Supplementary Information
The mutational oncoprint of recurrent cytogenetic abnormalities in adult
patients with de novo acute myeloid leukemia
Ann-Kathrin Eisfeld1,*, Krzysztof Mrózek1,*, Jessica Kohlschmidt1,2, Deedra Nicolet1,2,
Shelley Orwick3, Christopher J. Walker1, Karl W. Kroll3, James S. Blachly3, Andrew J. Carroll4,
Jonathan E. Kolitz5, Bayard L. Powell6, Eunice S. Wang7, Richard M. Stone8, Albert de la
Chapelle1, John C. Byrd3,#, and Clara D. Bloomfield1,#
1. The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
2. Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
3. Division of Hematology, Department of Internal Medicine, The Ohio State University
Comprehensive Cancer Center, Columbus, OH, USA
4. University of Alabama at Birmingham, Birmingham, AL, USA
5. Monter Cancer Center, Hofstra North Shore-Long Island Jewish School of Medicine,
Lake Success, NY, USA
6. Comprehensive Cancer Center of Wake Forest University, Winston-Salem, NC, USA
7. Roswell Park Cancer Institute, Buffalo, NY, USA
8. Dana-Farber/Partners CancerCare, Boston, MA, USA
The authors declare no conflicts of interest.
* These authors contributed equally to this work.# These senior authors contributed equally to this work.
Running title: Mutational oncoprint of recurrent cytogenetic groups in AML
1
Participating institutions
The following Cancer and Leukemia Group B (CALGB)/Alliance for Clinical Trials in
Oncology (Alliance) institutions participated in this study and contributed at least five patients.
For each of these institutions, the current or last principal investigator and the cytogeneticists
who analyzed the cases are listed as follows:
The Ohio State University Medical Center, Columbus, OH: Richard M. Goldberg, Karl S. Theil,
Diane Minka and Nyla A. Heerema; North Shore University Hospital, Manhasset, NY: Daniel R.
Budman, Prasad R. K. Koduru, Ayala Aviram-Goldring and Chandrika Sreekantaiah; Wake
Forest University School of Medicine, Winston-Salem, NC: Heidi Klepin, P. Nagesh Rao,
Wendy L. Flejter and Mark Pettenati; Roswell Park Cancer Institute, Buffalo, NY: Ellis G.
Levine and AnneMarie W. Block; Dana Farber Cancer Institute, Boston, MA: Harold J. Burstein,
Ramana V. Tantravahi, Leonard L. Atkins, Cynthia C. Morton and Paola Dal Cin; Washington
University School of Medicine, St. Louis, MO: Nancy L. Bartlett, Michael S. Watson, Eric C.
Crawford, Jaime Garcia-Heras, Peining Li and Shashikant Kulkarni; University of Iowa
Hospitals, Iowa City, IA: Daniel A. Vaena and Shivanand R. Patil; University of Chicago
Medical Center, Chicago, IL: Hedy L. Kindler, Diane Roulston, Katrin M. Carlson, Yanming
Zhang and Michelle M. LeBeau; University of North Carolina, Chapel Hill, NC: Thomas C.
Shea and Kathleen W. Rao; Duke University Medical Center, Durham, NC: Jeffrey Crawford,
Sandra H. Bigner, Mazin B. Qumsiyeh, John Eyre and Barbara K. Goodman; University of
Maryland Cancer Center, Baltimore, MD: Martin J. Edelman, Joseph R. Testa, Maimon M.
Cohen, Judith Stamberg and Yi Ning; Dartmouth Medical School, Lebanon, NH: Konstantin
Dragnev, Doris H. Wurster-Hill and Thuluvancheri K. Mohandas; Rhode Island Hospital,
Providence, RI: Howard Safran, Teresita Padre-Mendoza, Jennifer A. Ahearn, Hon Fong L.
2
Mark, Shelly L. Kerman and Aurelia Meloni-Ehrig; Ft. Wayne Medical Oncology/Hematology,
Ft. Wayne, IN: Sreenivasa Nattam and Patricia I. Bader; Christiana Care Health Services, Inc.,
Newark, DE: Gregory Masters, Digamber S. Borgaonkar, Jeanne M. Meck, Kathleen Richkind
and Eduardo Cantu; Weill Medical College of Cornell University, New York, NY: Scott
Tagawa, Ram S. Verma, Prasad R.K. Koduru, Andrew J. Carroll and Susan Mathew; Western
Pennsylvania Hospital, Pittsburgh, PA: John Lister and Gerard R. Diggans; Massachusetts
General Hospital, Boston, MA: David Ryan, Justin Gainor, Leonard L. Atkins, Cynthia C.
Morton and Paola Dal Cin; University of Vermont Cancer Center, Burlington, VT: Claire
Verschraegen, Elizabeth F. Allen and Mary Tang; SUNY Upstate Medical University, Syracuse,
NY: Stephen L. Graziano, Larry Gordon and Constance K. Stein; Moores University of
California San Diego Cancer Center, San Diego, CA: Barbara A. Parker, Renée Bernstein and
Marie L. Dell'Aquila; Eastern Maine Medical Center, Bangor, ME: Thomas H. Openshaw,
Laurent J. Beauregard and Sarah South; Long Island Jewish Medical Center, Lake Success, NY:
Daniel R. Budman, Prasad R. K. Koduru, Ayala Aviram-Goldring and Chandrika Sreekantaiah;
University of Massachusetts Medical Center, Worcester, MA: William V. Walsh, Philip L.
