Clinical Validation of Cytocell Pathology Probes

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1 Clinical Validation of Cytocell Pathology Probes Shivanand Richardson Specialized Technician Molecular Pathology Department of Pathology, University Medical Center Utrecht The Netherlands 5th annual Cytocell FISH User Group Meeting 2017

2 Molecular Pathology UMC Utrecht

3 Disclosures Collaboration with Cytocell

4 Content FISH diagnostics at University Medical Center Utrecht Cytocell Project workflow at University Medical Center Utrecht CytoVision Scanning and Image Analysis Clinical Validation of Cytocell Pathology Probes

5 Cytocell UMC Utrecht collaboration Cytocell Designs and manufactures FISH probes Validate FISH probes on patient material Designs new probes for new diagnostic purposes Quality requirements (ISO certification) clinical evaluation UMC Utrecht JCI Accredited institute Pathology department ISO-norm Experienced with FISH Cannot give away patient material Continuous improvement in FISH diagnostics Collaboration essential for creating and validating new FISH probes

6 Cytocell UMC Utrecht collaboration Pathology department of UMC Utrecht conducted clinical validation of FISH probes (provided by Cytocell) on patient material relevant for that probe. With this collaboration Cytocell has a partner for probe validation on patient material, and UMC Utrecht would be the first to have new validated probes in a diagnostic setting.

7 Molecular Pathology UMC Utrecht Mutation analysis NGS, Sanger, HRM Translocations FISH, RT-PCR CNV Copy number variation MLPA, FISH, SNP array Molecular Pathology UMC Utrecht HPV Human papillomavirus Methylation Array, MS-MLPA MSI Microsatellite instability B- and T- cel clonality

8 Content FISH diagnostics at University Medical Center Utrecht Cytocell Project workflow at University Medical Center Utrecht CytoVision Scanning and Image Analysis Clinical Validation of Cytocell Pathology Probes

9 UMC Utrecht FISH workflow Day 1 FISH Request (LMS) Evt. Slide sectioning HE scoring (tumor area & percentage) FISH slide in oven FISH starts 14:00, pretreatment, area marking on glass and probe o/n FISH: Monday Thursday (entire workflow) Friday (image analysis + report) FISH results: Within 2-3 days Max. 1 week (repeat analysis) Day 2 FISH stringent wash, DAPI + Cytovision scanning CytoVision analysis of images (technician + KMBP) CytoVision pdf report in UDPS (KMBP) (Uniform Decentralized System PALGA) Autorisation in UDPS (pathologist) Min. 40 FISH requests per week Daily max. 28 FISH slides (routine diagnostics + Cytocell FISH validation)

10 UMC Utrecht FISH Normal Deletion Breakapart Amplification ALK BCL2 BCL6 CEP6 CHOP cmet cmyc b.a. cmyc fusion COL1A/P DGFRB CCND1 ETV6 EWSR1 FGFR1 FGFR3 FKHR (FOXO1) FUS HER2 MALT MAML2 MDM2 MUM1 MYB NMYC PLAG-1 RET ROS1 SYT (SS18) 32 FISH Probes for diagnostic use Various manufacturers (Cytocell, Vysis, Zytolight) 1 FISH protocol (in-house method) TFE3 USP6 X-Y-18 YWHAE

11 UMC Utrecht FISH amounts

12 UMC Utrecht FISH diagnostics started 2008 LeicaDM5500 manual microscoop +LASX software Scanner Validated on 75 FISH cases Leica DM6000 Scanner + CytoVision software FISH diagnostics since 2014

13 Manual microscope vs Scanner RET Cytocell -Manual RET Cytocell -Scanner 100x 63x

14 Content FISH diagnostics at University Medical Center Utrecht Cytocell Project workflow at University Medical Center Utrecht CytoVision Scanning and Image Analysis Clinical Validation of Cytocell Pathology Probes

15 Cytocell Project Cytocell Defines the list of probes and references Phase 1 UMC Utrecht reviews the list of probes discusses/agrees with Cytocell checks the availability of tissue Cytocell probe and reference probe were tested per patient simultaneously Phase 2

16 Workflow Cytocell Project Request Receive FISH Probe request from Cytocell Tissue Pathologist advices what type of tissue to use Tissues is requested and provided by Biobank Tissue Facility UMC Utrecht FISH Slides sectioning, HE (tumor evaluation by pathologist) and FISH FISH is performed by trained technicians Analysis Imaging with scan microscope (or by manual microscope) Image analysis and scoring detailed categories Report results Images and results are evaluated by Clinical Molecular Biologist in Pathology Report Scoring results provided to Cytocell Digital Image are provided to Cytocell Clinical evaluation report

