Supplementary Information

DrugTargetSeqR: a genomics- and CRISPR/Cas9-based method for analyzing drug targets

Corynn Kasap, Olivier Elemento, and Tarun M. Kapoor*

Correspondence:
Kapoor@rockefeller.edu
The Rockefeller University
1230 York Avenue,
New York, NY10065
(212) 327 8176

Supplementary Results: Table of Contents

Supplementary Figures
Supplementary Tables

p 2 - 14
p 15 - 30

S1

Supplementary Figures

Log [ispinesib] (nM)

Supplementary Figure 1: Representative 8 point dose-response curves for analysis of
ispinesib-resistant clones. Clones I3 (green square), I11 (purple triangle), I12 (magenta diamond)
and parental cells (blue diamond) are shown. For this analysis, eight doses of ispinesib were tested.
The error bars (s.d.) in the curves were generated from three parallel Wst1 assays as described in
Methods. LD50 values were determined for three independent sets of experiments. Mean LD50 values
+/- s.d. for clones are provided in Supplementary Table 1.

S2

Supplementary Figure 2: Representative 4-point dose response curves for multi-drug

resistance analysis of ispinesib-resistant clones. Clones I1 (black square), I3 (orange triangle),
I12 (red diamond) and parental cells (black diamond) are shown. For this analysis, four doses of (a)
irinotecan, (b) vinblastine, (c) nocodazole, (d) taxol, and (e) mitoxantrone were tested. The error bars
(s.d.) in the curves were generated from three parallel Wst1 assays as described in Methods. LD50
values were determined for two independent sets of experiments. Clones which exhibited significant
proliferation in the presence of drug compared to parental cells for more than two doses of drug were
scored as moderately resistant (yellow box, Figure 1c). Clones which exhibited significant
proliferation in the presence of drug compared to parental for three or more doses of drug were
scored as highly resistant (red box, Figure 1c). The mean of the approximate LD50 values for all 12
clones are provided in Supplementary Table 2.

S3

Supplementary Figure 3: Representative 8-point dose response curves for multi-drug

resistance analysis of five ispinesib-resistant clones processed for whole transcriptome
sequencing. Representative curves for clones I1(red square), I4(purple triangle), I7(magenta
diamond), I9(blue triangle), I10(green line) and parental cells(black circle) are shown. For this
analysis, eight doses of (a) irinotecan, (b) mitoxantrone, and (c) taxol were tested. The error bars
(s.d.) in the curves were generated from three parallel Wst1 assays as described in Methods. LD50
values were determined for three independent sets of experiments. Mean LD50 values +/- s.d. for
clones are provided in Supplementary Table 3.

S4

Supplementary Figure 4: Expression analysis of (a) kinesin-12 and (b) EGFR in parental and
ispinesib-resistant clonal HCT116 cells. Parental HCT116 and 8 ispinesib-resistant clones were
subjected to RNA-Seq. After read alignment using TopHat (default parameters; hg19 reference
genome), expression levels were quantified using Cufflinks with GC and upper-quartile normalization
and are reported as fragments per kilobase of exon per million fragments mapped (FPKM).

S5

FUZ
HOXA3
DDX3Y
RPS4Y1
KLK5
GDF15
JUN
CDKN1A
ACTA2
TP53INP1
KRTAP3-1
SULF2
BTG2
C2
HIST1HSBD
HIST1H2AC
HIST1H2BE
HIST1H2BK
SPDYA
RPS10-NUDT3
MT1B
MT1E
MT1JP

Supplementary Figure 5: Transcriptome Analysis of Ispinesib-resistant Clones and Parental

HCT116: Upon read alignment using TopHat (default parameters; hg19 reference genome), we
quantified expression levels (FPKMs) for all 21,570 RefSeq genes using Cufflinks with GC and upperquartile normalization. Expression levels were averaged across clones for each gene. Fold
expression changes between parental HCT116 and average clone expression were calculated.
Down- and up-regulated genes with fold-change > 2 in at least 75% of resistant clones with FPKM>=5
were determined. We found 4 down-regulated genes and 19 down-regulated genes. Yellow =
maximum expression, blue = not expressed.

S6

Supplementary Figure 6: SURVEYOR analysis of genome editing by CRISPR/Cas9 of A133P

mutation in HeLa cells. A 390 bp amplicon was generated and hybridized using wildtype template
only (w), mutant template only (m), or a mix of both (b) before being treated with SURVEYOR
nuclease. Presence of 240bp band (arrow) indicates SURVEYOR cleavage of template.

S7

Supplementary Figure 7: Structure of ispinesib (purple) bound to kinesin-5. The motor domain
of kinesin-5 is shown. Amino acids Ser120, D130, and Ala133 lie within the drug-binding pocket
(inset, boxed). Rendered in PyMol using Eg5-ADP-ispinesib complex, PDB:4ap0.

S8

Supplementary Figure 8: Sanger Sequencing of bortezomib-resistant HeLa and HEK293E cell

lines. Genomic DNA was isolated from HeLa and HEK293E cells after transfection with px335
CRISPR/Cas9 nickase targeting constructs and homologous double-stranded DNA containing the
point mutant of interest (PSMB5 M104V or A108T) and selection in 40nM bortezomib. Arrow denotes
presence of mutant peak. Genomic DNA was sequenced in both directions.

S9

Clone 26

Clone 20

Clone 28

Clone 23

Clone 27

Clone 31

Clone 2

Clone 29

Clone 30

Clone 22

Supplementary Figure 9. Direct sequencing of subcloned PCR products from genome-edited

HeLa (kinesin-5 A133P). Genome-edited HeLa cells were assessed for kinesin-5 mutant allele
A133P transcript abundance. Total RNA was isolated from the HeLa kinesin-5 A133P line and used
as template for rtPCR. PCR products were subcloned in to pBlueScript and transformed in to DH5a
competent cells. Individual colonies were analyzed using Sanger sequencing. Raw sequencing traces
are shown above. Arrow denotes presence of mutant base in 9 of 10 colonies.

S10

expression (FPKM)

kinesin-5
120
100
80
60
40
20
0

expression (FPKM)

ABCB1
7
6
5
4
3
2
1
0

Supplementary Figure 10: Expression analysis of (a) kinesin-5 and (b) MDR transporter
ABCB1 in parental and ispinesib-resistant clonal HCT116 cells. Parental HCT116 and 8
ispinesib-resistant clones were subjected to RNA-Seq. After read alignment using TopHat (default
parameters; hg19 reference genome), expression levels were quantified using Cufflinks with GC and
upper-quartile normalization and are reported as fragments per kilobase of exon per million fragments
mapped (FPKM).

S11

Supplementary Figure 11: Cartoon of kinesin-5 homotetramer. The motor protein kinesin-5
functions as a homotetramer. In the setting of a heterozygous mutation, equivalent expression of
wildtype and mutant allele is predicted to produce only 6.25% motor protein complexes composed
solely of mutant motor protein.

