Integrative omics analyses for tumor stratification and CAR T cell therapy Hamid Bolouri Division of Human Biology Fred Hutchinson Cancer Research Center 1) Substantial differences in molecular profiles of pediatric and adult AML 2) Identification of gliomas enriched for CAR T cell therapy
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Integrative omics analyses for tumor stratification and CAR T cell … · 2017-09-22 · Integrative omics analyses for tumor stratification and CAR T cell therapy Hamid Bolouri Division
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Integrative omics analyses for
tumor stratification and CAR T cell therapy
Hamid Bolouri
Division of Human Biology
Fred Hutchinson Cancer Research Center
1) Substantial differences in molecular profiles of pediatric and adult AML
2) Identification of gliomas enriched for CAR T cell therapy
FHCRC (pediatric AML)
Soheil Meshinchi
Rhonda Ries
…
+ contractors at St Jude’s and BCCA
NIH
Daniela Gerhardt
Tanja Davidson,…
Todd Alonzo
Alan Gamis
Rob Gerbing
Phoenix Children’s (DNA.me)
Robert Arceci
Jason Farrar, …
Bioinformatics Working Group: Tim Triche Jr, Jason Farrar, Emilia Lim, HB
142 Infinium 450K methylation arrays (~600 more to come)
> 50 clinical data elements (incl. cytogenetics) per sample
Targeted sequencing of ~400 genes in
143 of the 197 whole-genome-sequenced samples
~ 650 additional ‘frequency validation’ samples
Plans/hopes for ‘full coverage’ of a total of ~2000 samples.
junctions
CNVs > 10Kbp
Indels ~ 1 – 10 bp
SNVs
CompleteGenomics whole genome sequencing: 31- to 35-base mate-paired reads up to 700bp apart
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hs a-m ir-10ahs a-m ir-100hs a-m ir-15b
hs a-m ir-155hs a-m ir-125ahs a-m ir-99b
hs a-le t-7ehs a-m ir-1468hs a-m ir-181a-1
hs a-m ir-181b-1hs a-m ir-181b-2hs a-m ir-181a-2
hs a-m ir-30dhs a-m ir-335hs a-m ir-181d
hs a-m ir-181chs a-m ir-146bhs a-m ir-146a
hs a-m ir-130ahs a-m ir-126hs a-m ir-424
hs a-m ir-542hs a-le t-7c
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hs a-m ir-505hs a-m ir-331hs a-m ir-186
hs a-m ir-148bhs a-m ir-652hs a-m ir-576
hs a-m ir-128-1hs a-m ir-128-2hs a-m ir-361
hs a-m ir-4677hs a-m ir-1287hs a-m ir-23b
hs a-m ir-330hs a-m ir-132hs a-m ir-150
hs a-m ir-342hs a-m ir-4772hs a-m ir-379
hs a-m ir-4746hs a-m ir-942hs a-m ir-151a
hs a-m ir-22hs a-m ir-140hs a-m ir-103a-1
hs a-m ir-107hs a-m ir-185hs a-m ir-3653
hs a-m ir-486hs a-m ir-451ahs a-m ir-144
hs a-m ir-183hs a-m ir-182hs a-m ir-629
hs a-m ir-192hs a-m ir-194-2hs a-m ir-194-1
hs a-m ir-3130-1hs a-m ir-30ahs a-m ir-10b
hs a-m ir-145hs a-m ir-143hs a-m ir-338
hs a-le t-7a-2hs a-le t-7a-1hs a-le t-7a-3
hs a-le t-7bhs a-m ir-339
hs a-m ir-34ahs a-m ir-1976hs a-m ir-3074
hs a-m ir-501hs a-m ir-500ahs a-m ir-532
hs a-m ir-660hs a-m ir-582hs a-m ir-196b
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hs a-m ir-152hs a-m ir-874hs a-m ir-106a
hs a-m ir-210hs a-m ir-664bhs a-m ir-664a
hs a-m ir-191hs a-m ir-345hs a-m ir-106b