Townes, Vikram Jaswaney, Kathleen Richkind, Michael J. Mitchell and Patricia Miron; Mount
Sinai School of Medicine, New York, NY: Lewis R. Silverman and Vesna Najfeld; Walter Reed
National Military Medical Center, Bethesda, MD: Mary Kwok, Rawatmal B. Surana, Digamber
S. Borgaonkar and Kathleen E. Richkind; University of Minnesota, Minneapolis, MN: Bruce A.
Peterson, Diane C. Arthur and Betsy A. Hirsch; University of Alabama at Birmingham,
Birmingham, AL: Robert Diasio and Andrew J. Carroll; University of Tennessee Cancer Center,
Memphis, TN: Harvey B. Niell and Sugandhi A. Tharapel; University of Illinois, Chicago, IL:
Arkadiusz Z. Dudek, Maureen M. McCorquodale, Kathleen E. Richkind and Valerie Lindgren;
University of Missouri/Ellis Fischel Cancer Center, Columbia, MO: Clint Kingsley, Jeffrey R.
3
Sawyer, Tim Hui-Ming Huang and Linda M. Pasztor; Virginia Commonwealth University,
Richmond, VA: Steven Grossman and Colleen Jackson-Cook; University of Puerto Rico, San
Juan, Puerto Rico: Eileen I. Pacheco, Ramana V. Tantravahi, Leonard L. Atkins, Cynthia C.
Morton and Paola Dal Cin; University of Nebraska Medical Center, Omaha, NE: Apar Ganti and
Warren G. Sanger; University of California at San Francisco, San Francisco, CA: Charalambos
Andreadis and Kathleen E. Richkind; Georgetown University Medical Center, Washington, DC:
Minnetta C. Liu, Jeanne M. Meck and Christine Bryke; Nevada Cancer Research Foundation
CCOP, Las Vegas, NV: John Ellerton and Marie L. Dell'Aquila.
4
Supplementary Table S1. Pretreatment clinical characteristics of patients with de novo acute myeloid leukemia, listed for the total
cohort and separately for the five major cytogenetic groups
Characteristic Alln = 1603
CN-AMLn = 716
Complex karyotypen = 137
CBF-AMLn = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
Age, years <0.001
Median Range
52 17-85
53 17-83
57 18-84
41 18-74
48 17-84
58 19-85
Sex, n (%) <0.001
Male 914 (57) 370 (52) 92 (67) 105 (59) 128 (57) 219 (63)
Female 689 (43) 346 (48) 45 (33) 72 (41) 96 (43) 130 (37)
Race, n (%) 0.007
White 1376 (88) 638 (91) 114 (87) 139 (81) 186 (85) 299 (86)
Non-white 195 (12) 66 (9) 17 (13) 32 (19) 32 (15) 48 (14)
Hemoglobin, g/dl 0.02
Median Range
9.2 2.3-25.1
9.3 4.2-25.1
9.1 5.5-14.7
8.9 3.1-14.2
9.4 5.6-15.8
9.1 2.3-14.1
Platelet count, x109/l <0.001
Median Range
55 4-989
57 5-850
50 4-376
38 7-369
64 8-387
60 4-989
WBC, x109/l <0.001
5
Median Range
23.2 0.4-475.0
29.5 0.6-475.0
7.6 0.7-225.3
22.8 0.4-244.3
25.9 1.0-320.0
13.2 0.6-276.8
Blood blasts, % <0.001
Median Range
52 0-99
57 0-99
34 0-99
49 1-97
57 0-99
44 0-99
Bone marrow blasts, % <0.001
Median Range
66 0-99
68 0-99
58 13-98
56 2-95
72 12-97
64 0-97
Extramedullary involvement, n (%)
377 (25) 200 (29) 19 (15) 48 (28) 56 (27) 54 (17)<0.001
Abbreviations: n, number; CN-AML, cytogenetically normal acute myeloid leukemia; CBF-AML, core-binding factor AML; WBC, white blood
count.
a P-values are from Wilcoxon rank-sum test for continuous variables and Fisher’s exact test for discrete variables. The P-values reported compare
the five major cytogenetic groups.
6
Supplementary Table S2. Frequencies of single gene mutations detected in patients with de novo acute myeloid leukemia, listed for the
total cohort and separately for the five major cytogenetic groups
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
AKT1, n (%) 1.00
Mutated 6 (0) 2 (0) 2 (1) 0 (0) 1 (0) 1 (0)
Wild-type 1597 (100) 714 (100) 135 (99) 177 (100) 223 (100) 348 (100)
ARAF, n (%) 0.77
Mutated 8 (0) 7 (1) 0 (0) 1 (1) 0 (0) 0 (0)
Wild-type 1595 (100) 709 (99) 137 (100) 176 (99) 224 (100) 349 (100)
ASXL1, n (%) Mutated 112 (7) 44 (6) 7 (5) 2 (1) 15 (7) 44 (13)
<0.001
Wild-type 1491 (93) 672 (94) 130 (95) 175 (99) 209 (93) 305 (87)
ATM, n (%) 1.00
Mutated 11 (1) 7 (1) 0 (0) 1 (1) 1 (0) 2 (1)
