GENOMIC ANALYSIS OF OVER 400 SARCOMAS

– Gregory M. Cote –

J. Butrynski, J. Shen, J. Morgan, Z. Duan, D. D’Adamo, G. Nielsen, S. George, F. Hornicek, G. Demetri, D. Harmon, C.

Raut, J. Hornick, E. Choy, A. Wagner

No Disclosures

Objective:

To identify the frequency and types of genomic alterations in sarcomas

– Allele-specific mutation analysis

(Profile)

– Targeted exome sequencing (FoundationOne)

Methods

Profile• Mass spectrometry-based

mutation hotspot analysis• 471 mutations in 41

cancer-related genes • Data collected

prospectively• Research study (internal

DFCI funding)

Methods

Profile• Mass spectrometry-based

mutation hotspot analysis• 471 mutations in 41

cancer-related genes • Data collected

prospectively• Research study (internal

DFCI funding)

FoundationOne• Next-generation

sequencing platform• 3,769 exons in 236 genes

and 47 introns from 19 genes commonly rearranged

• Data collected retrospectively

• Clinical study billed to insurance/patients

ProfileSarcoma Subtype Number of Samples

GIST 84 LMS 68

Unclassified STS 27 DDLPS 26

Angiosarcoma 15 Myxofibrosarcoma 15

Solitary fibrous tumor 15 Desmoid 10

Synovial sarcoma 10 myxLPS 9 PEComa 9 WDLPS 9 DFSP 7

Ewing Sarcoma 7 Endometrial Stromal Sarcoma 6

MPNST 6 Osteosarcoma 6

Pleomorphic liposarcoma 6 Chondrosarcoma 5

ASPS 4 DSRCT 4

IMT 4 PVNS 4

Epithelioid sarcoma 3 Low grade sarcoma 3 Clear cell sarcoma 2

EHE 2 FDCS 2

Phylloides 2 Undifferentiated uterine STS 2

extraskeletal myxoid chondrosarcoma

1

Intimal sarcoma 1 Myofibroblastic 1

Rhabdomyosarcoma 1 Unclassified liposarcoma 1

377 Patient Samples

Sarcoma Subtype Number of Samples Number of DNA Alterations

GIST 84 41 LMS 68 5

Unclassified STS 27 3 DDLPS 26 2

Angiosarcoma 15 3 Myxofibrosarcoma 15 0

Solitary fibrous tumor 15 0 Desmoid 10 6

Synovial sarcoma 10 1 myxLPS 9 5 PEComa 9 0 WDLPS 9 0 DFSP 7 0

Ewing Sarcoma 7 0 Endometrial Stromal Sarcoma 6 0

MPNST 6 1 Osteosarcoma 6 1

Pleomorphic liposarcoma 6 1 Chondrosarcoma 5 2

ASPS 4 0 DSRCT 4 0

IMT 4 0 PVNS 4 0

Epithelioid sarcoma 3 1 Low grade sarcoma 3 0 Clear cell sarcoma 2 0

EHE 2 0 FDCS 2 0

Phylloides 2 1 Undifferentiated uterine STS 2 0

extraskeletal myxoid chondrosarcoma

1 0

Intimal sarcoma 1 0 Myofibroblastic 1 1

Rhabdomyosarcoma 1 0 Unclassified liposarcoma 1 0

377 Patient Samples

- 74 mutations - 20% - 9% (excluding GIST and Desmoid)

Profile

83 mutations in 74 of 377 (20%) patient samples

Profile

83 mutations in 74 of 377 (20%) patient samples

Gene Mutation Sarcoma c-KIT 42/84 GIST

CTNNB1 6/10 Desmoid 1/26 LPS* 1/6 MPNST 1/3 Epithelioid 1/1 Myofibroblastic 1/27 STS NOS

RAS 3/15 Angiosarcoma 1/84 GIST 1/27 STS NOS

IDH1 1/5 Chondrosarcoma VHL 1/5 Chondrosarcoma

MLH1 1/26 LPS 1/84 GIST

PIK3CA 4/9 myxLPS 1/84 GIST 1/6 Osteosarcoma

AKT1 1/9 myxLPS

Profile

Targeted Exome Sequencing (3,769 exons in 236 genes and 47 introns from 19 genes

commonly rearranged)

71 patient samples from clinic

Sarcoma Subtype Number of Samples

Chordoma 11

LMS 11

STS 8

OS 7

ES 4

Chondrosarcoma 3

GIST 3

MPNST 3

Myxofibrosarcoma 3

SFT 3

Angiosarcoma 2

ASPS 2

DDLPS 2

myxLPS 2

RMS 2

Clear Cell Sarcoma 1

DSRCT 1

LGFMS 1

Sarcoma NOS 1

Synovial Sarcoma 1

Sarcoma Subtype Number of Samples Number of DNA Alterations

Chordoma 11 21

LMS 11 39

STS 8 17

OS 7 20

ES 4 7

Chondrosarcoma 3 7

GIST 3 4

MPNST 3 5

Myxofibrosarcoma 3 6

SFT 3 1

Angiosarcoma 2 7

ASPS 2 1

DDLPS 2 11

myxLPS 2 4

RMS 2 4

Clear Cell Sarcoma 1 2

DSRCT 1 0

LGFMS 1 2

Sarcoma NOS 1 1

Synovial Sarcoma 1 0

162 DNA alterations80% with >/= 1Median = 2 (range 0-8)

162 DNA alterations

PI3K/Akt16 (17%)

Cell Cycle56 (52%)

Receptor Tyrosine Kinase(Amplifications)

19 (13%) MAPK9 (13%)

Epigenetic21 (20%)

DNA repair6 (8%)

Other31 (38%)

Cell Cycle

M G1

SG2

p53MDM2

CDK4/6-Cyclin DCDK2-Cyclin E

p15, p16

Rb

Cell Cycle

18 (25%)

M G1

SG2

p53MDM2

CDK4/6-Cyclin DCDK2-Cyclin E

p15, p16

Rb

15 (21%)

8 (11%)

8 (11%)31 (44%)

12 (17%)

56 Aberrations (52% samples)

RTK

PI3K

PDK1 PIP3

AKT

TSC1/2

mTOR

p70S6K4EBP1

PTEN

RICTOR

AMP

RAPTOR

STK11

Rheb

PI3K/AKT

RTK

PI3K

PDK1 PIP3

AKT

TSC1/2

mTOR

p70S6K4EBP1

PTEN

RICTOR

AMP

RAPTOR

STK11

2

1

1

9 (13%)

2

1

Rheb

PI3K/AKT

16 Aberrations (17% samples)

19 RTK Amplifications, 3 RTK Activating Mutations

Summary

• Exome sequencing identified more alterations v. allele-specific analysis

• Alterations in sarcomas are heterogeneous

• Therapeutic/prognostic relevance unclear (I.e. EGFR amplification pathway addiction)

• Potential to guide clinical studies

Acknowledgements

MGH• J. Shen • Z. Duan• G. Nielsen• F. Hornicek• D. Harmon• E. Choy

Profile• Neal Lindeman

DFCI• J. Butrynski • J. Morgan• D. D’Adamo• S. George• G. Demetri• C. Raut• A. Wagner

BWH• J. Hornick