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SUPPLEMENTARY INFORMATION
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MATERIALS AND METHODS
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Patient samples
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Blood and marrow cells from both donor and recipient were obtained from the South
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Australian Cancer Research Biobank. Mesenchymal stromal cells (MSC) were cultured from
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BM aspirates as a source of germline control DNA. Whole exome sequencing (WES) was
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performed on three donor samples (MSC, AML diagnosis and relapse) and one recipient
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sample (AML diagnosis). In addition, paired diagnostic and remission samples from 12 other
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patients with DNMT3A-mutant AML were available for targeted sequencing. None of these
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12 patients had therapy-related AML or an antecedent diagnosis of a hematological
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neoplasm.
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Whole Exome Sequencing (WES) and Targeted Massively Parallel Sequencing
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WES was performed using a Roche NimbleGen capture kit and sequenced on the Illumina
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HiSeq2500. Briefly 1 g of genomic DNA was sheared to a mean fragment size of 200 bp
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using the Covaris S220 before conversion to barcoded DNA libraries using a TruSeq DNA
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LT Sample Preparation Kit (Illumina, San Diego, CA USA). After purification, libraries
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were quantified by Agilent Bioanalyzer HS DNA assay and combined equally into pools of 6
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prior to solution phase capture using the SeqCap EZ Exome Library v3.0 (Roche NimbleGen,
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Madison, WI USA). The three donor (mesenchymal stem cells, diagnosis, relapse) and one
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recipient (diagnosis) samples were sequenced together with other unrelated samples on five
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Illumina HiSeq2500 flowcells (v3 SBS chemistry 2x100PE), with 6 samples multiplexed per
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lane. All but the mesenchymal stem cell sample were included on two flowcells. The number
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of sequenced fragments for the mesenchymal stem cell sample was 30 million, while for the
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other three samples there were 121, 86 and 71 million fragments, respectively).
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Targeted Massively Parallel Sequencing was performed on a custom 29 gene panel (all
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coding regions) of myeloid genes (Supplementary Table 3) using an Ion Torrent AmpliSeq
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approach. Briefly, the targeted gene libraries were generated from 10 ng of genomic DNA
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using the Ion AmpliSeq Library Kit v2.0 and the custom primer pool as per the
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manufacturer’s protocol (Life Technologies, Guilford, CT USA). After adapter ligation and a
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5-cycle PCR amplification incorporating barcodes the libraries were quantified by Agilent
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Bioanalyzer HS DNA assay and combined equally into a pool of 12 samples. The library
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pool was diluted to 6 pM and templated onto Ion Sphere Particles (ISPs) by emulsion PCR
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using the automated Ion OneTouch2 system with the Ion P1 Template OT2 200 Kit (Life
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Technologies). ISP Sequencing was done using an Ion P1 chip (Ion P1 Sequencing 200 Kit
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v3 chemistry) on the Ion Proton.
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Sequence analysis
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The WES reads were mapped to the human genome (hg19) using bwa sampe (v0.6.2).
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Sorting and indexing was carried out using samtools (v0.1.12a) followed by duplicate
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marking using picard (v1.71). Mapping resulted in average coverage over the Nimblegen
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capture regions of 34.1, 96.5, 94.2 and 76.1 for the donor’s mesenchymal stem cells,
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diagnosis, relapse and the recipient’s diagnosis sample, respectively.
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The GATK toolkit (v2.5.2-v2.8.1) was used to realign indels, recalibrate quality scores and
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its UnifiedGenotyper was used to call variants (multi-sample calling) according to the
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Broad’s “best practices pipeline” for the GATK v2 series. Variants were annotated using the
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ACRF Cancer Genome Facility’s custom annotation pipeline based on SnpEff and SnpSift
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(v3.3)18. Annotation information was taken from Ensembl (v73)19, dbSNP (v137), the 1000
2
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Genomes project (integrated phase 1, v3)20, the Exome Sequencing project (6500SI-V2)21,
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COSMIC (v67)22, GERP scores23 as well as other public databases.
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A rudimentary filtering was imposed on variants to remove those that were relatively unlikely
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to be of interest by imposing two conditions. First, we demanded that the variant had to be
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rare (<0.5%) both in the 1092 individuals of the 1000 Genomes project and the 4300/2203
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European/African-Americans of the Exome sequencing project. Secondly, variants were only
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retained if they either showed evidence that they were evolutionarily conserved, either in
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mammalian (GERP ≥ 2) or other vertebrate (PhastCons ≥ 0.9) species, or if their predicted
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functional impact had the potential to be non-trivial (i.e. not synonymous coding and not
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classified by SnpEff to be a “modifier”), or if they were known somatic mutations occurring
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in the COSMIC database. Finally, we compared the variants passing the above criteria to an
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in-house collection of 51 exomes of patients with non-hematological malignancies, some of
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which were sequenced concurrently with the four exomes considered here. If the variant
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occurred more than once (heterozygous) in this collection then it was discarded. In total,
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these filters reduced the total number of sites to be considered further to 7480.