Wild-type 1592 (99) 709 (99) 137 (100) 176 (99) 223 (100) 347 (99)
AXL, n (%) 1.00
Mutated 25 (2) 12 (2) 1 (1) 4 (2) 4 (2) 4 (1)
7
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
Wild-type 1578 (98) 704 (98) 136 (99) 173 (98) 220 (98) 345 (99)
BCL2, n (%) 1.00
Mutated 1 (0) 1 (0) 0 (0) 0 (0) 0 (0) 0 (0)
Wild-type 1602 (100) 715 (100) 137 (100) 177 (100) 224 (100) 349 (100)
BCOR, n (%) <0.001
Mutated 83 (5) 27 (4) 6 (4) 1 (1) 18 (8) 31 (9)
Wild-type 1520 (95) 689 (96) 131 (96) 176 (99) 206 (92) 318 (91)
BCORL1, n (%) 0.96
Mutated 43 (3) 20 (3) 1 (1) 7 (4) 3 (1) 12 (3)
Wild-type 1560 (97) 696 (97) 136 (99) 170 (96) 221 (99) 337 (97)
BRAF, n (%) 0.16
Mutated 7 (0) 1 (0) 0 (0) 1 (1) 0 (0) 5 (1)
Wild-type 1596 (100) 715 (100) 137 (100) 176 (99) 224 (100) 344 (99)
BRD4, n (%) 0.56
Mutated 18 (1) 6 (1) 3 (2) 0 (0) 2 (1) 7 (2)
Wild-type 1585 (99) 710 (99) 134 (98) 177 (100) 222 (99) 342 (98)
8
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
BRINP3, n (%) 1.00
Mutated 24 (1) 10 (1) 2 (1) 2 (1) 5 (2) 5 (1)
Wild-type 1579 (99) 706 (99) 135 (99) 175 (99) 219 (98) 344 (99)
BTK, n (%) 1.00
Mutated 5 (0) 2 (0) 1 (1) 0 (0) 1 (0) 1 (0)
Wild-type 1598 (100) 714 (100) 136 (99) 177 (100) 223 (100) 348 (100)
CBL, n (%) 1.00
Mutated 29 (2) 14 (2) 0 (0) 2 (1) 3 (1) 10 (3)
Wild-type 1574 (98) 702 (98) 137 (100) 175 (99) 221 (99) 339 (97)
CCND1, n (%) 0.35
Mutated 8 (0) 4 (1) 2 (1) 2 (1) 0 (0) 0 (0)
Wild-type 1595 (100) 712 (99) 135 (99) 175 (99) 224 (100) 349 (100)
CCND2, n (%) 0.006
Mutated 17 (1) 6 (1) 0 (0) 8 (5) 2 (1) 1 (0)
Wild-type 1586 (99) 710 (99) 137 (100) 169 (95) 222 (99) 348 (100)
CEBPA, n (%) <0.001
9
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
Mutated 89 (6) 71 (12) 2 (2) 0 (0) 1 (1) 15 (5)
Wild-type 1286 (94) 540 (88) 118 (98) 177 (100) 172 (99) 279 (95)
CSNK1A1, n (%) 0.28
Mutated 3 (0) 0 (0) 0 (0) 0 (0) 0 (0) 3 (1)
Wild-type 1600 (100) 716 (100) 137 (100) 177 (100) 224 (100) 346 (99)
10
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
CTNNB1, n (%) 1.00
Mutated 4 (0) 2 (0) 0 (0) 0 (0) 2 (1) 0 (0)
Wild-type 1599 (100) 714 (100) 137 (100) 177 (100) 222 (99) 349 (100)
DNMT3A, n (%) <0.001
Mutated 375 (23) 255 (36) 18 (13) 1 (1) 13 (6) 88 (25)
Wild-type 1228 (77) 461 (64) 119 (87) 176 (99) 211 (94) 261 (75)
DNMT3A R882, n (%) <0.001
Mutated 251 (16) 177 (25) 7 (5) 0 (0) 8 (4) 59 (17)
Wild-type 1352 (84) 539 (75) 130 (95) 177 (100) 216 (96) 290 (83)
DNMT3A non-R882, n (%)
<0.001
Mutated 126 (8) 80 (11) 11 (8) 1 (1) 5 (2) 29 (8)
Wild-type 1477 (92) 636 (89) 126 (92) 176 (99) 219 (98) 320 (92)
ETV6, n (%) 1.00
Mutated 40 (2) 15 (2) 5 (4) 3 (2) 5 (2) 12 (3)
Wild-type 1563 (98) 701 (98) 132 (96) 174 (98) 219 (98) 337 (97)
EZH2, n (%) 1.00
11
Mutated 45 (3) 18 (3) 1 (1) 4 (2) 7 (3) 15 (4)
Wild-type 1558 (97) 698 (97) 136 (99) 173 (98) 217 (97) 334 (96)
FBXW7, n (%) 0.60
Mutated 2 (0) 0 (0) 1 (1) 0 (0) 0 (0) 1 (0)
Wild-type 1596 (100) 716 (100) 135 (99) 177 (100) 222 (100) 346 (100)
FLT3-ITD, n (%) <0.001
Present 342 (22) 242 (35) 8 (6) 6 (3) 25 (12) 61 (18)
Absent 1213 (78) 458 (65) 128 (94) 168 (97) 185 (88) 274 (82)
FLT3-TKD, n (%) 0.27
Present 118 (7) 68 (10) 5 (4) 11 (6) 12 (5) 22 (6)
Absent 1467 (93) 647 (90) 128 (96) 166 (94) 209 (95) 317 (94)
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
GATA1, n (%) 1.00
Mutated 1 (0) 0 (0) 0 (0) 0 (0) 0 (0) 1 (0)
Wild-type 1602 (100) 716 (100) 137 (100) 177 (100) 224 (100) 348 (100)
GATA2, n (%) 0.003
Mutated 68 (4) 41 (6) 1 (1) 1 (1) 6 (3) 19 (5)
12
Wild-type 1535 (96) 675 (94) 136 (99) 176 (99) 218 (97) 330 (95)
GSK3B, n (%) 0.84
Mutated 8 (0) 2 (0) 2 (1) 0 (0) 2 (1) 2 (1)
Wild-type 1595 (100) 714 (100) 135 (99) 177 (100) 222 (99) 347 (99)
HIST1H1E, n (%) 1.00
Mutated 17 (1) 5 (1) 2 (1) 1 (1) 3 (1) 6 (2)