17 Workflow diagram FISH probe validation Order reference probe Register in probe database Test on normal tissue (check if concordant to datasheet) Determine tumor test tissue Request test tissue Slide Sectioning Conduct FISH Image analysis and report Use of FISH scanner Use of TMA

18 Workflow diagram Probe validation Use of FISH scanner Marked FISH processed slide Determine Tumor area and percentage in HE Determine scan method based on tumor percentage, cell density and sample size Imaging (Manual, Semiautomatic or Automatic) Scoring / Results Use of TMA

19 Workflow diagram Probe validation Use of FISH scanner Use of TMA Request TMA Tissue selection in UDPS Slide sectioning for HE Tumor area selection on HE Submit marked slides and FFPE blocks TMA is designed and made TMA slide sectioning Tumor evaluation in HE Benefits: Less probe needed Specific tumor area Image analysis with different probes in same region

20 TMA Colon/ Lung / Tonsil

21 TMA NSCLC cases

22 Content FISH diagnostics at University Medical Center Utrecht Cytocell Project workflow at University Medical Center Utrecht CytoVision Scanning and Image Analysis Clinical Validation of Cytocell Pathology Probes

23 Scanning preparation Marking of tumor area on FISH slide. Automatic scanning: Mandatory for automatic region detection. Case 1 Case 1 Case 1 Case 1 HE FISH Semi-automatic: Guidance for manual region selection.

24 Manual scoring with detailed categories Frequently > 40 categories Extremely long Excel datasheets Labor intensive Error prone

25 CytoVision probe templates Standardized diagnostic scoring +/- 8 categories Cell monitoring (aberrant cells)

26 Break-apart spot counting configuration +

27 Break- Apart FISH spot counting configuration +

28 Region Markup Case 1

29 Region Markup Case 1

30 Region Markup Case 1

31 Region Markup Case 1

32 Region Markup Case 1

33 Scanning Case 1

34 Case analysis Case 1

35 Case analysis Case 1

36 Case analysis Case 1

37 Case analysis Case 1

38 Case analysis Case 1

39 Case analysis Case 1

40 Case analysis Case 1

41 Case analysis Case 1

42 Case analysis Case 1

43 Content FISH diagnostics at University Medical Center Utrecht Cytocell Project workflow at University Medical Center Utrecht CytoVision Scanning and Image Analysis Clinical Validation of Cytocell Pathology Probes

44 Cytocell Project Phase 1

45 Frequency of genomic alterations in lung adenocarcinoma

46 ALK break-apart probe (LPS019) Intended purpose: To identify FISH rearrangements of ALK gene on chromosome 2 in patients with Non-small-cell lung carcinoma. Test tissue: Lung Primary and Metastatic tissue Aberrant cells: break apart and single red ALK cut off criteria : <10% not translocated, 10%-15% equivocal (translocation unlikely), >15% translocation Round 1 Round 2 Reference method - Vysis ALK break-apart probe (06N38-020) Source of material Archive slides TMA Patients tissue N=28 10 positive for translocation Control tissue N=8 N=5 Result Positive cases showed breakapart and single red signals N=22 1 positive for translocation 100% Concordant results between Cytocell probe and reference method

47 Phase 1- ALK ALK Cytocell ALK Vysis

48 ROS1-GOPC (FIG) break-apart/deletion probe (LPS046) Intended purpose: To identify FISH rearrangements of ROS1 gene on chromosome 6 in patients with Non-small-cell lung carcinoma. Test tissue: Lung Primary and Metastatic tissue Aberrant cells: break apart and single green ROS1-GOPC (FIG) cut off criteria : <10% not translocated, 10%-15% equivocal (translocation unlikely), >15% translocation Round 1 Round 2 Reference method - Kreatech ROS1 (6q22) breakapart probe (KBI-10752) Source of material Archive slides TMA Patients tissue N=26 4 positive for translocation Control tissue N=5 N=5 Result Positive cases showed breakapart and single green signals N=22 2 positive for translocation 3 cases discordant, increased background and weak signal with Kreatech probe