S12

Supplementary Figure 12: Characterization of YM155-resistant clones. (a) Structure of YM155.

(b) LD50 values for HCT116 parental cells and 10 YM155-resistant clones (Y1-Y10). Average of n = 2

S13

independent experiments are provided. (c) Number of mutations found in each of the 6 sequenced
drug resistant clones (Y1-Y6) but absent in parental cell population. (d) Upon read alignment using
TopHat (default parameters; hg19 reference genome), we quantified expression levels (FPKMs) for
all 21,570 RefSeq genes using Cufflinks with GC and upper-quartile normalization. Expression levels
were averaged across clones for each gene. Fold expression changes between parental HCT116 and
average clone expression were calculated. Down- and up-regulated genes with fold-change > 2 in
75% or more of resistant clones were determined: 547 genes were down-regulated and 605 genes
were upregulated in resistant clones. Pathway analysis was then performed using the mutual
information-based iPAGE approach (Goodarzi et al, 2009) and Gene Ontology gene sets (>=300
genes, electronic annotations were filtered out). Randomizations were used to determine FDR < 10%.
In the Figure, rows correspond to pathways and columns to gene sets (stable, down-regulated and
up-regulated). Colors indicate enrichment of a given GO function (row) in a given gene set (column).
Red colors indicate strong enrichment (Bonferoni-corrected p<0.05) as calculated by the
hypergeometric distribution.

S14

Supplementary Tables:

Clone

LD50 (nM)

SD

parental

3.4

+/- 2.5

I1

470

+/- 310

I2

830

+/- 340

I3

940

+/- 340

I4

770

+/- 210

I5

600

+/- 270

I6

500

+/- 230

I7

530

+/- 240

I8

610

+/- 320

I9

670

+/- 150

I10

1200

+/- 270

I11

690

+/- 190

I12

900

+/- 320

Supplementary Table 1. Calculated ispinesib LD50 values of parental and 12 ispinesib-resistant

HCT116 clones. Wst1 proliferation assay was performed as described in Methods. Representative 8
point dose response curves are shown in Supplementary Figure 1. Three independent experiments
were performed for each clone. Mean LD50 values +/- s.d. are shown.

S15

Clone

Ispinesib IC50
(nM)

Irino. IC50
(uM)

Mitoxan. IC50
(nM)

Noca. IC50
(nM)

Taxol IC50
(nM)

Vinblst. IC50
(nM)

Parental

3.4

0.46

0.79

2.8

0.87

I1

280

0.43

10

0.78

1.4

0.8

I2

635

0.67

18

2.7

7.4

1.5

I3

760

0.85

21

0.8

190

1.1

I4

720

1.5

7.1

0.44

0.82

I5

720

0.81

6.3

0.67

4.3

0.53

I6

560

0.72

9.2

0.49

4.9

0.29

I7

420

0.25

29

1.5

0.3

I8

540

0.46

9.6

1.2

1.3

2.6

I9

620

0.11

1.8

2.6

0.79

I10

1000

0.86

12

1.7

4.1

0.38

I11

620

0.08

9.4

1.6

4.3

0.45

I12
720
3.7
620
12
1300
52
Supplementary Table 2. Calculated 4 point multi-drug resistance approximate LD50 values of
parental and 12 ispinesib-resistant HCT116 clones. Wst1 proliferation assay was performed as
described in Methods. Representative 4 point dose response curves are shown in Supplementary
Figure 2. Two independent experiments were performed for each clone. Values shown are mean of 2
independent experiments.

S16

Supplementary Table 3. Calculated 8 point multi-drug resistance LD50 values of parental and
12 ispinesib-resistant HCT116 clones. Wst1 proliferation assay was performed as described in
Methods. Representative 8 point dose response curves are shown in Supplementary Figure 3. Three
independent experiments were performed for each clone. Mean LD50 values +/- s.d. are shown.

S17

Clone
HCT116

I1

I2

I7

I9

DMSO
nocodazole
ispinesib
DMSO
nocodazole
ispinesib
DMSO
nocodazole
ispinesib
DMSO
nocodazole
ispinesib
DMSO
nocodazole
ispinesib

% mitotic
4.8 - 6.6
54 - 59
31 - 41
5.6 - 8.7
52 - 57
9.3 - 8.8
4.1 - 6.8
55 - 58
6.1 - 11
8.1 - 8.5
53 - 56
10 - 11
7.3 - 11
67 - 70
5.6 - 8.7

Supplementary Table 4. Spindle Assembly Checkpoint Assay. Cells were treated with DMSO,
ispinesib (50nM x 2 hours) or nocodazole (166nM x 14 hours) and processed for
immunofluorescence as described in Methods. The number of mitotic cells in >200 cells total was
counted. The range of 2 independent experiments is shown.

S18

Supplementary Table 5: Significant mutations identified in Clone 1

S19

chr
chr11
chr10

pos
65809515
53744808

chr7

56113568

chr2
chr15
chr10
chr19

2.42E+08
99258382
94356944
15087237

chr19

10131716

chr19
chr19
chr19
chr8

40688712
6702189
2758655
30046761

chr2
chr11

1.05E+08
1.34E+08

chr19

19093219

chr20

34669607

chr20
chr20
chr9
chr5
chr11

32341877
21278089
1.02E+08
1.41E+08
73618964

chr6
chr4
chr16

1E+08
17194289
56344544

chr1

1.55E+08

chr8
chr6

1.42E+08
28980378

chr19

45804266

chr22
chr1
chr2

17415996
2.18E+08
1.01E+08

chr12
chr16

88538063
82774872

chr17
chr16

77788335
70698759

chr8
chr17

1.45E+08
1886092

chr10
chr20
chr3

89270824
60327398
1.98E+08

chr17
chr7

33060982
1.49E+08

gene
YIF1A
DKK1

transcript
NM_020470
NM_012242
NM_001042470/NM_01
5411/NM_001042469/N
SUMF2
M_001146333
NM_005336/NM_20334
HDLBP
6
ALDH1A3 NM_000693
KIF11
NM_004523
ILVBL
NM_006844
NM_001379/NM_001130
DNMT1
823
NM_001126059/NM_001
126058/NM_033317/NM
_001126056/NM_00112
DMKN
6057
TRIP10
NM_004240
THOP1
NM_003249
TMEM66 NM_016127
NM_201557/NM_20155
5/NM_001450/NM_0010
FHL2
39492
NCAPD3 NM_015261
TMEM161
A
NM_017814
NM_018840/NM_19948
C20orf24 3
NM_001161766/NM_000
AHCY
687
XRN2
NM_012255
ERP44
NM_015051
HDAC3
NM_003883
PPME1
NM_016147
NM_005190/NM_00101
CCNC
3399
LAP3
NM_015907
KATNB1 NM_005886
NM_182679/NM_01559
GPATCH4 0
NM_153831/NM_00560
PTK2
7
TRIM27
NM_006510

