 17 (23%) 10 (13%) 9 (12%) 3 (4%) 2 (3%) 4 (5%) 0.08 Notes: * Data was missing for 347 patients. Analysis is by chi-squared test adverse cytogenetic risks were defined as those previous shown to be associated with poor outcome 2, namely-5/del(5q), -7/del(7q), t(9;22)(q34;q11), MLL translocations (except t(9;11)(p21;q23) and t(11;19)(q23;p13)) and abnormalities of 3q or 17p. 3

4 Table S4: Differential chromosome gain or loss among all 221 patients with hyperdiploid (49-65 chromosomes) AML; categorised by the presence of purely numerical changes (NUM), structural abnormalities (STR) or adverse cytogenetic risk aberrations (ACR). Total NUM Chromosome Gains STR ACR Total Chromosome Losses NUM STR ACR (n=221) (n=75) (n=49) (n=97) p value (n=221) (n=75) (n=49) (n=97) p value 1 46 (21%) 5 (7%) 10 (20%) 31 (32%) < (<1%) 1 (1%) (10%) 4 (5%) 8 (16%) 9 (9%) (7%) 3 (4%) 6 (12%) 7 (7%) (3%) 1 (1%) 0 6 (6%) (19%) 13 (17%) 9 (18%) 19 (20%) (3%) 1 (1%) 0 6 (6%) (9%) 4 (5%) 3 (6%) 12 (12%) (9%) (20%) < (28%) 15 (20%) 16 (33%) 30 (31%) (2%) 0 1 (2%) 3 (3%) (6%) 2 (3%) 3 (6%) 8 (8%) (6%) (14%) < (64%) 50 (67%) 34 (69%) 58 (60%) (2%) 0 1 (2%) 3 (3%) (20%) 13 (17%) 9 (18%) 23 (24%) (<1%) (1%) (28%) 20 (27%) 8 (16%) 33 (34%) (<1%) (2%) (29%) 16 (21%) 5 (10%) 43 (44%) < (<1%) (1%) (9%) 9 (12%) 3 (6%) 7 (7%) (3%) (6%) (38%) 33 (44%) 16 (33%) 36 (37%) (5%) 1 (1%) 0 10 (10%) (27%) 22 (29%) 10 (20%) 27 (28%) (<1%) 1 (1%) 0 1 (1%) (12%) 6 (8%) 6 (12%) 14 (14%) (2%) 1 (1%) 0 4 (4%) (6%) 4 (5%) 3 (6%) 6 (6%) (2%) (4%) (3%) 0 3 (6%) 3 (3%) (6%) (13%) < (11%) 5 (7%) 8 (16%) 12 (12%) (3%) (7%) (28%) 20 (27%) 11 (22%) 31 (32%) (<1%) (1%) (14%) 7 (9%) 9 (18%) 14 (14%) (5%) (10%) (39%) 24 (32%) 15 (31%) 48 (49%) (2%) 0 1 (2%) 4 (4%) (15%) 4 (5%) 2 (4%) 28 (29%) < (<1%) (1%) X 24 (11%) 8 (11%) 5 (10%) 11 (11%) (2%) 1 (1%) 0 3 (3%) Y 16 (7%) 5 (7%) 2 (4%) 9 (9%) (2%) 1 (1%) 0 4 (4%) Chi-squared calculations carried out on all individual variables. 4

5 Table S5 : Demographic and clinical data for AML non-hyperdiploid patients with three or more chromosomal abnormalities presented according to the presence or absence of specific adverse cytogenetic abnormalities. Adverse cytogenetic abnormalities p values Present Absent No. of cases 1061 (79%) 281 (21%) Age Median (range) 61 (0-90) 45 (0-82) (6%) 60 (21%) (40%) 138 (49%) < a (55%) 83 (30%) Sex Female 462 (44%) 118 (42%) Male 599 (56%) 163 (58%) Secondary disease 227 (21%) 31 (11%) < WCC x10 9 /L 1 Median Range ( ) ( ) < (69%) 136 (49%) (20%) 78 (28%) < (12%) 64 (23%) Trial AML10/12/ (47%) 204 (73%) AML11/14/ (53%) 77 (27%) < Treatment Non-intensive 144 (14%) 16 (6%) Intensive 917 (86%) 265 (94%) Complete remission 2 50% 75% Unadjusted OR/HR ( ) < Adjusted OR/HR ( ) < year Survival 2 8% 29% Unadjusted OR/H ( ) < Adjusted OR/HR ( ) < year RFS 12% 31% Unadjusted OR/HR ( ) < Adjusted OR/HR ( ) < year CIR 73% 58% Unadjusted OR/HR ( ) < Adjusted OR/HR ( ) < adverse cytogenetic risks were defined as those previous shown to be associated with poor outcome 2, namely-5/del(5q), -7/del(7q), t(9;22)(q34;q11), MLL translocations (except t(9;11)(p21;q23) and t(11;19)(q23;p13)) and abnormalities of 3q or 17p. Notes: (1) Data was missing for 6 patients; (2) Outcome data restricted to those patients treated intensively; (3) Odds/Hazard Ratios ACR vs not (95% CI); (4) Mantel- Haenszel test for trend all other tests using chi-square 5