hs a-m ir-25hs a-m ir-93hs a-m ir-625
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hs a-m ir-328hs a-m ir-324hs a-m ir-1307
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hs a-m ir-624hs a-m ir-15a
hs a-m ir-628hs a-m ir-454hs a-m ir-32
hs a-m ir-590
-4 -2 0 2 4
Value
00
.10
.20
.30
.40
.5
Color Key
and Density Plot
De
nsity
Normal 1 Normal 2 MLL 1 MLL 2 MLL 3
T(8;21) Inv(16)
Pui et al, J Clin Oncol 2011, 29:551-565. PML-RARA
CBF
NK
CV
CV MLL-PTD
mutTP53
0 1 2 3 4 5 6 7 years Blo
od
, 20
12
12
0:
29
63
-29
72
100
80
60
40
20
2
3
4
1
miRNA-seq (n=637)
hemoglobin
inhibition of apoptosis
RNA processing
immune response
ribosomal genes
RNA-seq(n=158)
Emilia Lim
Unsupervised clustering of DNA methylation probes (n=142)
(Tim Triche Jr and Jason Farrar)
Normal blood cells
CGI WGS
SNVs
indels
CNVs
junctions
197 tumor samples
matched remission CGI WGS
som
atic
var
ian
t ca
lls
Targeted seq 143 tumor samples
matched remission Targeted seq
som
atic
var
ian
t ca
lls
sam
e
sa
mp
les
507 tumor samples
matched remission
som
atic
var
ian
t ca
lls
Targeted seq
Targeted seq
146 tumor samples Targeted seq
pri
vate
SN
Vs,
ind
els
freq
uen
cy v
alid
atio
n 1
fr
equ
ency
val
idat
ion
2
dis
cove
ry s
et
vari
ant
veri
fica
tio
n
Clinical cytogenetics
SNVs
indels
fusions
SNP6.0 arrays
mRNA-seq
72%
SNVs/junc.s
impacting expression
76%
focal (75% CN-, 85% CN+)
high confidence discovery SNVs high confidence discovery indels
SNVs
indels
SNVs
indels
freq. indels within 3bp
freq. indels within 3bp
freq. exact matches
freq. exact matches
Removed avgNormalizedCvg < 20 Removed standard deviation of LAF > 0.22 Removed ploidyScore < 30 Checked no chrM == OK Removed CNVs in centromeric/telomeric regions Removed 6 CNV regions < 10Kbp Per patient, merged CNV regions within 10Kbp distance Marked chr-arm level CNVs (footprint > 50%) Added-in chr CNV data from CDEs (115 of 197 samples have CNVs) Matched the selected CGI CNVs (475 up, 488 down) to
recurrent SNP6 CNV regions in 192 matched Dx samples:
recur in at least 5 samples (2.5%)
803,917,882bp amplified in 894 segments
533,421,564bp deleted in 1434 segments
402 (85%) match for CN up
367 (75%) match for CN down
Example variant filtering steps - CNVs
confirmed on 2 platforms
not confirmed
15/15 predicted ELF1 deletions were confirmed by a nanoString tiling array
Expression of ELF1
ELF1
delet
ion
ELF1
WT
0
200
400
600
800
1000
1200
Exp
ressio
n V
alu
e
ELF1
exp
ress
ion
del WT
ELF1 deletions are not part of global aberrations P ~ 0.008
KMT2A MLLT3 (AF9) NRAS
MBNL1 ZEB2
RAS mutations are mutually exclusive with MLL-MLLT3 fusions (cf. FLT3)
Focal co-deletions of MBNL1 (chr3) and ZEB2 (chr2) (hyper-geometric p-value in 684 samples = 1.9e-14, p in MLL-fusion cases = 0.006)
KRAS FLT3
MBNL1
ZEB2
Example sub-populations enriched for specific targets
Nat Commun. 2015
Co-occurrence patterns (N = 684, p < 0.001)
Mutual exclusivity patterns
found by CoMEt (N = 684, p < 0.001)
Substantial differences in the genomic landscapes of pediatric and adult AML