aa change
A185T
M122V
G167E/G2
51E/G236
E/G144E

#reads parental
0/52
0/84

#reads clone
58/61
48/83

adjp
2.8E-24
2.06E-15

0/83

47/81

2.76E-15

E1156G
V322M
S120P
Y575C
A340T/A35
6T

0/79
0/71
0/25
0/45

43/84
43/80
27/28
32/45

1.43E-12
2.91E-12
8.38E-11
8.43E-11

0/67

39/76

9.46E-11

P65T/P352
T/P382T/P
364T
P536S
G368V
R213H

0/74
0/65
0/56
0/59

33/65
35/65
33/57
33/59

9.46E-11
1.16E-10
4.21E-10
4.21E-10

C104Y
A864T

0/55
0/40

38/72
25/35

2.01E-09
5.5E-09

H271Y

1/61

33/60

6.41E-09

0/56

34/70

2.4E-08

0/78
0/50
0/39
0/45
0/48

30/79
26/49
26/42
28/51
29/58

4.68E-08
1.26E-07
1.62E-07
1.62E-07
3.38E-07

0/63
0/52
0/46

23/52
25/53
21/39

3.83E-07
8.72E-07
1.29E-06

0/61

23/55

1.45E-06

1/50
1/52

25/48
24/47

3.39E-06
3.74E-06

1/31

26/38

5.76E-06

0/47
0/41
1/43

23/51
22/46
22/42

9.55E-06
2.27E-05
4.08E-05

0/29
0/45

21/37
18/42

8.25E-05
9.91E-05

1/92
0/43

23/90
16/36

0.000133
0.000167

0/32
0/30

20/40
17/31

0.000213
0.000234

0/28
0/56
0/26

18/32
16/47
21/38

0.000239
0.000307
0.000319

0/37
0/23

16/36
17/28

0.000598
0.000623

P64Q
N270S/N2
98S
A643T
H1552N
A136T
M143I
Q240R/Q1
55R
V156M
R304H
A233D/A2
38D
I844V/I866
V
I330T
C359Y/C3
NM_003573/NM_00104 29Y/C396
LTBP4
2545/NM_001042544
Y
NM_005137/NM_001184 R321H/R3
781/NM_001173533/NM 18H/R280
DGCR2
_001173534
H/R277H
EPRS
NM_004446
Q362R
RNF149 NM_173647
A384P
NM_001682/NM_00100
ATP2B1
1323
R558W
TAF1C
NM_005679
H51Y
NM_001042422/NM_00
SLC16A3 1042423/NM_004207
L134P
DHX38
NM_014003
Y874C
A1636V/A
NM_201379/NM_20138 1795V/A16
0/NM_201382/NM_2013 58V/A1626
81/NM_201384/NM_201 V/A1662V/
383/NM_201378/NM_00 A1644V/A1
PLEC
0445
685V
DPH1
NM_001383
L125M
NM_001178118/NM_004 Y128C/Y3
MINPP1 897
29C
LAMA5
NM_005560
L2313F
MFI2
NM_005929
A464T
NM_152300/NM_00701 L191S/L29
DDX52
0
9S
ZNF282
NM_003575
E579D

Supplementary Table 6: Significant mutations identified in Clone 2

S20

chr

pos

chr2

2.28E+08

chr12
chr3

1.09E+08
52497029

chr11
chr2

61654428
45628215

chr16
chr1
chr8

66538791
1.49E+08
1.45E+08

gene

transcript
NM_001135189/NM_001
135188/NM_001135187/
AGFG1
NM_004504
NM_032300/NM_001143
TCHP
852
NISCH
NM_007184
NM_001040694/NM_02
INCENP 0238
SRBD1
NM_018079
NM_005072/NM_001145
964/NM_001145962/NM
_001145961/NM_00114
SLC12A4 5963
VPS72
NM_005997
C8orf30A NM_016458

chr18
chr1

46053228
2.02E+08

MBD1
SOX13

chr7

44703134

OGDH

chr16
chr10

82771136
79284067

TAF1C
DLG5

chr8
chr9
chr12
chr12

1.04E+08
1.32E+08
1.32E+08
50034463

FZD6
NCS1
POLE
GALNT6

chr7
chr19
chr10
chr12
chr6

1942905
11183527
17317297
93946359
31707520

MAD1L1
DOCK6
VIM
NR2C1
BAT2

NM_015847/NM_00238
4/NM_015845/NM_0158
44/NM_015846
NM_005686
NM_002541/NM_001165
036
NM_139353/NM_00567
9
NM_004747
NM_003506/NM_001164
615/NM_001164616
NM_014286
NM_006231
NM_007210
NM_003550/NM_00101
3837/NM_001013836
NM_020812
NM_003380
NM_003297
NM_080686

aa change #reads parental

A495V/A5
33V/A557
V/A535V
0/48

#reads clone

adjp

13/34

0.000859

R195Q
H828Y

0/20
0/24

18/29
14/24

0.001186
0.0016

I285T
G572E

1/37
0/20

18/38
13/20

0.001741
0.002405

0/18
1/45
0/39

19/31
19/51
10/23

0.002708
0.003621
0.003645

0/38
0/23

15/41
14/26

0.003915
0.004654

0/38

15/42

0.004785

0/34
0/18

15/40
14/24

0.006905
0.01114

1/27
0/23
1/34
1/20

14/26
10/19
13/29
14/22

0.0127
0.01819
0.01839
0.019

0/30
1/19
0/13
0/17
0/17

12/31
15/24
23/40
12/22
9/15

0.02268
0.0265
0.03803
0.04358
0.04639

A672V/A6
41V/A674
V/A666V
A313T
C228R
A511V/A45
8V/A491V/
A504V/A5
60V
V619A
K667N/K6
63N
R445G/R5
39G
D201E
D111G/D7
9G
L16P
N1717D
P612L
V584I
H1559Y
R378H
M489V
Y2222C

.
Supplementary Table 6: Significant mutations identified in Clone 2

S21

chr
chr11

pos
65809515

chr3
chr15

12855931
99258382

chr19

40688712

chr7

56113568

chr2

2.42E+08

chr19

10131716

chr1
chr10

94415784
53744808

chr20
chr11

32341877
62201651

chr1
chr10
chr20
chr4
chr19
chr11

1.55E+08
94356944
60327398
17194289
6702189
73618964

chr6

1E+08

gene
YIF1A

transcript
NM_020470
NM_000994/NM_00100
RPL32
7074/NM_001007073
ALDH1A3 NM_000693
NM_001126059/NM_001
126058/NM_033317/NM
_001126056/NM_00112
DMKN
6057
NM_001042470/NM_01
5411/NM_001042469/N
SUMF2
M_001146333
NM_005336/NM_20334
HDLBP
6
NM_001379/NM_001130
DNMT1
823
ARHGAP
29
NM_004815
DKK1
NM_012242
NM_001161766/NM_000
AHCY
687
UBXN1
NM_015853
NM_182679/NM_01559
GPATCH4 0
KIF11
NM_004523
LAMA5
NM_005560
LAP3
NM_015907
TRIP10
NM_004240
PPME1
NM_016147
NM_005190/NM_00101
CCNC
3399
NM_201379/NM_20138
0/NM_201382/NM_2013
81/NM_201384/NM_201
383/NM_201378/NM_00
0445
NM_018840/NM_19948
3
NM_006510
NM_005886
NM_005137/NM_001184
781/NM_001173533/NM
_001173534
NM_014003
NM_003249
NM_201557/NM_20155
5/NM_001450/NM_0010
39492