Wild-type 1586 (99) 711 (99) 135 (99) 176 (99) 221 (99) 343 (98)
HNRNPK, n (%) 1.00
Mutated 10 (1) 5 (1) 1 (1) 1 (1) 0 (0) 3 (1)
Wild-type 1593 (99) 711 (99) 136 (99) 176 (99) 224 (100) 346 (99)
IDH1, n (%) <0.001
Mutated 122 (8) 83 (12) 5 (4) 0 (0) 5 (2) 29 (8)
Wild-type 1480 (92) 633 (88) 132 (96) 177 (100) 219 (98) 319 (92)
IDH2, n (%) <0.001
Mutated R140 R172
181 (11)13942
94 (13)8212
8 (6)53
0 (0)00
8 (4)44
71 (20)4823
Wild-type 1422 (89) 622 (87) 129 (94) 177 (100) 216 (96) 278 (80)
IKZF1, n (%) 0.26
13
Mutated 25 (2) 8 (1) 2 (1) 0 (0) 5 (2) 10 (3)
Wild-type 1578 (98) 708 (99) 135 (99) 177 (100) 219 (98) 339 (97)
14
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
IKZF3, n (%) 1.00
Mutated 4 (0) 3 (0) 0 (0) 1 (1) 0 (0) 0 (0)
Wild-type 1599 (100) 713 (100) 137 (100) 176 (99) 224 (100) 349 (100)
IL7R, n (%) 0.34
Mutated 1 (0) 0 (0) 1 (1) 0 (0) 0 (0) 0 (0)
Wild-type 1600 (100) 716 (100) 135 (99) 177 (100) 223 (100) 349 (100)
JAK1, n (%) 1.00
Mutated 15 (1) 7 (1) 1 (1) 3 (2) 2 (1) 2 (1)
Wild-type 1588 (99) 709 (99) 136 (99) 174 (98) 222 (99) 347 (99)
JAK2, n (%) 0.51
Mutated 10 (1) 3 (0) 0 (0) 4 (2) 1 (0) 2 (1)
Wild-type 1539 (99) 699 (100) 128 (100) 173 (98) 212 (100) 327 (99)
JAK3, n (%) 0.96
Mutated 14 (1) 4 (1) 1 (1) 3 (2) 4 (2) 2 (1)
Wild-type 1589 (99) 712 (99) 136 (99) 174 (98) 220 (98) 347 (99)
KIT, n (%) <0.001
15
Mutated 51 (3) 4 (1) 3 (2) 35 (20) 3 (1) 6 (2)
Wild-type 1452 (97) 672 (99) 122 (98) 142 (80) 202 (99) 314 (98)
KLHL6, n (%) 1.00
Mutated 1 (0) 1 (0) 0 (0) 0 (0) 0 (0) 0 (0)
Wild-type 1602 (100) 715 (100) 137 (100) 177 (100) 224 (100) 349 (100)
KMT2A, n (%) 0.06
Mutated 21 (1) 8 (1) 4 (3) 1 (1) 7 (3) 1 (0)
Wild-type 1582 (99) 708 (99) 133 (97) 176 (99) 217 (97) 348 (100)
KRAS, n (%) 0.003
Mutated 60 (4) 19 (3) 2 (1) 9 (5) 20 (9) 10 (3)
Wild-type 1541 (96) 697 (97) 134 (99) 168 (95) 204 (91) 338 (97)
16
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
MAPK1, n (%) 1.00
Mutated 1 (0) 1 (0) 0 (0) 0 (0) 0 (0) 0 (0)
Wild-type 1602 (100) 715 (100) 137 (100) 177 (100) 224 (100) 349 (100)
MAPK3, n (%) 0.71
Mutated 4 (0) 1 (0) 1 (1) 1 (1) 1 (0) 0 (0)
Wild-type 1599 (100) 715 (100) 136 (99) 176 (99) 223 (100) 349 (100)
MED12, n (%) 0.48
Mutated 23 (1) 9 (1) 3 (2) 0 (0) 2 (1) 9 (3)
Wild-type 1580 (99) 707 (99) 134 (98) 177 (100) 222 (99) 340 (97)
MYD88, n (%) 1.00
Mutated 2 (0) 1 (0) 0 (0) 0 (0) 0 (0) 1 (0)
Wild-type 1601 (100) 715 (100) 137 (100) 177 (100) 224 (100) 348 (100)
NOTCH1, n (%) 0.46
Mutated 24 (1) 6 (1) 3 (2) 4 (2) 2 (1) 9 (3)
Wild-type 1579 (99) 710 (99) 134 (98) 173 (98) 222 (99) 340 (97)
NPM1, n (%) <0.001
17
Mutated 492 (31) 407 (57) 6 (5) 0 (0) 11 (5) 68 (20)
Wild-type 1086 (69) 305 (43) 123 (95) 177 (100) 207 (95) 274 (80)
NRAS, n (%) 0.02
Mutated 213 (13) 89 (12) 12 (9) 40 (23) 29 (13) 43 (12)
Wild-type 1390 (87) 627 (88) 125 (91) 137 (77) 195 (87) 306 (88)
PHF6, n (%) 0.21
Mutated 47 (3) 18 (3) 8 (6) 2 (1) 4 (2) 15 (4)
Wild-type 1556 (97) 698 (97) 129 (94) 175 (99) 220 (98) 334 (96)
PIK3CD, n (%) 1.00
Mutated 14 (1) 7 (1) 0 (0) 2 (1) 1 (0) 4 (1)
Wild-type 1589 (99) 709 (99) 137 (100) 175 (99) 223 (100) 345 (99)
18
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
PIK3CG, n (%) 1.00
Mutated 24 (1) 13 (2) 3 (2) 4 (2) 2 (1) 2 (1)
Wild-type 1579 (99) 703 (98) 134 (98) 173 (98) 222 (99) 347 (99)
PLCG2, n (%) 1.00
Mutated 39 (2) 15 (2) 4 (3) 2 (1) 9 (4) 9 (3)
Wild-type 1564 (98) 701 (98) 133 (97) 175 (99) 215 (96) 340 (97)
PLEKHG5, n (%) 1.00
Mutated 2 (0) 1 (0) 0 (0) 0 (0) 0 (0) 1 (0)
Wild-type 1588 (100) 712 (100) 133 (100) 177 (100) 222 (100) 344 (100)
PRKCB, n (%) 0.64
Mutated 17 (1) 5 (1) 4 (3) 3 (2) 2 (1) 3 (1)
Wild-type 1586 (99) 711 (99) 133 (97) 174 (98) 222 (99) 346 (99)
PRKD3, n (%) 1.00
Mutated 11 (1) 6 (1) 0 (0) 0 (0) 2 (1) 3 (1)
Wild-type 1592 (99) 710 (99) 137 (100) 177 (100) 222 (99) 346 (99)
