Supplementary Table 1. A Summary of published cancer genome sequencing projects
Type
Source
Primary
tumour
Acute
myeloid
leukemia
(AML) - M1
H
e
m
at
olo
gi
ca
l
Acute
myeloid
leukemia
(AML) - M5
Follicular
lymphoma (FL)
and germinalcenter B-cell
type diffuse
large B-cell
lymphoma
(GBC DLBCL)
Primary
tumour
Primary
tumour
9 primary
tumours
Target
Highlights of Genetic Findings
Myeloid neoplasms: Acute myeloid leukemia
First cancer genome ever sequenced by massively parallel
Genome
sequencing. Identified mutations in FLT3 and NPM1,
previously known drivers of tumorigenesis.
IDH1 mutations were present in 13 of 80 (16%) of
Genome
cytologically normal AML genomes.
Newer sequencing techniques identified a base pair
insertion in DNA methyltransferase 3A (DNMT3A) not
found in the original AML-M1 genome first published by
Genome
Ley et al. in 2008. DNMT3A mutations are present in 62
of 281 (22.1%) AMLs and are independently associated
with poor outcome.
Identified a recurrent somatic mutation affecting the
DNMT3A in 23 of 112 (20.5%) AML-M5 tumors. Further
analysis of DNMT3A in AML-M4 cases revealed
Exome
mutations in 9 of 66 (13.6%). Mutations in DNMT3A were
shown to affect the protein’s enzymatic activity and alter
expression profiles. Leukemias with DNMT3A are
associated with poor prognosis.
Lymphoid neoplasms: Mature B-cell neoplasms
1 primary
FL
31 primary
Identified a recurrent somatic mutation affecting the
GCB
Exome and polycomb-group oncogene EZH2, encoding a histone
DLBCLs
transcriptome methyltransferase, in 18 of 83 (21.7%) DLBCLs and 16 of
and 7 GCB
221 (7.2%) FLs.
DLBCL cell
lines
Ref
[1]
[2]
[3]
[4]
[5]
Activated B-cell
like diffuse
large B-cell
lymphoma
(ABC DLBCL)
4 primary
tumours
Multiple
myeloma (MM)
38 primary
tumours
Chronic
lymphocytic
leukemia (CLL)
4 primary
tumours
Hairy-cell
leukemia (HCL)
Primary
tumor
Hodgkin
lymphoma
2 cancer cell
lines
Identified a single mutation, L265P, in MYD88 that was
present in 111 of 382 lymphomas (29%). Additionally
Transcriptom L265P was present in 9% of mucosa-associated lymphod
e
tissue lymphomas. Analysis of this mutation demonstrated
a gain-of-function promoting cell survival through the
NF-kB and JAK-STAT3 pathway.
Analysis of 23 multiple myeloma genomes as well as 16
multiple myeloma exomes (including one that was
analysed by both methods) revealed mutations involving
Genome and
genes that regulate: RNA processing, protein homeostasis,
exome
the NF-kB pathway, gene imprinting and the coagulation
cascade. Additionally, mutations in BRAF and in noncoding regions were discovered.
Identified 45 genes with mutations in protein-coding
sequences. Analysis of these 45 genes in an additional 363
CLL patients identified 4 genes that are recurrently
mutated: NOTCH1, MYD88, XPO1 and KLHL6.
Genome
Mutations identified in NOTCH1 and MYD88 are
activating mutations present in 31/255 (12.2%) and 9/310
(2.9%) respectively. Mutations in NOTCH1 are associated
with decreased overall survival.
Exome sequencing identified 5 nonsynonymous mutations
one of which was BRAF V600E. An additional 47 patients
with HCL were examined. All had BRAF V600E
Exome
mutations and virtually all were present in the original
clone. None were found in 195 patients with other
peripheral B-cell lymphomas and leukemias.