chr8

1.45E+08

PLEC

chr20
chr6
chr16

34669607
28980378
56344544

C20orf24
TRIM27
KATNB1

chr22
chr16
chr19

17415996
70698759
2758655

DGCR2
DHX38
THOP1

chr2

1.05E+08

chr19

19093219

chr2
chr9
chr1
chr14

2.28E+08
1.02E+08
2.18E+08
22414180

FHL2
TMEM161
A
NM_017814
NM_001135189/NM_001
135188/NM_001135187/
AGFG1
NM_004504
ERP44
NM_015051
EPRS
NM_004446
LRP10
NM_014045

chr19

45804266

LTBP4

chr12
chr20
chr1
chr20
chr5

88538063
21278089
1.49E+08
60183025
1.41E+08

ATP2B1
XRN2
VPS72
SS18L1
HDAC3

chr16
chr11
chr19

82771136
1.34E+08
15087237

TAF1C
NCAPD3
ILVBL

NM_003573/NM_00104
2545/NM_001042544
NM_001682/NM_00100
1323
NM_012255
NM_005997
NM_198935
NM_003883
NM_139353/NM_00567
9
NM_015261
NM_006844

aa change #reads parental

A185T
0/52

#reads clone
54/59

adjp
1.46E-21

K65R
V322M

53/98
44/64

4.39E-17
2.88E-16

44/66

3.11E-16

48/80

3.11E-16

E1156G
0/79
A340T/A35
6T
0/67

45/76

5.22E-15

34/58

1.07E-11

A959V
M122V
N270S/N29
8S
P189T
A233D/A23
8D
S120P
L2313F
V156M
P536S
M143I
Q240R/Q1
55R
R3595H/R3
754H/R361
7H/R3585H
/R3621H/R
3603H/R36
44H

0/68
0/84

37/66
32/64

1.09E-11
2.07E-11

0/78
0/69

37/83
34/72

3.91E-10
1.48E-09

0/61
0/25
0/56
0/52
0/65
0/48

25/48
26/31
29/58
24/43
27/61
26/47

1.68E-08
3.69E-08
4.14E-08
5.34E-08
8.63E-08
1.05E-07

0/63

22/47

2.32E-07

0/75

26/69

2.79E-07

P64Q
I330T
R304H
R321H/R31
8H/R280H/
R277H
Y874C
G368V

0/56
1/52
0/46

25/59
24/48
16/29

2.34E-06
6.22E-06
6.81E-06

0/47
0/43
0/56

20/43
19/38
22/57

1.44E-05
1.72E-05
1.72E-05

C104Y

0/55

22/57

2.1E-05

H271Y
A495V/A53
3V/A557V/
A535V
H1552N
Q362R
C98Y

1/61

22/53

2.72E-05

0/48
0/39
0/41
0/35

16/35
17/33
18/39
21/43

4.95E-05
5.37E-05
0.000104
0.000112

C359Y/C32
9Y/C396Y 1/31

24/41

0.000175

0/29
0/50
1/45
0/17
0/45

15/25
17/46
21/47
14/18
16/42

0.000203
0.000291
0.000322
0.00063
0.000665

0/34
0/40
0/45

18/40
14/32
16/43

0.000732
0.000734
0.000824

0/100
0/71

P65T/P352
T/P382T/P
364T
0/74
G167E/G2
51E/G236E
/G144E
0/83

R558W
A643T
A313T
Q366H
A136T
R445G/R5
39G
A864T
Y575C

Supplementary Table 7: Significant mutations identified in Clone 4

S22

chr

pos

chr17

77788335

chr1

1.52E+08

chr7
chr12

44703134
1.32E+08

chr18

46053228

chr1

1.7E+08

chr17
chr8
chr17

33878913
1.46E+08
77576639

chr10
chr2

89270824
1.01E+08

chr17

24110776

chr12
chr17

1.21E+08
1886092

chr5
chr16
chr1
chr9

88054322
87126087
2.02E+08
95447861

chr8

1.45E+08

chr17
chr22
chr12
chr3
chr6
chr15

33060982
18156478
50034463
52497029
31707520
41953564

chr16
chr3

66538791
1.98E+08

chr12
chr20

1469594
37083989

gene

transcript
aa change #reads parental
NM_001042422/NM_00
SLC16A3 1042423/NM_004207
L134P
1/92

#reads clone

adjp

20/88

0.000948

GATAD2B NM_020699
NM_002541/NM_001165
OGDH
036
POLE
NM_006231

0/19

16/25

0.001964

0/38
1/34

15/38
19/39

0.002151
0.002174

0/38

14/35

0.002359

0/23

16/29

0.002445

0/16
1/51
0/47

8/9
20/60
13/42

0.003045
0.003403
0.006038

0/28
1/43

13/28
13/31

0.006473
0.006506

0/19

11/17

0.006612

0/18
0/30

15/25
12/28

0.006884
0.0104

0/9
0/22
0/23
0/21

8/8
12/24
13/28
11/21

0.01234
0.01977
0.02224
0.02308

0/32

13/37

0.0253

0/37
0/21
1/20
0/24
0/17
1/19

8/21
10/19
12/19
14/34
10/17
14/23

0.02829
0.0289
0.03299
0.03483
0.037
0.03996

0/18
0/26

12/23
13/34

0.04158
0.04343

0/16
0/21

7/10
7/12

0.04392
0.04444

K362E
K667N/K66
3N
N1717D
A511V/A45
NM_015847/NM_00238 8V/A491V/
4/NM_015845/NM_0158 A504V/A56
MBD1
44/NM_015846
0V
NM_014955/NM_01593 S181G/S26
METTL13 5
7G
ARHGAP
23
NM_020876
E457G
CPSF1
NM_013291
R355H
LRRC45 NM_144999
N210S
NM_001178118/NM_004 Y128C/Y32
MINPP1 897
9C
RNF149 NM_173647
A384P
NM_018182/NM_00107
C17orf63 7498
A109V
TMEM120
B
NM_001080825
V114M
DPH1
NM_001383
L125M
NM_001131005/NM_002 S416G/S42
MEF2C
397
6G
ZFPM1
NM_153813
C297Y
SOX13
NM_005686
V619A
PHF2
NM_005392
F144L
A1636V/A1
NM_201379/NM_20138 795V/A165
0/NM_201382/NM_2013 8V/A1626V
81/NM_201384/NM_201 /A1662V/A
383/NM_201378/NM_00 1644V/A16
PLEC
0445
85V
NM_152300/NM_00701 L191S/L29
DDX52
0
9S
GNB1L
NM_053004
R246H
GALNT6 NM_007210
P612L
NISCH
NM_007184
H828Y
BAT2
NM_080686
Y2222C
FRMD5
NM_032892
T508I
NM_005072/NM_001145
964/NM_001145962/NM A672V/A64
_001145961/NM_00114 1V/A674V/
SLC12A4 5963
A666V
MFI2
NM_005929
A464T
NM_178040/NM_17803 I1097V/I10
ERC1
9
69V
DHX35
NM_021931
A531T