6 Table S6: Karyotypes of the 49 patients with hyperdiploid karyotype (49-65 chromosomes) classified in the STR subgroup. LRCG Karyotype (ISCN) RegID ,XX,+4,del(12)(p?),+13,+19[29] ,XX,t(7;12)(q36;p13),+8[9]/48,sl,+19[2]/ 50,sdl1,+4,+8[2]/ 51,sdl2,+X[6] ,XY,der(15)t(1;15)(q11;p11),+8,+8,+19[11] ,XY,+8,+11,+der(11)t(6;11)(p21;p13),+14,+21c[1]/50,idem,del(20)(p11p12)[2] ,XY,+8,+8,+8,t(11;19)(q23;p13.1)[30] ,XY,+4,+6,+9,del(11)(q23q25),+21[6] ,XX,+8,del(11)(q23),+13,+19[19] ~49,XX,del(1)(q31)[3],+6[11],+13[7],+19[15],+20[2][cp16] ,XX,+6,+7,+8,+10,der(13)t(2;13)(q14;p11),der(18)t(15;18)(q22;q23),+19,+21[3] ,XX,+3,-8,der(14)t(1;14)(q32;q32),+der(14)t(1;14)(q32;q32)x2,der(16)t(8;16)(q13;p13),+21,+22[17] ,XX,+2,del(7)(p11),+13,dup(15)(q11q22),+19,+21c,+21,+22[8] 46,XY,del(12)(p11p12)[3]/46,idem,del(13)(q14q22)[8]/46,idem,t(5;15)(q12~13;q14~15) 6629 /51~53,idem,+2,+6,+11,del(13)(q14q22),+del(13)(q14q22),+19,+21[cp3] ~49,XY,t(1;2)(q21;q37),+8,+9,add(13)(p1?),del(19)(q1?),+add(21)(q2?),add(22)(q2?),+mar[cp5] ,XY,+del(6)(q21)[1]/48,idem,+21[3]/49,idem,+8,+21[2] ~63,XY,+1,+2,+3,add(3)(p?),+5,+6,+8,+i(14)(q10),add(16)(p?),+21,add(21)(p?),+8~12mar[cp12] ,XX,t(4;17)(q28;q23),+8,+8,+9,t(11;19)(q23;p13),+der(19)t(11;19)(q23;p13) ~50,XY,-6,+15,+15,+18,+2r[cp9] ~50,XX,+X[2],+4[5],+14[7],+21[3],+22[6][cp8] ~60,XY,+X,+4,+4,+5,+6,+8,+8,add(10)(p1?3),+12,+16,+17,+18,+19,+20,+22[cp12] ,XY,t(6;9)(q21;q22),der(7)t(1;7)(q23~25;p13~15)[9]/50,idem,+der(6)t(6;9),+13,+15,+20[3]/51,XY,idem,+der(6)t(6;9),+8,+18,+18,+20[5] ,XX,+20[4]/48,sl,+8[5]/49,sdl1,+8[2]/47,sdl1,add(15)(q2?5),-20[3] ~61,XX,+1,+2,+2,+3,+4,+6,+8,+8,add(9)(q11),+13,+18,add(19)(p13),+20,+21,+21,+der(?)t(?;9)(?;q?21)[cp6] ,XX,r(21)(p1q22),+r(21)(p1q22)x2,+r[8]/50,idem,+r[2] ,X,t(X;18)(q2?6;q21),+6,+8,+13,+19[10] ,XY,+1,der(1;15)(q10;q10),+8[6]/48,idem,+8[2]/49,idem,+8,+13[20] ,XX,+X,t(1;22)(p13;q13),+6,+7,+8,+8,+10,+19,+20,+21,+22[20] ,XY,+1,+3,add(8)(p?),add(11)(p?)/50,idem,+add(8)(p?),+mar ,XY,+8,+9,+13,+mar/50,idem,add(4)(q?) ,XX,+8,del(11)(q?23),+13,+14,+19,+21, ,XY,+4,+10,add(12)(p?)x2,+14,+21,+22/53,idem, ,XX,+8,del(11)(q23),+13,+19,+21 6