PTEN, n (%) 0.20
19
Mutated 8 (0) 2 (0) 2 (1) 2 (1) 2 (1) 0 (0)
Wild-type 1595 (100) 714 (100) 135 (99) 175 (99) 222 (99) 349 (100)
PTPN11, n (%) 0.02
Mutated 101 (6) 59 (8) 5 (4) 1 (1) 15 (7) 21 (6)
Wild-type 1502 (94) 657 (92) 132 (96) 176 (99) 209 (93) 328 (94)
RAD21, n (%) 0.05
Mutated 33 (2) 24 (3) 0 (0) 4 (2) 2 (1) 3 (1)
Wild-type 1570 (98) 692 (97) 137 (100) 173 (98) 222 (99) 346 (99)
RAF1, n (%) 1.00
Mutated 10 (1) 6 (1) 1 (1) 0 (0) 1 (0) 2 (1)
Wild-type 1593 (99) 710 (99) 136 (99) 177 (100) 223 (100) 347 (99)
20
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
RUNX1, n (%) <0.001
Mutated 174 (11) 70 (10) 12 (9) 1 (1) 25 (11) 66 (19)
Wild-type 1429 (89) 646 (90) 125 (91) 176 (99) 199 (89) 283 (81)
SAMHD1, n (%) 1.00
Mutated 15 (1) 6 (1) 1 (1) 3 (2) 4 (2) 1 (0)
Wild-type 1588 (99) 710 (99) 136 (99) 174 (98) 220 (98) 348 (100)
SETBP1, n (%) 1.00
Mutated 38 (2) 20 (3) 2 (1) 1 (1) 5 (2) 10 (3)
Wild-type 1565 (98) 696 (97) 135 (99) 176 (99) 219 (98) 339 (97)
SF1, n (%) 1.00
Mutated 13 (1) 7 (1) 1 (1) 0 (0) 3 (1) 2 (1)
Wild-type 1590 (99) 709 (99) 136 (99) 177 (100) 221 (99) 347 (99)
SF3A1, n (%) 1.00
Mutated 15 (1) 6 (1) 0 (0) 2 (1) 1 (0) 6 (2)
Wild-type 1588 (99) 710 (99) 137 (100) 175 (99) 223 (100) 343 (98)
SF3B1, n (%) 0.03
21
Mutated 53 (3) 27 (4) 1 (1) 3 (2) 15 (7) 7 (2)
Wild-type 1550 (97) 689 (96) 136 (99) 174 (98) 209 (93) 342 (98)
SMARCA2, n (%) 1.00
Mutated 26 (2) 11 (2) 3 (2) 3 (2) 2 (1) 7 (2)
Wild-type 1577 (98) 705 (98) 134 (98) 174 (98) 222 (99) 342 (98)
SMC1A, n (%) 1.00
Mutated 59 (4) 30 (4) 2 (1) 3 (2) 8 (4) 16 (5)
Wild-type 1544 (96) 686 (96) 135 (99) 174 (98) 216 (96) 333 (95)
SMC3, n (%) 0.59
Mutated 50 (3) 31 (4) 3 (2) 3 (2) 7 (3) 6 (2)
Wild-type 1553 (97) 685 (96) 134 (98) 174 (98) 217 (97) 343 (98)
22
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
SRSF2, n (%) <0.001
Mutated 145 (9) 67 (9) 9 (7) 1 (1) 8 (4) 60 (17)
Wild-type 1446 (91) 647 (91) 124 (93) 175 (99) 215 (96) 285 (83)
STAG2, n (%) 0.08
Mutated 51 (3) 26 (4) 4 (3) 0 (0) 5 (2) 16 (5)
Wild-type 1552 (97) 690 (96) 133 (97) 177 (100) 219 (98) 333 (95)
SYK, n (%) 1.00
Mutated 11 (1) 6 (1) 0 (0) 2 (1) 1 (0) 2 (1)
Wild-type 1592 (99) 710 (99) 137 (100) 175 (99) 223 (100) 347 (99)
TET2, n (%) <0.001
Mutated 226 (14) 117 (16) 23 (17) 3 (2) 22 (10) 61 (17)
Wild-type 1377 (86) 599 (84) 114 (83) 174 (98) 202 (90) 288 (83)
TGM7, n (%) 1.00
Mutated 6 (0) 3 (0) 0 (0) 0 (0) 1 (0) 2 (1)
Wild-type 1577 (100) 705 (100) 132 (100) 176 (100) 220 (100) 344 (99)
TP53, n (%) <0.001
23
Mutated 73 (5) 2 (0) 52 (38) 0 (0) 13 (6) 6 (2)
Wild-type 1530 (95) 714 (100) 85 (62) 177 (100) 211 (94) 343 (98)
TYK2, n (%) 1.00
Mutated 32 (2) 12 (2) 4 (3) 4 (2) 3 (1) 9 (3)
Wild-type 1571 (98) 704 (98) 133 (97) 173 (98) 221 (99) 340 (97)
U2AF1, n (%) <0.001
Mutated 61 (4) 17 (2) 2 (1) 0 (0) 5 (2) 37 (11)
Wild-type 1542 (96) 699 (98) 135 (99) 177 (100) 219 (98) 312 (89)
WT1, n (%) Mutated 109 (7) 66 (9) 4 (3) 10 (6) 11 (5) 18 (5)
0.06
Wild-type 1494 (93) 650 (91) 133 (97) 167 (94) 213 (95) 331 (95)
24
Mutation frequenciesAll
n = 1603
CN-AML
n = 716
Complex karyotypen = 137
CBF-AML
n = 177
Balanced rearrangements
n = 224
Unbalanced abnormalities
n = 349
Pa
XPO1, n (%) 1.00
Mutated 7 (0) 5 (1) 0 (0) 0 (0) 0 (0) 2 (1)
Wild-type 1596 (100) 711 (99) 137 (100) 177 (100) 224 (100) 347 (99)
ZMYM3, n (%) 1.00
Mutated 2 (0) 1 (0) 0 (0) 0 (0) 1 (0) 0 (0)
Wild-type 1601 (100) 715 (100) 137 (100) 177 (100) 223 (100) 349 (100)
ZRSR2, n (%) 1.00
Mutated 82 (5) 34 (5) 10 (7) 7 (4) 14 (6) 17 (5)
Wild-type 1521 (95) 682 (95) 127 (93) 170 (96) 210 (94) 332 (95)
Total number of mutations
<0.001
Median Range
3 (0, 9)
3 (0, 9)
2 (0, 7)
1 (0, 5)
2 (0, 7)
3 (0, 9)
Abbreviations: n, number; CN-AML, cytogenetically normal acute myeloid leukemia; CBF-AML, core-binding factor AML.