Supplementary Table 7: Significant mutations identified in Clone 4

S23

chr
chr16
chr19

pos
88529669
3928302

gene
TUBB3
EEF2

chr19

18884836

COPE

chr19
chr22
chrX
chr9
chr17
chrX
chr1
chr16

40449269
40354172
53627358
1.39E+08
77439510
37590541
2.18E+08
667089

LSR
XRCC6
HUWE1
FAM69B
THOC4
DYNLT3
EPRS
RHBDL1

chr19

55068200

AKT1S1

chr17
chr10
chr10
chr20
chr22
chr11
chr6

70379774
94358757
1.06E+08
54525418
49069639
64634644
1.6E+08

FDXR
KIF11
SLK
C20orf43
PLXNB2
C11orf2
ACAT2

chr5

1.8E+08

MAPK9

chr2
chr16

64714691
66470486

chr3

52704253

chr19

8409331

chr1
chr16

1.84E+08
2439858

chr2

2.01E+08

chr11

9157053

chr6
chr9
chr17
chr6
chr7
chr16
chr2

76022694
32439023
34819634
3977287
1.4E+08
30014218
36602822

chr2
chr9
chr19

1.75E+08
38386456
7500511

chr10

74498714

chr14
chr7

67118549
91795123

chr19
chr1

55444182
2.3E+08

chr14
chr5
chr1
chr14

90438905
14518705
27581421
34943490

chr12

44028113

transcript
NM_006086
NM_001961
NM_199442/NM_00
7263/NM_199444
NM_205835/NM_20
5834/NM_015925
NM_001469
NM_031407
NM_152421
NM_005782
NM_006520
NM_004446
NM_003961
NM_032375/NM_00
1098633/NM_00109
8632
NM_004110/NM_02
4417
NM_004523
NM_014720
NM_016407
NM_012401
NM_013265
NM_005891
NM_139068/NM_00
2752/NM_00113504
4

aa change
Y437C
R765W

#reads parental
0/77
0/99

#reads clone
59/76
44/98

adjp
7.1E-23
5.06E-13

D49H

0/79

44/85

8.47E-13

S296N/S364N/S345N
S63N
R1802C
V369A
G228R
A15V
V530I
R247H

0/88
0/91
0/29
0/24
0/92
0/21
0/59
0/17

43/90
39/85
22/23
22/22
33/91
19/19
25/49
20/20

1.11E-12
4.93E-12
2.21E-10
2.98E-10
5.59E-09
1.39E-08
4.56E-08
9.42E-08

A55V

0/46

27/48

1.15E-07

T53M
D130G
G521V
A205T
R376H
T665I
N22D

0/59
0/28
0/26
0/69
0/48
0/65
0/31

31/71
13/14
20/25
22/55
21/42
23/63
12/15

1.96E-07
6.46E-07
7.88E-07
1.03E-06
3.01E-06
6.12E-06
1.01E-05

I224T

0/29

18/27

1.8E-05

SERTAD2 NM_014755
EDC4
NM_014329
NM_018446/NM_15
2932/NM_00101098
GLT8D1 3
NM_016496/NM_00
1005416/NM_00100
MARCH2 5415
IVNS1AB
P
NM_006469
CCNF
NM_001761
NM_004071/NM_00
CLK1
1162407
DENND5
A
NM_015213
TMEM30 NM_018247/NM_00
A
1143958
ACO1
NM_002197
MED1
NM_004774
PRPF4B NM_003913
MKRN1
NM_013446
YPEL3
NM_031477
CRIM1
NM_016441
NM_001172712/NM
_001017371/NM_00
SP3
3111
ALDH1B1 NM_000692
MCOLN1 NM_020533
NM_001142596/NM
_000917/NM_00114
2595/NM_00101796
P4HA1
2

W940G
L472I

0/36
0/32

16/28
18/31

4.59E-05
5.63E-05

R306H

0/44

17/36

5.9E-05

R215C/R145C

0/32

24/46

6.67E-05

G425D
L477I

1/47
0/43

15/29
14/30

0.000199
0.000221

Y372C/Y414C

0/30

16/29

0.00034

V533A

0/28

14/23

0.000343

M310T/M274T
R834Q
E789*
T180A
T461A
R29H
A764V

0/33
1/40
0/25
0/28
1/48
0/8
0/26

18/37
18/37
15/25
16/30
18/44
15/16
9/15

0.000401
0.000685
0.00069
0.00084
0.000998
0.004839
0.005604

T512I/T447I/T515I
I238V
V425I

0/36
1/34
0/24

13/33
16/34
13/25

0.005726
0.006586
0.007529

Y120H

0/30

11/24

0.009618

PLEKHH1 NM_020715
ANKIB1
NM_019004
NM_001077186/NM
_024729/NM_00114
MYH14
5809
EXOC8
NM_175876
NM_004755/NM_18
RPS6KA5 2398
TRIO
NM_007118
CD164L2 NM_207397
NFKBIA
NM_020529
NM_001142678/NM
_001142680/NM_00
1142679/NM_00102
ANO6
5356

R1099H
T254I

0/12
0/15

10/12
9/12

0.01223
0.01634

D486G/D478G
D659N

0/21
0/16

12/23
7/9

0.02156
0.02435

Q373R
A1907V
R104H
M37I

0/13
0/17
0/16
0/27

5/5
7/10
9/14
19/55

0.03674
0.04098
0.04192
0.04238

A110T/A128T

0/22

8/15

0.04904

Supplementary Table 8: Significant mutations identified in Clone 7

S24

chr
chr11
chr3

pos
1.3E+08
1.43E+08

gene
ST14
ATP1B3

transcript
NM_021978
NM_001679

chr2
chr20

55068194
55179554

RTN4
BMP7

chr1
chr10

39814074
94358757

PABPC4
KIF11

NM_020532/NM_
007008/NM_2075
21/NM_207520/N
M_153828
NM_001719
NM_001135654/N
M_003819/NM_0
01135653
NM_004523

chr6
chr14
chr19
chr3

31711023
53977755
1031071
1.21E+08

BAT2
CNIH
HMHA1
C3orf1

NM_080686
NM_005776
NM_012292
NM_016589

chr9

1.31E+08

NUP188

NM_015354

chr13

32242601

PDS5B

chr10
chr10
chr11

45578926
1.05E+08
67515822

FAM21C
PDCD11
UNC93B1

chr17
chr17
chr11

53048343
70745181
64358349

MSI2
GGA3
CDC42BPG

chr1
chr12

2.4E+08
1.08E+08

EXO1
SSH1

chr16
chr22
chr12
chr9
chr11

88171486
48663268
56215798
38567109
1.19E+08

CPNE7
ZBED4
DCTN2
ANKRD18A
MCAM

NM_015032
NM_001169106/N
M_015262/NM_0
01169107
NM_014976
NM_030930
NM_138962/NM_
170721
NM_001172704
NM_017525
NM_130398/NM_
006027/NM_0036
86
NM_018984
NM_014427/NM_
153636
NM_014838
NM_006400
NM_147195
NM_006500