Lymphoid neoplasms: Hodgkin lymphoma
Identified a gene fusion involving CIITA that was found to
be recurrent in 29 of 77 B-cell lymphomas (38%) and 8 of
Transcriptom
55 (15%) classical Hodgkin lymphomas. CIITA gene
e
fusions result in down-regulation of surface HLA class II
expression and up-regulation of ligands of PDL1/2
[6]
[7]
[8]
[9]
[10]
Br
ea
st
an
d
O
va
ria
n
Lobular breast
cancer
Lung
metastasis
Basal-like
breast cancer
Primary
tumour,
brain
metastasis
and mouse
xenograft
[11]
Genome
Point mutations were predominantly C>T/G>A
transitions. Comparing the mutational spectrum of the
primary tumour with that of the metastases and xenograft,
suggested that all the mutations necessary for metastases
were already present in the primary tumour.
[12]
Triple negative
breast cancer
2 primary
tumours and
liver
metastasis
Copy number
variation of a
singlenucleus for
100 cells of
each tumour
Phylogenetic reconstruction demonstrated that tumour
progression is characterized by a “punctuated clonal
evolution”. Findings also show that metastatic potential is
achieved in the late stages of tumour evolution.
[13]
Granuolsa-cell
tumour (GCT)
4 primary
tumours
Transcriptom
e
8 primary
tumours
Exome
Ovarian clearcell carcinoma
(OCCC)
L
un
g
allowing the tumour cell to escape immune detection.
Five mutations (in ABCB11, HAUS3, SLC24A4, SNX4 and
Genome and PALB2) were prevalent in both the primary and the
transcriptome metastatic tumour. RNA-editing events contribute to the
transcriptional variation of lobular breast cancer.
Small-cell
lung cancer
18 OCCCs
and 1
OCCC cell
line
NCI-H209
cell line
Identified a single recurrent mutation 402C>G (C134W)
in FOXL2 in all 4 GCTs. Sequencing of an additional 89
GCTs revealed the same mutation in 86 (97%).
Identified PPP2R1A and ARID1A mutations in two
tumours.
Resequencing 42 OCCCs revealed PPP2R1A mutations
were present in 7% and ARID1A mutations in 57% of
OCCCs.
ARID1A mutations were present in 55 of 119 (46%)
Exome and
ovarian clear-cell carcinomas, and 10 of 33 (30%)
transcriptome
endometrioid carcinomas.
Genome
Tabocco carcinogens predominantly cause G>T/C>A
transversions, preferentially at methylated CpGs.
Mutational signatures showed evidence of transcriptioncoupled nucleotide excision repair as well as expression-
[14]
[15]
[16]
[17]
M
el
an
o
m
a
Br
ai
n
Non-small-cell
lung cancer
Primary
tumour
Malignant
pleural
mesothelioma
Primary
tumour
Melanoma
COLO-829
cell line, a
malignant
cell line
Uveal
Melanoma class
2
2 tumours
with
monosomy
3
Glioblastoma
multiforme
21 primary
tumours
Medulloblastom
a
(MB)
17 primary
tumours,
4
xenografts,
1 cell line
coupled repair.
The mutational signature was similar to that observed in
small-cell lung cancer. The predominant point mutations
Genome
were G>T/C>A transversions and in methylated CpGs
with evidence of transcription-coupled repair.
A DPP10 deletion was identified in the primary tumour.
Resequencing of this gene in 53 tumour samples was
Genome
detected in 31 (55%) and showed loss of DPP10 is
associated with a poorer survival.
The mutational imprint left by UV damage is
characterized predominantly by C>T/G>A transitions,
particularly between two adjacent pyrimidines. These
Genome
mutations occur more frequently at the 3’ base of a
pyrimidine dinucleotide and in CpG dinucleotides. There
was also evidence for transcription-coupled nucleotide
excision repair.
Both tumours contained inactivating mutations in
BRCA1-associated protein 1 (BAP1) at 3p21.1. An
additional 26 of 31 (84%) class 2 (high metastatic risk)
UMs showed mutations in BAP1, while only 1 of 26 class
Exome
1 (low metastatic risk) UMs contained BAP1 mutations.