a P-values are from Fisher’s exact test and compare the five major cytogenetic groups.
25
Supplementary Table S3. Proportions of patients with de novo acute myeloid leukemia classified into the five major cytogenetic groups
among patients aged <60 years and those aged ≥60 years
Major cytogenetic group Patients aged <60 years (n=1080)
Patients aged ≥60 years (n=523)
P-valuea
CN-AML, n (%) 485 (45) 234 (45) 0.96Complex karyotype, n (%) 76 (7) 61 (12) 0.003CBF-AML, n (%) 163 (15) 14 (3) <0.001Balanced rearrangements, n (%) 170 (16) 54 (10) 0.003Unbalanced rearrangements, n (%) 186 (17) 160 (31) <0.001
Abbreviations: n, number; CN-AML, cytogenetically normal acute myeloid leukemia; CBF-AML, core-binding factor AML.
a P-values are from Fisher’s exact test and compare older and younger AML patients.
26
Supplementary Table S4. Frequencies of gene mutations assigned to the functional groups detected in patients with cytogenetically
normal de novo acute myeloid leukemia, listed for the total cohort and separately for patients <60 and ≥60 years of age
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Chromatin remodeling, n (%) 0.009
Mutated 105 (15) 59 (12) 46 (20)
Wild-type 611 (85) 425 (88) 186 (80)
Cohesin complex, n (%) 0.82
Mutated 110 (15) 73 (15) 37 (16)
Wild-type 606 (85) 411 (85) 195 (84)
Kinases, n (%) 0.05
Mutated 318 (46) 230 (49) 88 (41)
Wild-type 369 (54) 240 (51) 129 (59)
Methylation-related, n (%) <0.001
Mutated 438 (61) 266 (55) 172 (74)
Wild-type 278 (39) 218 (45) 60 (26)
NPM1, n (%) 0.26
Mutated 407 (57) 282 (59) 125 (54)
27
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Wild-type 305 (43) 199 (41) 106 (46)
RAS pathway, n (%) 0.09
Mutated 174 (24) 127 (26) 47 (20)
Wild-type 542 (76) 357 (74) 185 (80)
Spliceosome, n (%) <0.001
Mutated 136 (19) 49 (10) 87 (38)
Wild-type 578 (81) 433 (90) 145 (63)
Transcription factors, n (%) 0.01
Mutated 131 (21) 76 (18) 55 (27)
Wild-type 502 (79) 350 (82) 152 (73)
28
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Tumor suppressors, n (%) 0.81
Mutated 84 (12) 58 (12) 26 (11)
Wild-type 632 (88) 426 (88) 206 (89)
Abbreviation: n, number.a Chromatin remodeling is mutated if ASXL1, BCOR, BCORL1, EZH2 or SMARCA2 is mutated. Cohesin complex is mutated if RAD21, SMC1A,
SMC3 or STAG2 is mutated. Kinases is mutated if AXL, FLT3-ITD, FLT3-TKD, KIT or TYK2 is mutated. Methylation-related is mutated if
DNMT3A, IDH1, IDH2, or TET2 is mutated. NPM1 is mutated if NPM1 is mutated. RAS pathway is mutated if CBL, KRAS, NRAS or PTPN11 is
mutated. Spliceosome is mutated if SF3B1, SRSF2, U2AF1 or ZRSR2 is mutated. Transcription factors is mutated if CEBPA, ETV6, IKZF1,
GATA2, NOTCH1 or RUNX1 is mutated. Tumor suppressors is mutated if PHF6, TP53 or WT1 is mutated. b P-values are from Fisher’s exact test and compare patients aged <60 years with those aged ≥60 years.