chr11

1.2E+08

ARHGEF12

NM_015313

chr19

10085931

chr11
chr8

1.18E+08
95935226

NM_001040664/N
PPAN-P2RY11/P2RY11 M_002566
NM_005797/NM_
MPZL2
144765
INTS8
NM_017864

chr20
chr19
chr14
chr1

32794547
51079977
91670183
2.14E+08

NCOA6
IRF2BP1
CPSF2
KCTD3

chr14
chr11

94627175
597143

DICER1
PHRF1

chr6

75882348

COL12A1

aa
change #reads parental
I404T
0/53
T89S
0/80

#reads clone
35/37
36/64

adjp
9.64E-19
1.22E-12

S1053
C/S60C
/S847C
/S253C
/S234C 1/83
P388Q 0/24

38/77
21/21

2.46E-10
1.18E-09

0/60
0/28

33/61
17/17

1.56E-09
3.43E-09

0/70
0/49
0/26
0/46

33/72
25/40
19/28
19/43

5.27E-09
1.39E-08
5.6E-05
9.93E-05

0/67

19/61

0.00018

A1323V 0/20

14/18

0.000399

0/38
0/44
0/33

13/25
14/33
15/30

0.000568
0.00102
0.001274

0/42
0/35
0/24

17/43
18/42
16/28

0.001297
0.002
0.002431

A761T
E852D

1/43
0/21

15/32
15/25

0.002431
0.004907

V72M

0/58
0/23
0/64
0/7
0/25

16/61
8/11
14/58
18/19
13/25

0.005696
0.006669
0.008214
0.008305
0.009737

R1338L 0/37

15/41

0.009737

G635S/
G215S 0/26

10/18

0.01156

0/15
0/42

17/26
12/36

0.01333
0.0184

0/22
1/35
0/38
0/34

15/30
15/34
11/31
11/29

0.02127
0.02131
0.02565
0.0297

1/27
0/32

8/12
10/25

0.03353
0.03877

0/19

12/22

0.0415

M46L
D130G
D2222
G
L14M
P553H
E53D
E1189
G

D574G/
D550G
P541S
V521M
K185N/
K181N
P579L
M793V

G68C
F894Y
A44V

T7A
Y554H
R1058
NM_014071
M
NM_015649
D299N
NM_017437
G76R
NM_016121
E708G
NM_177438/NM_ R1851
030621
C
NM_020901
A562V
M1359
NM_080645/NM_ T/M252
004370
3T

Supplementary Table 9: Significant mutations identified in Clone 8

S25

chr
chr11
chr9

pos
65380016
1.39E+08

chr1
chr4
chr10

94412133
1695387
53746432

chr2

9464448

chr9
chr5
chr6

1.39E+08
1.59E+08
26653396

chr19

10765480

chr19

16205382

chr19
chr16
chr10
chr17
chr12

7524841
66474489
94358765
71548613
1.24E+08

chr13

72234202

chr11

2998104

chr5

1.32E+08

chr2

gene
CFL1
TUBB2C
ARHGAP
29
TACC3
DKK1
ITGB1BP
1

transcript
NM_005507
NM_006088

aa change
K92N
R309C

#reads parental
1/100
0/89

#reads clone
46/100
40/85

adjp
1.2E-11
1.2E-11

NM_004815
NM_006342
NM_012242

Q1222R
K100E
T221A

1/73
0/66
1/82

41/71
36/64
41/86

1.69E-11
5.74E-11
4.67E-10

0/62

29/58

2.4E-08

NM_004763/NM_022334 A190T/A140T
P379S
E50K

0/50
0/63
0/53

27/47
30/68
28/56

5.01E-08
1.44E-07
2.3E-07

A360T

0/53

26/55

1.06E-06

I388T/I376T

0/41

26/46

1.07E-06

C743Y/C791Y/C781Y/C716Y
P1253H
A133P
S522L
P341S

0/31
1/57
0/26
0/76
1/98

24/35
23/44
16/19
25/76
29/98

1.27E-06
2.03E-06
2.63E-06
4.43E-06
4.52E-06

P734Q/P704Q

0/38

26/48

5.66E-06

E313G/E303G/E396G

1/48

25/49

1.39E-05

A36T

0/29

18/26

1.39E-05

1.31E+08

TMEM203 NM_053045
TTC1
NM_003314
HMGN4
NM_006353
NM_004945/NM_001005
362/NM_001005361/NM
DNM2
_001005360
NM_001130524/NM_032
AP1M1
493
NM_006702/NM_001166
111/NM_001166114/NM_
001166113/NM_0011661
PNPLA6 12
EDC4
NM_014329
KIF11
NM_004523
SRP68
NM_014230
UBC
NM_021009
NM_014953/NM_001128
DIS3
226
NM_001751/NM_139273
/NM_001014438/NM_00
CARS
1014437
NM_004199/NM_001017
974/NM_001142599/NM
_001142598/NM_001017
P4HA2
973
NM_001171083/NM_017
951/NM_017751/NM_00
SMPD4
1171084

G703D/G805D/G776D/G554D

0/53

20/50

4.78E-05

chr14

98994388

SETD3

Y219H

1/45

21/40

4.88E-05

chr7
chr13
chr9

72647918
21076244
36579541

MLXIPL
EFHA1
MELK

N746S/N763S/N765S/N744S
G15C
P52A

0/34
0/22
0/31

17/29
20/32
19/39

5.15E-05
0.000567
0.000822

chr17
chr12

35762184
1.32E+08

RARA
FBRSL1

I139T/I231T/I236T
D176E

0/30
0/19

17/33
10/12

0.000846
0.001077

chr14

54695033

DLGAP5

NM_199123/NM_032233
NM_032952/NM_032953
/NM_032951/NM_03295
4
NM_152726
NM_014791
NM_001145302/NM_001
024809/NM_000964/NM
_001145301
NM_001142641
NM_014750/NM_001146
015

A611V

1/35

18/35

0.001707

chr1
chr12
chr18
chr15
chr8
chr16
chr16
chr19

33006899
63432746
16803147
26081871
25402012
74239758
68841824
568322

KIAA1522
GNS
ROCK1
HERC2
CDCA2
TERF2IP
EXOSC6
POLRMT

V175M
A84P
M947T
S3570F
V521A
G160S
A494T
G1249V

0/27
0/26
0/26
0/26
1/38
0/25
0/55
0/42

22/46
16/30
14/25
13/23
16/35
19/43
11/42
9/25

0.001967
0.002176
0.002176
0.002615
0.004914
0.01212
0.02057
0.02261

chr17
chr1

1584094
28210106

WDR81
EYA3

NM_020888
NM_002076
NM_005406
NM_004667
NM_152562
NM_018975
NM_058219
NM_005035
NM_001163673/NM_152
348/NM_001163811/NM_
001163809
NM_001990