Additionally, one patient had a germline BAP1 mutation,
suggesting that germline mutations in BAP1 could be a
novel cancer predisposition gene. BAP1 regulates a
number of genes involved in metastatic transformation.
Mutations in IDH1 were found in 18 of 149 (12%) GBMs
Exome and
and all affect amino acid R132. Mutations affecting R132
transcriptome
are associated with a better prognosis.
The number of nonsilent (nonsynonymous, missense,
nonsense, indels or splice site) mutations per
Exome
medulloblastoma, a childhood cancer, was only 8.3, five
to ten times fewer mutations compared to adult solid
tumours. The discovery of recurring mutations in MLL2
[18]
[19]
[20]
[21]
[22]
[23]
7 metastic
MBs
R
en
al
G
as
tr
oint
es
tin
al
Clear cell renal
carcinoma
(ccRCC)
7 primary
tumours
Colorectal
cancer
3 cell lines
and 8
xenografts
all derived
from liver
metastases
Pancreatic
adenocarcinoma
Exome
Exome
24 primary
tumours
Exome
24 primary
tumours
Exome
Primary
tumour and
metastasis
from
thirteen
patients
and MLL3, genes regulating transcription and chromatin
remodeling, suggests that MB is caused by mechanisms
that subvert normal brain development, explaining its
rarity in adult populations.
Identified truncating mutations in PBRM1. Sequencing of
an additional 257 renal cell carcinomas identified
truncating mutations in 88 (34%). PBRM1 maps to 3p, the
same position as tumour suppressor genes, VHL and
SETD2. This may be why 3p loss-of-heterozygosity is
commonly seen in ccRCC.
IDH1 mutations affecting R132 were overlooked as driver
mutations, however they were retrospectively recognized
after discovering similar mutations in glioblastoma
multiforme (Parsons 2008)
Grouped mutated genes into 69 gene sets of which 31
could be further grouped into 12 core signalling pathways.
Expression data of these 31 gene sets suggest that they
contribute to pancreatic tumourigenesis.
Identified one pancreatic tumor, which harbored both a
germline and somatically acquired deleterious mutation in
PALB2. Sequencing PALB2 in 96 patients with familial
pancreatic cancer identified 3 patients with germline
PALB2 truncating mutations, while none were found in
1084 controls.
Genomic
rearrangemen “Fold-back inversions” are a distinct pattern of genomic
ts by paired- instability in pancreatic cancer indicative of telomere
end
erosion and dysregulation of the G1-to-S transition.
sequencing
[24]
[25]
[26]
[27]
[28]
Pro
stat
e
Primary
tumour and
metastases
from seven
patients
Genome
Pancreatic
neuroendocrine
tumour
(PanNET)
10 sporadic
PanNETs
Exome
Hepatocellular
carcinoma
(HCC)
1 primary
tumour
Genome and
exome
Prostate
7 tumours
Genome
Analysis of the genome of pancreatic cancers at various
spatial and temporal stages of its evolution demonstrate
that it is initiated by a single parental clone, from which
progressor mutations accumulate and drive clonal
evolution. Estimated time from the initiated tumour cell to
parental clone is 11.7 years, while another 3.4 years
elapses before subclones with metastatic potential are
achieved. This suggests that metastatic cells arise late in
tumour development.
Identified and validated mutations in 58 PanNETs in
chromatin remodeling genes (MEN1 in 44% and either
DAXX or ATRX in 43%) as well as mutations involving
the mTOR pathway (14%).
Whole genome sequencing of a hepatitis C virus induced
HCC revealed a predominance of T>C/A>G transitions
with evidence of transcription-coupled repair. Exome
sequencing of the same tumour sample at a higher
sequence depth revealed sub-clones with mutations in the
tumour suppressor gene, TSC1.
Complex genomic rearrangements in prostate cancer are
characterized by balanced translocations. Furthermore, a
single closed chain of rearrangements can disrupt multiple
known cancer genes.
[29]
[30]
[31]
[32]
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