7 ~51,XY,der(4)ins(4;5)(q2?8;q?1q?3),add(8)(p23)x2,add(9)(p11),t(12;19)(q1?1;q13),+14,+16,-21,+mar1,+mar2,+mar3x2[cp24] ~49,XY,+3mar[cp] ,XY,+del(1)(p1?),+8, ,X,add(X)(p22),t(1;12)(p?32;q?13),+i(1)(q10),+8,del(12)(q?22),+19[cp10] ~64,XY,+X,+1,del(1)(p13),+2,+3,+6,+8,+9,+10,+11,+12,+13,+14,+i(15)(q?),+16,+17,+18,+19,+20,+21,+22[cp4] ,XY,+8[2]/49,sl,+4,+8[3]/49,sdl1,del(9)(q22)[3]/49,sdl2,-4,+15,add(15)(q24)x2[4] ,XY,+i(1)(q10),+6,+8[10] ,XY,+8,+8,+add(8)(q24),del(13)(q12q14)[4]/50,idem,+mar[2] 54,X,der(Y)t(Y;7)(p11;p13),+2,+3,+6,+add(8)(p23)x2,add(13)(p1?)x2,+14,dic(14;19)(p11;q13.3)x2,der(15)t(13;15)(q14;p11)x2,+19,der(21;22)(q10;q10) x2,+5r[5] ,XY,del(11)(q23)[10]49,sl,+6,+8,+13[1]/50,sdl1,+19[2] ,XX,+9,+13,del(16)(q21q22),+22[10] ,XY,+1,der(1;21)(q10;q10),+2,+4,+7,del(7)(p15)x2,+8,der(8)t(7;8)(p15;q23)x2,+10,+19[5] ,XX,t(6;9)(p23;q34)[7]/52,idem,+5,+8,+9,+10,+13,+15[2] ,XY,+8,inv(12)(p13q1?3),+18,+20[51] ~62,XY,+1,+2,+6,+8,+9,+10,+11,+13,+14,+14,+add(15)(p11.2),+17,+18,+18,+20,+22,+mar1[cp8] ~51,XY,+4,+4,+8,del(9)(q1q3),+18,+18[cp6] ,XY,+Y[3]/48,idem,+Y[12]/49,idem,+Y,+Y[5] ,XY,+Y,add(7)(p21),+8,+9,+10,+11,add(11)(p15)x2,+12,+14,+20,+21,+22[7] Cell numbers are provided where known, where no cell numbers are given the abnormalities were clonal: present in 2 or more abnormal cells. The number of normal cells are omitted from the karyotypes. 7

8 Figure S1 : Kaplan-Meier plot of overall survival for 1387* intensively treated AML patients with three or more chromosomal abnormalities stratified by the presence or absence of a hyperdiploid karyotype (HK, chromosomes) (a) without further stratification, (b) in the absence of adverse features; (c) in the presence of adverse features. (a) (b) (c) * Survival data unavailable for 6 patients 8

9 Figure S2 : Forest plot of overall survival for 1387* intensively treated AML patients with three or more chromosomal abnormalities stratified by the presence or absence of a hyperdiploid karyotype (HK, chromosomes) in the presence or absence of adverse features. 9

10 Figure S3: (a) Overall survival, (b) Relapse-free survival and (c) Cumulative incidence of relapse in patients with hyperdiploid (49-65 chromosomes) AML defined by the presence of purely numerical (NUM), structural abnormalities (STR) or adverse cytogenetic risk aberrations (ACR). Patients were stratified by age into children (up to the age of 15) and adults (aged 16 or over). (a) (b) 10

11 (c) 11

CLINICAL STUDY REPORT SYNOPSIS

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