V469M/V621M/V445M/V1672M 0/19
T283A
0/12

10/17
10/13

0.03455
0.0388

Supplementary Table 10: Significant mutations identified in Clone 9

S26

chr
chrX
chr19
chrX
chr14
chr2

pos
1.53E+08
2197787
1.09E+08
23677160
15675837

chrX
chr10

40341499
94356944

chr14
chr6
chr11

1.02E+08
79968749
1.18E+08

gene
HCFC1
SF3A2
ACSL4
PSME1
DDX1
ATP6AP
2
KIF11
DYNC1
H1
HMGN3
HYOU1

transcript
NM_005334
NM_007165
NM_022977/NM_004458
NM_006263/NM_176783
NM_004939

aa change
A1313T
S131N
V612M/V571M
V152I
R400K

#reads parental
0/33
1/85
0/30
0/75
0/64

#reads clone
47/48
49/92
27/27
45/93
38/67

adjp
3.46E-17
1.39E-12
1.39E-12
2.45E-11
2.57E-11

NM_005765
NM_004523

E119G
S120P

0/32
0/25

23/26
25/27

1.01E-09
2.37E-09

NM_001376
NM_004242
NM_001130991/NM_006389

R4140H
T75A
H123D

1/67
0/50
0/62

34/64
32/60
30/69

4.05E-09
4.63E-08
1.97E-07

chr10
chr21

74680668
44369028

MRPS16 NM_016065
PWP2
NM_005049

A121T
A653V

1/65
0/58

30/65
29/67

4.46E-07
6.71E-07

chr4
chr11
chr9
chr19

57555607

POLR2B NM_000938

V132A

0/46

27/53

1.07E-06

1.34E+08
1.3E+08
4861888

NCAPD3 NM_015261
PTRH1 NM_001002913
UHRF1 NM_013282
NM_017836/NM_001164475/
SLC41A NM_001008487/NM_0010084
3
86/NM_001008485
AGPAT5 NM_018361
WDR61 NM_025234
RRAS
NM_006270
TMEM14
1
NM_032928
CHERP NM_006387

S517P
C150R
A11T

0/38
0/46
0/55

23/38
28/57
21/46

1.31E-06
1.57E-06
3.51E-06

chr3
chr8
chr15
chr19

1.27E+08
6602192
76367703
54832131

V267M/V150M/V241M/V2
31M
S324L
Y213C
G74D

0/41
1/50
0/45
0/46

21/38
26/51
22/45
24/52

4.81E-06
5.51E-06
8.63E-06
9.97E-06

chr9
chr19

1.39E+08
16497468

V35I
Y442C

1/53
1/46

26/55
26/50

9.97E-06
1.13E-05

chr19
chr19

4380498
49954677

CHAF1A NM_005483
BCL3
NM_005178
NM_032638/NM_001145662/
GATA2 NM_001145661
TRIB3
NM_021158

M557L
P444L

0/51
0/41

20/45
23/49

1.49E-05
3.32E-05

chr3
chr20

1.3E+08
324935

A300T
G227R

1/35
0/31

15/22
25/49

8.79E-05
0.000144

chr5

1.46E+08

TCERG1 NM_001040006/NM_006706
NM_004524/NM_001031803/
LLGL2
NM_001015002
NM_000213/NM_001005619/
ITGB4
NM_001005731
NM_198569/NM_020455/NM
GPR126 _001032395/NM_001032394
PITX1
NM_002653
RLTPR NM_001013838

R891H/R912H

1/45

23/49

0.00015

chr17

71066223

chr17

71257879

H98Y

0/50

22/61

0.000182

A1137V

1/63

22/63

0.00028

chr6
chr5
chr16

1.43E+08
1.34E+08
66245905

G104R
L194F
T1131I

0/22
0/44
0/38

13/18
19/50
18/42

0.000513
0.000593
0.00069

chr3

1.93E+08

R114H

0/39

18/44

0.000932

P461S/P508S
I1801T/I1831T
G471C

0/17
0/39
0/11

11/13
15/35
10/10

0.000954
0.001161
0.001688

R327W/R507W/R742W
R234Q
V368A
R1053H

1/36
0/25
0/37
0/30

22/47
16/29
16/39
19/42

0.001766
0.001874
0.001993
0.00212

32440156
1.46E+08

CCDC50 NM_174908/NM_178335
NM_007297/NM_007300/NM
BRCA1 _007294
ABCA2 NM_001606/NM_212533
TLX3
NM_021025
COL18A NM_130445/NM_030582/NM
1
_130444
SH3BP4 NM_014521
SPG7
NM_003119/NM_199367
MTMR4 NM_004687
CCDC28
B
NM_024296
FBXL6
NM_024555/NM_012162

chr17
chr9
chr5

38499551
1.39E+08
1.71E+08

chr21
chr2
chr16
chr17

45721802
2.36E+08
88125927
53927343

chr1
chr8

P12S
C291Y/C297Y

0/14
0/68

19/26
17/73

0.002664
0.002664

chr1
chr3

65045568
47118029

RAVER2 NM_018211
SETD2 NM_014159

P489T
L1646P

0/25
0/25

17/33
16/31

0.00311
0.003763

chr8

1.45E+08

1/53

22/70

0.004666

64936614
1.73E+08
1.05E+08
1.04E+08

FAM83H NM_198488
NM_033228/NM_033227/NM
TRIM23 _001656
STC2
NM_003714
RINT1
NM_021930
MGEA5 NM_001142434/NM_012215

T1108A

chr5
chr5
chr7
chr10

V353G
Q282L
V569M
S693C/S746C

0/13
0/39
0/22
0/50

17/23
14/39
16/31
15/55

0.005591
0.006778
0.009014
0.009441

chr2
chr1

38666389
1.01E+08

T149I/T144I
A207T/A220T

0/40
0/30

12/34
11/24

0.01077
0.01107

chr19

15886652

R390W

0/36

13/37

0.01651

chr17

58866829

S119N

1/41

18/50

0.01685

chr10

50620907

HNRPLL NM_138394/NM_001142650
RTCD1 NM_003729/NM_001130841
CYP4F1
1
NM_021187/NM_001128932
NM_001915/NM_001017917/
CYB561 NM_001017916
NM_018245/NM_001143997/
OGDHL NM_001143996