29
Supplementary Table S5. Frequencies of gene mutations assigned to the functional groups detected in patients de novo acute myeloid
leukemia with complex karyotype, listed for the total cohort and separately for patients <60 and ≥60 years of age
Functional groupa Alln = 137
<60 yearsn = 76
≥60 yearsn = 61
Pb
Chromatin remodeling, n (%) 0.20
Mutated 17 (12) 12 (16) 5 (8)
Wild-type 120 (88) 64 (84) 56 (92)
Cohesin complex, n (%) 0.73
Mutated 9 (7) 6 (8) 3 (5)
Wild-type 128 (93) 70 (92) 58 (95)
Kinases, n (%) 0.02
Mutated 19 (15) 15 (22) 4 (7)
Wild-type 106 (85) 53 (78) 53 (93)
Methylation-related, n (%) 0.85
Mutated 43 (31) 23 (30) 20 (33)
Wild-type 94 (69) 53 (70) 41 (67)
NPM1, n (%) 0.23
Mutated 6 (5) 5 (7) 1 (2)
30
Functional groupa Alln = 137
<60 yearsn = 76
≥60 yearsn = 61
Pb
Wild-type 123 (95) 67 (93) 56 (98)
RAS pathway, n (%) 0.13
Mutated 19 (14) 14 (18) 5 (8)
Wild-type 118 (86) 62 (82) 56 (92)
Spliceosome, n (%) 0.008
Mutated 21 (16) 6 (8) 15 (25)
Wild-type 113 (84) 69 (92) 44 (75)
Transcription factors, n (%) 1.00
Mutated 22 (18) 12 (17) 10 (19)
Wild-type 101 (82) 57 (83) 44 (81)
31
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Tumor suppressors, n (%) 0.12
Mutated 63 (46) 30 (39) 33 (54)
Wild-type 74 (54) 46 (61) 28 (46)
Abbreviation: n, number.a Chromatin remodeling is mutated if ASXL1, BCOR, BCORL1, EZH2 or SMARCA2 is mutated. Cohesin complex is mutated if RAD21, SMC1A,
SMC3 or STAG2 is mutated. Kinases is mutated if AXL, FLT3-ITD, FLT3-TKD, KIT or TYK2 is mutated. Methylation-related is mutated if
DNMT3A, IDH1, IDH2, or TET2 is mutated. NPM1 is mutated if NPM1 is mutated. RAS pathway is mutated if CBL, KRAS, NRAS or PTPN11 is
mutated. Spliceosome is mutated if SF3B1, SRSF2, U2AF1 or ZRSR2 is mutated. Transcription factors is mutated if CEBPA, ETV6, IKZF1,
GATA2, NOTCH1 or RUNX1 is mutated. Tumor suppressors is mutated if PHF6, TP53 or WT1 is mutated. b P-values are from Fisher’s exact test and compare patients aged <60 years with those aged ≥60 years.
32
Supplementary Table S6. Frequencies of gene mutations assigned to the functional groups detected in patients with de novo core-
binding factor acute myeloid leukemia, listed for the total cohort and separately for patients <60 and ≥60 years of age
Functional groupa Alln = 177
<60 yearsn = 163
≥60 yearsn = 14
Pb
Chromatin remodeling, n (%) 0.37
Mutated 16 (9) 14 (9) 2 (14)
Wild-type 161 (91) 149 (91) 12 (86)
Cohesin complex, n (%) 0.55
Mutated 56 (32) 53 (33) 3 (21)
Wild-type 118 (68) 107 (67) 11 (79)
Kinases, n (%) 0.28
Mutated 4 (2) 3 (2) 1 (7)
Wild-type 173 (98) 160 (98) 13 (93)
Methylation-related, n (%) --
Mutated 0 (0) 0 (0) 0 (0)
Wild-type 177 (100) 163 (100) 14 (100)
NPM1, n (%) 0.23
Mutated 51 (29) 45 (28) 6 (43)
33
Functional groupa Alln = 177
<60 yearsn = 163
≥60 yearsn = 14
Pb
Wild-type 126 (71) 118 (72) 8 (57)
RAS pathway, n (%) 1.00
Mutated 11 (6) 10 (6) 1 (7)
Wild-type 165 (94) 152 (94) 13 (93)
Spliceosome, n (%) 1.00
Mutated 8 (5) 8 (5) 0 (0)
Wild-type 169 (95) 155 (95) 14 (100)
Transcription factors, n (%) 1.00
Mutated 12 (7) 11 (7) 1 (7)
Wild-type 165 (93) 152 (93) 13 (93)
34
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Tumor suppressors, n (%) 0.37
Mutated 16 (9) 14 (9) 2 (14)
Wild-type 161 (91) 149 (91) 12 (86)
Abbreviation: n, number.a Chromatin remodeling is mutated if ASXL1, BCOR, BCORL1, EZH2 or SMARCA2 is mutated. Cohesin complex is mutated if RAD21, SMC1A,
SMC3 or STAG2 is mutated. Kinases is mutated if AXL, FLT3-ITD, FLT3-TKD, KIT or TYK2 is mutated. Methylation-related is mutated if
DNMT3A, IDH1, IDH2, or TET2 is mutated. NPM1 is mutated if NPM1 is mutated. RAS pathway is mutated if CBL, KRAS, NRAS or PTPN11 is
mutated. Spliceosome is mutated if SF3B1, SRSF2, U2AF1 or ZRSR2 is mutated. Transcription factors is mutated if CEBPA, ETV6, IKZF1,
GATA2, NOTCH1 or RUNX1 is mutated. Tumor suppressors is mutated if PHF6, TP53 or WT1 is mutated. b P-values are from Fisher’s exact test and compare patients aged <60 years with those aged ≥60 years.
35
Supplementary Table S7. Frequencies of gene mutations assigned to the functional groups detected in patients with de novo acute
myeloid leukemia with balanced rearrangements, listed for the total cohort and separately for patients <60 and ≥60 years of age
Functional groupa Alln = 224
<60 yearsn = 170
≥60 yearsn = 54
Pb
Chromatin remodeling, n (%) 0.16
Mutated 42 (19) 28 (16) 14 (26)
Wild-type 182 (81) 142 (84) 40 (74)
Cohesin complex, n (%) 0.79
Mutated 21 (9) 17 (10) 4 (7)
Wild-type 203 (91) 153 (90) 50 (93)
Kinases, n (%) 0.56
Mutated 45 (22) 32 (21) 13 (26)
Wild-type 156 (78) 119 (79) 37 (74)
Methylation-related, n (%) 0.02
Mutated 41 (18) 25 (15) 16 (30)
Wild-type 183 (82) 145 (85) 38 (70)
NPM1, n (%) 0.005
Mutated 11 (5) 4 (2) 7 (13)
36
Functional groupa Alln = 224
<60 yearsn = 170
≥60 yearsn = 54
Pb
Wild-type 207 (95) 162 (98) 45 (87)
RAS pathway, n (%) 0.02
Mutated 65 (29) 56 (33) 9 (17)
Wild-type 159 (71) 114 (67) 45 (83)
Spliceosome, n (%) 0.68
Mutated 41 (18) 30 (18) 11 (21)
Wild-type 182 (82) 140 (82) 42 (79)
Transcription factors, n (%) 0.53
Mutated 39 (21) 28 (20) 11 (25)
Wild-type 143 (79) 110 (80) 33 (75)
37
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Tumor suppressors, n (%) 0.63
Mutated 26 (12) 21 (12) 5 (9)
Wild-type 198 (88) 149 (88) 49 (91)
Abbreviation: n, number.a Chromatin remodeling is mutated if ASXL1, BCOR, BCORL1, EZH2 or SMARCA2 is mutated. Cohesin complex is mutated if RAD21, SMC1A,
SMC3 or STAG2 is mutated. Kinases is mutated if AXL, FLT3-ITD, FLT3-TKD, KIT or TYK2 is mutated. Methylation-related is mutated if
DNMT3A, IDH1, IDH2, or TET2 is mutated. NPM1 is mutated if NPM1 is mutated. RAS pathway is mutated if CBL, KRAS, NRAS or PTPN11 is
mutated. Spliceosome is mutated if SF3B1, SRSF2, U2AF1 or ZRSR2 is mutated. Transcription factors is mutated if CEBPA, ETV6, IKZF1,
GATA2, NOTCH1 or RUNX1 is mutated. Tumor suppressors is mutated if PHF6, TP53 or WT1 is mutated. b P-values are from Fisher’s exact test and compare patients aged <60 years with those aged ≥60 years.
