Slide deck (no audio) from Caris Life Sciences' Virtual Molecular Tumor Board hosted by COE member MedStar Washington Cancer Institute (Dr. Avani S. Mohapatra)

1. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Virtual Molecular Tumor Board
October 15th 2015
Host: MedStar Washington Cancer Institute
Leader: Dr. Avani S. Mohapatra

2. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
• Clinical Case 1
• Clinical Case 2
• Clinical Case 3
Agenda

3. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Presentation
• Early 50’s, white female with T1N0M0 L breast IDC
– ER 90%, PR <5%, HER2 neg (FISH 1.1)
tamoxifen/toremifene.
• metastatic disease – R axilla, multiple regional lymph
nodes, bone
– ER 95%, PR 10%, HER2 FISH 4.5
• Year 1-2 after DX: treated with exemestane,
fulvestrant, letrozole, THP

4. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Presentation
• Initial MWHC visit
– Pt on letrozole and HP
– Stable disease in R axilla, L 6th rib
• Progressed - biopsy of L axillary LN
– Poorly differentiated ductal carcinoma
– ER 95%, PR neg, HER2 neg by IHC but FISH 2.2
• Treatment
– Progressed on fulvestrant/trastuzumab/pertuzumab
– 1 year: Rapid progression T-DM1
• Tumor sent for Next-Generation Sequencing analysis

5. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Family History
• Mother: breast cancer, died late 40’s
• Maternal grandmother: breast cancer, died early 50’s
• Maternal aunt: breast cancer, died early 40’s
• BRCA and BART testing - Negative

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Biopsy of L axillary LN:
ER/PR
ER+ 95% PR- negative

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HER-2/neu- Negative 1+, Positive FISH
• Sent out for FISH based on
pathologist instinct
• FISH positive (HER-2/CEP 17
ratio- 2.2)
HER-2: 1+
IHC

8. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
NGS Results
• 9 genomic alterations:
– FGFR1 amplification
– AURKA amplification
– GNAS amplification
– LYN amplification
– MYC amplification
– ARFRP1 amplification
– GATA3 mutation
– ZNF217 amplification
– ZNF703 amplification

9. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
MYC Amplification
• Chr 8q2411
• Family of transcription factors containing basic helix-
loop-helix/leucine zipper domain
• Amplified in 12-18% of breast cancer
– Co-expression with HER2 associated with aggressive
behavior
• Targeted therapies: in vitro and in vivo studies show
response to 5FU and oxaliplatin
Dang Cell 2014
Nair Oncogene 2014
Chen Int J Biol Sci 2014
Arango Canc Res 2001
Augenlicht Canc Res 1997

10. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
ARFRP1 Amplification
• Chr 20q13
• ADP ribosylation factor-related protein 1
• Encodes membrane-associated GTPase
• Breast cancer: strong association between ARFRP1
amplification and cyclin gene amplification
• Targeted therapies: CDK 4/6 inhibitors (via inhibition
of CDK 4/6-cyclin D1 pathway)
Schwaederle Oncotarget 2014

11. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.

12. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Other genomic alterations
• FGFR1: Chr 8p11, amplified in 10% HR positive breast
cancer
• AURKA: Chr 20q13, overexpressed in 12-62% breast
cancers
• LYN: Chr 8q13, upregulated in breast cancer cell lines
resistant to hormonal therapy
Dienstmann Annals Onc 2014
Crane Biology of the Cell 2003
Kalous Breast Canc Res and Treat 2013
Harder Immunity 2001
Ingley Cell Comm and Sig 2012
Schwarz JCI 2014
Tabaries Oncotarget 2015

13. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
• GATA3: Chr 10p15, mutation in > 10% breast cancers,
considered marker of luminal A
• ZNF217: Chr 20q13, amplified in 20% breast cancer
• ZNF703: Chr 8p11, seen in luminal B subtype,
expressed in up to 91% of stage 1-3 breast cancers,
confers tam resistance
Krug NEJM 2015
Izzo Breast Can Res 2014
Krig Oncogene 2010
Vendrell Canc Res 2012
Nguyen Mol Onc 2014
Gala Clin Can Res 2014
Holland Mol Med 2011
Zhang PLOS 2013

14. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Take Home Message
• Chr 20q13 and 8q24 primarily implicated
• Schwaederle: association between cyclin gene and
majority of the other amplifications and mutations
present in patient’s tumor
• Lebok: 8p deletion strongly linked to poor prognosis
• Myc amplification: response to 5-FU and oxaliplatin
from colorectal studies

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Treatment Recommendation
• Target cyclin: palbociclib
• Target myc: 5-fu and oxaliplatin
Arango BJC 2003

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Palbociclib
• CDK 4/6 inhibitor
• Inhibits cell cycle progression from G1 to S phase
• Side effects: neutropenia, weakness, fatigue, anemia,
nausea

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Palbociclib
Schwaederle Oncotarget 2014

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Study 2011-219 at GUH
• Phase 1
• Purpose: test the safety and effectiveness of PD-
0332991 and 5-Fluorouracil and Oxaliplatin for
patients with advanced solid tumor malignancies
www.clinicaltrials.gov

19. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
3 yrs post-DX (upon progression)

20. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
3 months later (after four cycles on study)

21. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
• Clinical Case 1
• Clinical Case 2
• Clinical Case 3
Agenda

22. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
History
• Female early 30’s with no significant PMHx
– Recurrent abdominal pain and obstruction of increasing severity
and frequency
• Intermittent obstruction and food intolerance
• 15 Ibs weight loss
– CT Abdomen and Pelvis
• Ascending colon and abdominal masses
• Abdominal ascites
– Colonoscopy recommended
• Bx: Malignant adenocarcinoma of the ascending colon
– Started on FOLFOX with Vectibix
• 8 cycles
– CT Chest, Abdomen, and Pelvis:
• Indeterminate changes in liver
• Lesion within ascending colon, stranding in adjacent peritoneal fat
• Both ovaries enlarged
– Presents to WHC Surgical Oncology

23. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• PMHx: None
• PSHx: Colonoscopy
• Social: (-) EtOH, (-) Tobacco, (-) Illicit
• Family: Noncontributory
• Meds: None
• All: NKDA
• ROS: Abdominal Pain

24. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• Physical Exam
– General: Well appearing, NAD, AAOx3
– Resp: CTA B/L
– CV: RRR
– Abdomen: Soft, Non-tender, Non-distended. No palpable
masses. Concern for intraperitoneal fluid, but no fluid
wave appreciated
– Rectal: No palpable masses within cul-de-sac
• Laboratory and Other Studies
– CA 15-3: 2.8, CA 125: 22.8, CA 19-9: 64↑, CEA: 2.5.

25. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• Imaging
– CT Chest, Abdomen, and Pelvis
• No evidence of pulmonary metastasis
• Small right liver lobe lesion
• Infiltrating R colon mass with evidence of infiltration into the
ileocolic mesentery
• Small adjacent mesenteric nodes present
• Left adnexal cyst 6 x 4.8 cm

26. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• Exploratory Laparotomy, Greater Omentectomy, Left
Oophorectomy, Right Colon Resection, and HIPEC
– No diaphragm, omentum, or peritoneal seeding
– Single pelvic nodule identified and removed
• Fibrosis, no evidence of malignancy
– Normal R ovary and tube. L ovary with ruptured cyst
– Ascending (7 x 13 cm) colon mass
• Dilated distal small bowel
• Normal appearing appendix
– Palpable enlarged lymph nodes of R colon mesentery

27. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• Pathology
– Abdominal Wall Tissue
• Skin and soft tissue with scar fibrosis
– Pelvic Nodules
• Small foci of adenocarcinoma with background mucin
– Ruptured Left Ovarian Cyst
• Two small foci of metastatic adenocarcinoma with signet-ring cells
measuring 2 mm in the ovarian parenchyma
• Hemorrhagic corpus luteum, few small inclusion cysts
– Right Fallopian Tube
• Parasalpingeal Cyst

28. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Case
• Pathology
– Right Colon, Terminal Ileum, Greater Omentum
• Poorly differentiated mucinous adenocarcinoma with signet-ring
cells infiltrating the entire wall of the colon and attached fatty
tissue involving the cecum and ascending colon. Tumor size 6.4 x
3.5 cm
• Margins negative for carcinoma
• 8 LNs negative for metastatic carcinoma
– Appendix
• Negative for carcinoma
– Peritoneal Fluid
• No malignant cells identified

29. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Pathology
H&E 10x H&E 60x

30. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Caris Molecular Intelligence Results

31. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.

32. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.

33. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
• Clinical Case 1
• Clinical Case 2
• Clinical Case 3
Agenda

34. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Clinical Presentation/ History
• Male early 20’s, college athlete presented with 3 mos hx
of large soft tissue mass involving the right axilla thought
initially to be caused by trauma
• CT chest and axilla showed a right axillary mass 12 x 8 x
6cm with no lung metastasis.
• Received 3 cycles of neoadjuvant AIM
• Underwent radical resection with reconstruction of the
latissimus dorsal.
• Pathology c/w monophasic synovial sarcoma. Confirmed
t(x;18)
• Received 3 cycles adjuvant AIM
• Then postoperative radiation 6-10 months post- DX.

35. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
History
2 years after DX
• CT scan showed 2 possible pulmonary nodules, 4 and 6 mm RUL
• Seen at NCI for possible metasectomy. Decision to continue surveillance scans.
• Repeat CT scan, stable lung nodules. Went to NFL Combine
• 5 months later: CT scan progression of lung nodules. Had a Left VATS and right
thoracotomy , path c/w synovial sarcoma
3 years after DX
• CT scan new left lung apex pleural base
• Ineligible for NY-ESO trial, HLA-02 negative. Restarted on ifosfamide
4 years after DX
• Underwent left posterolateral thoracotomy with resection of posterior portions of
ribs 2 through 6, resection of left lower lobe metastasis with diaphragmatic
resection and primary repair
• CT scan showed new left pleural based lesion, inferior to the post-op bed. Therapy
offered, patient declined due to job interviews
• CT scan persistent left pleural based lesion new PET avid right anterior pulmonary
nodule

36. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
History - Continued
4 years after DX (6 months)
• Redo left thoracotomy, resection of posterior mediastinum
metastasis, resection of left lower lobe metastasis and
pericardial window. He also underwent a right VATS resection
of RUL metastasis with adhesiolysis
• CT scan new posterior left pleural based lesion in the
mid/lower posterior pleura.
• Received low dose Cytoxan/Sorafenib at NCI.
• CT scan progression of pleural based masses.
• Pembrolizumab trial. Received 2 cycles
• Disease progression, taken off Pembrolizumab
• Biopsy left pleural mass. Sent to Caris
• Started on pazopanib

37. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Comparison of CT scan
Pre-Pembrolizumab treatment
new right anterior chest mediastinal mass
Post-Pembrolizumab treatment

38. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Pathology
Post-Pembrolizumab treatment

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Specimen sent to Caris Life Sciences
H&E 10x H&E 20x

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IHC results
Biomarker Result Therapies
TOPO1 Positive Irinotecan/Topotecan
TOP2A Positive Anthracyclines
TLE3* Positive Taxanes
TUBB3 Negative Taxanes
PGP Negative Taxanes
ERCC1 Negative Platinums

41. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
IHC Results
Pgp
TOP2A
TLE3
TUBB3

42. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Caris Molecular Intelligence Summary
• No mutations or translocations identified.
• IHC studies, Paclitaxel possible active agent with Pazopanib.
Tan A. et al. (2010). The Oncologist, 15, 1253-1261.
Kendra K. et al. (2015). Molecular Cancer Therapeutics, 14, 461-469.

43. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
MI Profile™ for Solid Tumors: Current Biomarker List
IHC CISH FISH
Next-Gen.
Seq.
Sanger
Seq.
Fragment
Analysis
Pyro
Seq.
MI
Profile™
ALK, AR, cMET, EGFR (H-score;
NSCLC only), EGFR (excluding
NSCLC), ER, ERCC1 (ovarian
only), HER2, MGMT (excluding
glioma), MLH1 (CRC only), MSH2
(CRC only), MSH6 (CRC only), PD-
1, PD-L1, Pgp, PMS2 (CRC only),
PR, PTEN, RRM1, TLE3, TOP2A
(excluding breast), TOPO1, TS,
TUBB3
cMET,
EGFR,
HER2,
MDM2,
TOP2A
1p19q
(glioma only),
ALK
(NSCLC only),
ROS1
(NSCLC only)
See
Next-Gen
Sequencing
Cancer
Service
IDH2
(glioma only)
EGFRvIII
(glioma only),
MSI
(CRC only)
MGMT
Methylation
Analysis
(glioma only)
MI Profile X Selected Gene Fusion List

44. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
Expanded NGS Biomarker Panel (1 of 2)
ABI1 ARHGEF12 BCL11A BRIP1 CBL CDKN1B COPB1 DDB2 EML4 ETV6 FCGR2B FLT1 GNA13 HMGA2 IL21R
ABL1 ARID1A BCL11B BTG1 CBLB CDKN2A COX6C DDIT3 EP300 EWSR1 FCRL4 FLT3 GNAQ HNF1A IL6ST
ABL2 ARID2 BCL2 BTK CBLC CDKN2B CREB1 DDR2 EPHA3 EXT1 FEV FLT4 GNAS
HNRNPA2B
1 IL7R
ACSL3 ARNT BCL2L11 BUB1B CCDC6 CDKN2C CREB3L1 DDX10 EPHA5 EXT2 FGF10 FNBP1 GOLGA5 HOOK3 INHBA
ACSL6 ASPSCR1 BCL2L2 C11orf30 CCNB1IP1 CDX2 CREB3L2 DDX5 EPHB1 EZH2 FGF14 FOXA1 GOPC HOXA11 IRF4
AFF1 ASXL1 BCL3 C15orf21 CCND1 CEBPA CREBBP DDX6 EPS15 EZR FGF19 FOXL2 GPC3 HOXA13 IRS2
AFF3 ATF1 BCL6 C15orf55 CCND2 CHCHD7 CRKL DEK ERBB2 FAM123B FGF23 FOXO1 GPHN HOXA9 ITK
AFF4 ATIC BCL7A C15orf65 CCND3 CHEK1 CRLF2 DICER1 ERBB3 FAM22A FGF3 FOXO3 GPR124 HOXC11 JAK1
AKAP9 ATM BCL9 C16orf75 CCNE1 CHEK2 CRTC1 DNM2 ERBB4 FAM22B FGF4 FOXO4 GRIN2A HOXC13 JAK2
AKT1 ATP1A1 BCOR C2orf44 CD274 CHIC2 CRTC3 DNMT3A ERC1 FAM46C FGF6 FOXP1 GSK3B HOXD11 JAK3
AKT2 ATP2B3 BCORL1 CACNA1D CD74 CHN1 CSF1R DOT1L ERCC1 FANCA FGFR1 FSTL3 H3F3A HOXD13 JAZF1
AKT3 ATR BCR CALR CD79A CIC CSF3R DUX4 ERCC2 FANCC FGFR1OP FUBP1 H3F3B HRAS JUN
ALDH2 ATRX BIRC3 CAMTA1 CD79B CIITA CTCF EBF1 ERCC3 FANCD2 FGFR2 FUS HERPUD1 HSP90AA1 KAT6A
ALK AURKA BLM CANT1 CDC73 CLP1 CTLA4 ECT2L ERCC4 FANCE FGFR3 GAS7 HEY1 HSP90AB1 KCNJ5
AMER1 AURKB BMPR1A CARD11 CDH1 CLTC CTNNA1 EGFR ERCC5 FANCF FGFR4 GATA1 HGF IDH1 KDM5A
APC AXIN1 BRAF CARS CDH11 CLTCL1 CTNNB1 EIF4A2 ERG FANCG FH GATA2 HIP1 IDH2 KDM5C
AR AXL BRCA1 CASC5 CDK12 CNBP CXCR7 ELF4 ESR1 FANCL FHIT GATA3 HIST1H3B IGF1R KDM6A
ARAF BAP1 BRCA2 CASP8 CDK4 CNOT3 CYLD ELK4 ETV1 FAS FIP1L1 GID4 HIST1H4I IKBKE KDR
ARFRP1 BARD1 BRD3 CBFA2T3 CDK6 CNTRL CYP2D6 ELL ETV4 FBXO11 FLCN GMPS HLF IKZF1 KDSR
ARHGAP26 BCL10 BRD4 CBFB CDK8 COL1A1 DAXX ELN ETV5 FBXW7 FLI1 GNA11 HMGA1 IL2 KEAP1
COSMIC (Catalogue of Somatic Mutations in Cancer) defined oncology-related genes with HUGO Gene Nomenclature Committee (HGNC) symbol

45. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
KIAA1549 MAF MLF1 MTOR NFE2L2 NUP98 PDGFRA PPARG RAF1 RUNDC2A SLC34A2 SSX2 TERT TPR WHSC1L1
KIF5B MAFB MLH1 MUC1 NFIB OLIG2 PDGFRB PPP2R1A RALGDS RUNX1 SLC45A3 SSX4 TET1 TRAF7 WIF1
KIT MALT1 MLL MUTYH NFKB2 OMD PDK1 PRCC RANBP17 RUNx1T1 SMAD2 STAG2 TET2 TRIM26 WISP3
KLF4 MAML2 MLL2 MYB NFKBIA P2RY8 PER1 PRDM1 RAP1GDS1 SBDS SMAD4 STAT3 TFE3 TRIM27 WRN
KLHL6 MAP2K1 MLL3 MYC NIN PAFAH1B2 PHF6 PRDM16 RARA SDC4 SMARCA4 STAT4 TFEB TRIM33 WT1
KLK2 MAP2K2 MLLT1 MYCL1 NKX2-1 PAK3 PHOX2B PRF1 RB1 SDHAF2 SMARCB1 STAT5B TFG TRIP11 WWTR1
KRAS MAP2K4 MLLT10 MYCN NONO PALB2 PICALM PRKAR1A RBM15 SDHB SMARCE1 STIL TFPT TRRAP XPA
KTN1 MAP3K1 MLLT11 MYD88 NOTCH1 PATZ1 PIK3CA PRKDC RECQL4 SDHC SMO STK11 TFRC TSC1 XPC
LASP1 MAX MLLT3 MYH11 NOTCH2 PAX3 PIK3CG PRRX1 REL SDHD SOCS1 SUFU TGFBR2 TSC2 XPO1
LCK MCL1 MLLT4 MYH9 NPM1 PAX5 PIK3R1 PSIP1 RET SEPT5 SOX10 SUZ12 THRAP3 TSHR YWHAE
LCP1 MDM2 MLLT6 MYST4 NR4A3 PAX7 PIK3R2 PTCH1 RHOH SEPT6 SOX2 SYK TLX1 TTL ZBTB16
LGR5 MDM4 MN1 NACA NRAS PAX8 PIM1 PTEN RICTOR SEPT9 SPECC1 TAF15 TLX3 U2AF1 ZMYM2
LHFP MDS2 MNX1 NBN NSD1 PBRM1 PLAG1 PTPN11 RNF213 SET SPEN TAL1 TMPRSS2 UBR5 ZNF217
LIFR MECOM MPL NCKIPSD NT5C2 PBX1 PML PTPRC RNF43 SETBP1 SPOP TAL2 TNFAIP3 USP6 ZNF331
LMO1 MED12 MRE11A NCOA1 NTRK1 PCM1 PMS1 RABEP1 ROS1 SETD2 SRC TBL1XR1 TNFRSF14 VEGFA ZNF384
LMO2 MEF2B MSH2 NCOA2 NTRK2 PCSK7 PMS2 RAC1 RPL10 SF3B1 SRGAP3 TCEA1 TNFRSF17 VEGFB ZNF521
LPP MEN1 MSH6 NCOA4 NTRK3 PDCD1 POLE RAD21 RPL22 SFPQ SRSF2 TCF12 TOP1 VHL ZNF703
LRIG3 MET MSI2 NDRG1 NUMA1 PDCD1LG2 POT1 RAD50 RPL5 SFRS3 SS18 TCF3 TP53 VTI1A ZRSR2
LRP1B MITF MSN NF1 NUP214 PDE4DIP POU2AF1 RAD51 RPN1 SH2B3 SS18L1 TCF7L2 TPM3 WAS
LYL1 MKL1 MTCP1 NF2 NUP93 PDGFB POU5F1 RAD51L1 RPTOR SH3GL1 SSX1 TCL1A TPM4 WHSC1
COSMIC (Catalogue of Somatic Mutations in Cancer) defined oncology-related genes with HUGO Gene Nomenclature Committee (HGNC) symbol
Expanded NGS Biomarker Panel (2 of 2)

46. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.

47. The information contained in these slides is provided for educational purposes only and has been permanently de-identified.
The next VMTB will be presented by Anthony Shields M.D., Ph.D.
at Barbara Ann Karmanos Cancer Institute
Date: Wednesday October 28, 2015
Time: 5pm EST
Look for an invitation coming soon!
Please direct questions regarding the VMTB to
cariscentersofexcellence@carisls.com