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The Ion Torrent targeted sequencing data was processed with the Torrent Suite™ software
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v4.0.1 using the AmpliSeq workflow. This suite automates the generation of sequence reads,
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trimming of adapter sequences and the removal of poor quality reads. Variant calls were
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made using the Torrent Variant Caller plugin (4.0-5, 72041) using the Somatic Mutation
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default settings except for ‘SNP minimum allele frequency’ (0.5%) and ‘Indel min allele
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frequency’ (1.25%). Variants were annotated using SnpEff, COSMIC and local in-house
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databases as detailed above.
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3
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Additional cases of DNMT3A-mutant AML
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DNMT3A mutation load of paired diagnostic and remission samples from 12 AML patients
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with DNMT3A (R882H/C) was performed using a custom Sequenom MassArray assay
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(Sequenom, Inc., San Diego, CA USA). Allele loads of concurrent mutations in isocitrate
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dehydrogenase 1 and 2 (IDH1/2), Kirsten rat sarcoma oncogene homolog (KRAS) and NPM1
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were measured using a custom Sequenom assay, Sanger sequencing and a restriction
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fragment length polymorphism assay, respectively.
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Study oversight
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The research was approved by the Royal Adelaide Hospital Human Research Ethics
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Committee and all patients gave written informed consent.
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Supplementary Table 1. Gene mutations in the two brothers.
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Gene
DNMT3A
NPM1
FLT3
IDH1
NOTCH4
WT1
SMC1A
Genome (hg19)
chr2:g.25457242C>T
chr5:
g.170837544_170837547dupTCTG
chr13:g.28592642C>A
chr2:g.209113112C>T
chr6:g.32178533C>T
chr11:g.32413566G>A
chrX:g.53423420T>C
mRNA Transcript
NM_022552; c.2645G>A
NM_002520;
c.860_863dupTCTG
NM_004119; c.2503G>T
NM_005896; c.395G>A
NM_004557; c.2861G>A
NM_024424; c.1180C>T
NM_006306; c.2680A>G
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5
Protein
p.Arg882His
p.Trp288Cysfs*12
p.Asp835Tyr
p.Arg132His
p.Cys954Tyr
p.Arg394Trp
p.Ile894Val
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91
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Supplementary Table 2. Mutation allele loads of 12 DNMT3A-mutant AML patients
who achieved complete remission after induction chemotherapy.
Patient Age at Sex
#
Diagnosis
(years)
Karyotype
Duration Sample
DNMT3A
IDH1
IDH2
NPM1
KRAS
of CR1
type R882H R882C R132C R132H R140Q R172K W288Cfs*12 G12D
(days)
1
65
M
46,XY,ins(17;2)
(p13;p21p23)[20]/
46,XY[1]
268
Dx
95
2
39
F
46,XX-7,+8[23]/
46,XX[7]
NA
CR1
Dx
54
45
3
69
F
46, XX
71
4
37
M
46, XY
360
49
58
47
48
29
56
53
5
64
F
46, XX
>1,460
6
63
F
46, XX
767
7
53
M
46,XY,+1~22
dmin[cp29].ish
dmin(ETO-,c-MYC,MLL-,RUNX1-)/
46,XY[6]
1188
CR1
Dx
CR1
Dx
CR1
Rel
CR2
Dx
CR1
CR1
Dx
CR1
Rel
CR2
Dx
55
15
27
41
54
45
12
17
0
0
491
CR1
CR2
Dx
8
50
F
46,XX,del(7)
(q?31.2)[10]/
46,XX,-7,+mar[2]/
91~92,XXXX,-7,
-7,+marx1~2[6]/
46,XX[2]
9
60
F
46, XX
230
10
65
M
46, XY
100
11
64
M
47,XY,+4,del(4)
(q12q31)[7]/
46,XY[13]
181
12
60
F
46, XX
159
32
0
48
0
48
0
NA
0
43
0
46
0
50
0
60
13
41
CR1
CR2
P1
P2
Dx
CR1
Dx
CR1
Dx
58
0
53
CR1
Dx
CR1
0
30
0
6
26
0
0
0
72
5
5
0
0
0
70
0
0
0
0
0
55
0
49
0
93
94
95
Supplementary Table 3. AmpliSeq 29 Gene Panel list. The entire coding region of each
gene was encompassed by massively parallel sequencing for mutation detection.
Genes
ASXL1
BAP1
BRAF
CBL
CEBPA
DNMT3A
EGFR
EZH2
GATA2
IDH1
IDH2
JAK1
JAK2
KIT
KRAS
MET
MPL
MYD88
NOTCH1
NPM1
NRAS
PTPN11
RUNX1
SF3B1
SRP72
SRSF2
TET2
U2AF1
XPO1
96
97
98
7
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
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