38
Supplementary Table S8. Frequencies of gene mutations assigned to the functional groups detected in patients with de novo acute
myeloid leukemia with unbalanced rearrangements, listed for the total cohort and separately for patients <60 and ≥60 years of age
Functional groupa Alln = 349
<60 yearsn = 187
≥60 yearsn = 161
Pb
Chromatin remodeling, n (%) 0.004
Mutated 85 (24) 34 (18) 51 (31)
Wild-type 264 (76) 153 (82) 111 (69)
Cohesin complex, n (%) 1.00
Mutated 41 (12) 22 (12) 19 (12)
Wild-type 308 (88) 165 (88) 143 (88)
Kinases, n (%) 0.005
Mutated 95 (30) 62 (37) 33 (22)
Wild-type 219 (70) 104 (63) 115 (78)
Methylation-related, n (%) <0.001
Mutated 188 (54) 77 (41) 111 (69)
Wild-type 161 (46) 110 (59) 51 (31)
NPM1, n (%) 0.007
Mutated 68 (20) 46 (25) 22 (14)
39
Functional groupa Alln = 349
<60 yearsn = 187
≥60 yearsn = 161
Pb
Wild-type 274 (80) 135 (75) 139 (86)
RAS pathway, n (%) 1.00
Mutated 80 (23) 43 (23) 37 (23)
Wild-type 269 (77) 144 (77) 125 (77)
Spliceosome, n (%) < 0.001
Mutated 112 (32) 35 (19) 77 (48)
Wild-type 233 (68) 150 (81) 83 (52)
Transcription factors, n (%) 0.03
Mutated 101 (33) 47 (27) 54 (40)
Wild-type 207 (67) 125 (73) 82 (60)
40
Functional groupa Alln = 716
<60 yearsn = 484
≥60 yearsn = 232
Pb
Tumor suppressors, n (%) 0.39
Mutated 38 (11) 23 (12) 15 (9)
Wild-type 311 (89) 164 (88) 147 (91)
Abbreviation: n, number.a Chromatin remodeling is mutated if ASXL1, BCOR, BCORL1, EZH2 or SMARCA2 is mutated. Cohesin complex is mutated if RAD21, SMC1A,
SMC3 or STAG2 is mutated. Kinases is mutated if AXL, FLT3-ITD, FLT3-TKD, KIT or TYK2 is mutated. Methylation-related is mutated if
DNMT3A, IDH1, IDH2, or TET2 is mutated. NPM1 is mutated if NPM1 is mutated. RAS pathway is mutated if CBL, KRAS, NRAS or PTPN11 is
mutated. Spliceosome is mutated if SF3B1, SRSF2, U2AF1 or ZRSR2 is mutated. Transcription factors is mutated if CEBPA, ETV6, IKZF1,
GATA2, NOTCH1 or RUNX1 is mutated. Tumor suppressors is mutated if PHF6, TP53 or WT1 is mutated. b P-values are from Fisher’s exact test and compare patients aged <60 years with those aged ≥60 years.
41
Supplementary Figure S1. Oncoprint of mutations found in patients with de novo acute myeloid leukemia who had specific
cytogenetic findings, using only mutations which were detected with a VAF of ≥30%. The color coding of rows indicate the
assignment of recurrent cytogenetic abnormalities to five major cytogenetic groups. Columns represent single gene mutations that are
clustered into the previously described functional groups (Cancer Genome Atlas Research Network. N Engl J Med 2013; 368: 2059-
2074). The frequency of each mutation detected within a given cytogenetic subset is indicated by a black-to-white color gradient, with
black indicating a mutation frequency ≥50%, and white indicating a mutation frequency <1% of patients. In addition, the specific
frequencies (in percent) are indicated in each cell.
Supplementary Figure S2. Pie charts showing how frequently mutations in each functional group are the first, second, third, fourth,
fifth or later mutational events within individual patient samples (based on their VAFs).
Supplementary Figure S3. Oncoprint of mutations found in patients with de novo acute myeloid leukemia and monosomal karyotype
(Breems et al. J Clin Oncol 2008; 26: 4791-4797). Columns represent single gene mutations that are clustered into the previously
described functional groups (Cancer Genome Atlas Research Network. N Engl J Med 2013; 368: 2059-2074). The frequency of each
mutation detected in patients with monosomal karyotype is indicated by a black-to-white color gradient, with black indicating a
mutation frequency ≥50%, and white indicating a mutation frequency <1% of patients. In addition, the specific frequencies (in
42
percent) are indicated in each cell. The respective mutation frequencies observed in the total patient cohort (n=1603 patients) have
been added as a reference.
43
Supplementary Figure S1.
44
Supplementary Figure S2.
45
Supplementary Figure S3.
46