G662R/G453R/G605R

0/16

14/24

0.03106

chr17
chr6

71979328
1.53E+08

L851P/L822P
K46R

0/39
0/28

14/48
9/20

0.03256
0.03608

chr12
chr13
chr1

49670891
59446550
35342847

RHBDF2 NM_024599/NM_001005498
FBXO5 NM_012177
NM_000617/NM_001174125/
NM_001174126/NM_0011741
SLC11A 29/NM_001174128/NM_0011
2
74127/NM_001174130
DIAPH3 NM_030932/NM_001042517
ZMYM1 NM_024772

V510M/V539M/V506M
E266V/E529V
E233G

1/20
0/25
0/20

19/34
10/22
13/27

0.04289
0.04441
0.0488

chr22

43271691

LDOC1L NM_032287

V137M

0/14

12/19

0.0488

Supplementary Table 11: Significant mutations identified in Clone 10

S27

chr
chr9
chr11
chr10
chr4
chr10

pos
1.39E+08
65380016
94358765
1695387
53746432

chr2
chr5

9464448
1.59E+08

chr1
chr6

94412133
26653396

gene
TUBB2C
CFL1
KIF11
TACC3
DKK1
ITGB1BP
1
TTC1
ARHGAP
29
HMGN4

transcript
NM_006088
NM_005507
NM_004523
NM_006342
NM_012242
NM_004763/NM_022
334
NM_003314

aa change
R309C
K92N
A133P
K100E
T221A

#reads parental
0/89
1/100
0/26
0/66
1/82

#reads clone
46/93
45/100
35/38
39/72
45/93

adjp
6.81E-13
1.85E-11
5.08E-11
6.55E-11
9.64E-11

A190T/A140T
E50K

0/62
0/63

36/69
38/78

1.1E-09
2.85E-09

1/73
0/53

40/86
35/66

7.32E-09
1.28E-08

chr19

10765480

DNM2

0/53

36/70

2.15E-08

chr9
chr17

1.39E+08
71548613

P379S
S522L

chr2
chr16

1.31E+08
66474489

chr11
chr12

2998104
1.24E+08

chr13

72234202

chr19
chr19
chr16

16205382
568322
68841824

chr14
chr8
chr16

98994388
25402012
74239758

TMEM203 NM_053045
SRP68
NM_014230
NM_001171083/NM_0
17951/NM_017751/N
SMPD4
M_001171084
EDC4
NM_014329
NM_001751/NM_139
273/NM_001014438/
CARS
NM_001014437
UBC
NM_021009
NM_014953/NM_0011
DIS3
28226
NM_001130524/NM_0
AP1M1
32493
POLRMT NM_005035
EXOSC6 NM_058219
NM_199123/NM_032
SETD3
233
CDCA2
NM_152562
TERF2IP NM_018975

0/50
0/76

31/60
31/86

1.22E-07
2.58E-07

G703D/G805D/G776D/G554D 0/53
P1253H
1/57

32/68
32/63

2.58E-07
2.67E-07

E313G/E303G/E396G
P341S

1/48
1/98

30/52
32/100

3.53E-07
5.85E-07

P734Q/P704Q

0/38

28/55

1.09E-05

I388T/I376T
G1249V
A494T

0/41
0/42
0/55

26/53
25/56
20/54

1.15E-05
4.61E-05
9.36E-05

Y219H
V521A
G160S

1/45
1/38
0/25

27/58
23/43
23/39

9.43E-05
0.000162
0.000244

chr9

1.11E+08

CTNNAL1 NM_003798

A3T

0/21

20/31

0.000587

chr11

68435570

IGHMBP2 NM_002180
NM_001145302/NM_0
01024809/NM_00096
RARA
4/NM_001145301
NM_006702/NM_0011
66111/NM_001166114
/NM_001166113/NM_
PNPLA6 001166112
GNS
NM_002076
FBRSL1 NM_001142641
MELK
NM_014791
NM_032952/NM_032
953/NM_032951/NM_
MLXIPL
032954
SCYL2
NM_017988

I212T

0/18

22/32

0.0006

chr17

35762184

I139T/I231T/I236T

0/30

20/40

0.00069

chr19
chr12
chr12
chr9

7524841
63432746
1.32E+08
36579541

C743Y/C791Y/C781Y/C716Y
A84P
D176E
P52A

0/31
0/26
0/19
0/31

15/31
22/45
9/11
21/49

0.002251
0.002278
0.002565
0.002565

chr7
chr12

72647918
99230350

N746S/N763S/N765S/N744S
P214H

0/34
0/18

12/25
27/47

0.003009
0.004171

chr1
chr15

33006899
26081871

KIAA1522 NM_020888
HERC2
NM_004667
NM_004199/NM_001
017974/NM_0011425
99/NM_001142598/N
P4HA2
M_001017973
NM_014750/NM_0011
DLGAP5 46015
EFHA1
NM_152726
NM_080599/NM_015
UPF2
542
KPTN
NM_007059
LAMB2
NM_002292
LAMA5
NM_005560
MTMR10 NM_017762

V175M
S3570F

0/27
0/26

21/47
16/34

0.004961
0.008539

chr5

1.32E+08

A36T

0/29

14/31

0.00877

chr14
chr13

54695033
21076244

A611V
G15C

1/35
0/22

18/41
12/22

0.01043
0.01571

chr10
chr19
chr3
chr20
chr15

12049355
52675879
49133730
60332608
29021535

H686L
E183G
E1777K
A1897V
P588L

1/21
0/23
1/38
1/48
0/24

20/34
13/26
17/44
19/62
15/35

0.01794
0.01965
0.02238
0.0232
0.03757

chr18

27708571

KIAA1012 NM_014939
NM_013352/NM_001
DSE
080976
ROCK1
NM_005406

G608R

1/18

17/27

0.04051

chr6
chr18

1.17E+08
16803147

Y950C
M947T

0/13
0/26

19/31
17/45

0.04343
0.04582

NM_004815
Q1222R
NM_006353
NM_004945/NM_001
005362/NM_0010053
61/NM_001005360
A360T

Supplementary Table 12: Significant mutations identified in Clone 11

S28

GENE
KIF11

NCAPD3
EPRS
MELK
ARHGAP29
BAT2
EDC4
LAMA5
DKK1

NUMGRP
5
2
2
2
2
2
2
2
2

MUT
A133P
D130G
S120P
A864T
S517P
Q362R
V530I
P52A
A959V
Q1222R
D2222G
Y2222C
L472I
P1253H
A1897V
L2313F
M122V

1,8
X
X
X
-

10
X
X
-

11,9
X
X
X
X
X
-

2,4
X
X
X
X
X
X
X

7
X
X
X
-

T221A

Description
kinesin-like protein KIF11

condensin-2 complex subunit D3

bifunctional aminoacyl-tRNA synthetase
maternal embryonic leucine zipper kinase
rho GTPase-activating protein 29
large proline-rich protein BAT2
enhancer of mRNA-decapping protein 4
laminin subunit alpha-5 precursor
dickkopf-related protein 1 precursor

Supplementary Table 13: Significant genes mutated in ispinesib-resistant clones. Genes

containing mutations present in more than 1 cluster of ispinesib-resistant clones but absent in the
parental cell line are shown.

S29