49 Phase 1 ROS1- GOPC (FIG) ROS1 Cytocell ROS1 Kreatech

50 RET break-apart probe (LPS045) Intended purpose: To identify FISH rearrangements of RET gene on chromosome 10 in patients with Non-small-cell lung carcinoma. Test tissue: Lung Primary and Metastatic tissue Aberrant cells: break apart and single red RET cut off criteria : <10% not translocated, 10%-15% equivocal (translocation unlikely), >15% translocation Round 1 Round 2 Reference method - ZytoLight SPEC RET Dual Color break-apart probe (Z ) Source of material Archive slides TMA Patients tissue N=24 2 positive for translocation Control tissue N=5 N=5 Result Positive cases showed breakapart and single red signals N=22 0 positive for translocation RET translocations are very rare <2% 100% Concordant results between Cytocell probe and reference method

51 Phase 1 RET RET Cytocell RET ZytoLight

52 Phase 1 ALK / ROS1 / RET Probe Remarks Moderate Good signal quality. Increased background caused by collagen in Lung tissue. Cellient (Cytological material) displayed increased background. Signal strength varies per case and per probe. ROS1 probe frequently display 1 signal pair per cell. Overall, the ALK, ROS1 and RET Cytocell probe works good enough for diagnostic purposes, as compared to the reference probes.

53 Cytocell Project Phase 2

54 TFE3 break-apart probe (LPS051) Intended purpose: To identify FISH rearrangements of TFE3 gene on the X chromosome in patients with Renal Cell Carcinoma. Test tissue: Renal (kidney) Aberrant cells: break apart Aberrant signal pattern gender specific: Male (XY): break-apart single red and single green signal (no fusion pair) Female (XX): fusion pair + break-apart single red and single green signal TFE3 cut off criteria : 10% translocation Reference method Source of material Round 1 ZytoLight SPEC TFE3 Dual Color break-apart probe (Z ) Sectioned slides Patients tissue N=25 1 positive for translocation (rare translocation) Control tissue Result N=7 (tonsil) 100% Concordant results between Cytocell probe and reference method

55 Phase 2 TFE3 TFE3 Cytocell TFE3 ZytoLight

56 Phase 2 TFE3 probe remarks All cases concordant. Moderate Good signal quality. Interpretation in low quality tissue material is difficult. Signal strength varies per case. Overall, the Cytocell TFE3 (LPS051) probe works good enough for diagnostic purposes, as compared to the ZytoLight probe.

57 FOXO1(FKHR) break-apart probe (LPS049) Intended purpose: To identify FISH rearrangements of FOXO1 gene on chromosome 13 in patients with Alveolar Rhabdomyosarcoma. Test tissue: Sarcoma Aberrant cells: break apart FOXO1 cut off criteria : 10% translocation Reference method Source of material Round 1 Vysis FOXO1 break-apart probe (03N60-020) Sectioned slides Patients tissue N=22 3 positive for translocation Control tissue Result N=7 (tonsil) 100% Concordant results between Cytocell probe and reference method

58 Phase 2 FOXO1 FOXO1 Cytocell FOXO1 Vysis

59 Phase 2 FOXO1 probe remarks All cases concordant. Moderate Good signal quality. Interpretation in low quality tissue material is difficult. Signal strength varies per case. Overall, the Cytocell FOXO1 (LPS049) probe works good enough for diagnostic purposes, as compared to the Vysis probe.

60 FUS break-apart probe (LPS050) Intended purpose: To identify FISH rearrangements of FUS gene on chromosome 16 in patients with a Soft Tissue Sarcoma. Test tissue: Sarcoma Aberrant cells: break apart FUS cut off criteria : 10% translocation Reference method Source of material Round 1 Vysis FUS break-apart probe (03N58-020) Sectioned slides Patients tissue N=28 13 positive for translocation Control tissue Result N=7 (tonsil) 1 case discordant, 7 cases not interpretable

61 Phase 2 FUS FUS Cytocell FUS Vysis

62 Phase 2 FUS probe remarks Moderate signal quality Most cases concordant 27 cases concordant, 1 case discordant. discordance: Cytocell: 6% break-apart - no translocation Vysis: 45% break-apart- translocation High background signals and weak FISH signal with both probes. 7 cases not interpretable: Cytocell: 7 cases Vysis: 3 cases Interpretation in low quality tissue is more difficult using the Cytocell FUS break apart probe, although the Vysis probe gives in some cases still a weak but interpretable signal. If a sample shows too much background and weak fluorescent signal, do not try to interpret the FISH signals -> Repeat analysis.

63 Take home message FISH diagnostics can be fast, accurate and robust Standardized protocols are essential for FISH diagnostics High throughput & automated image analysis is validated Critical clinical evaluation on tissue samples is necessary

64 Cytocell project Collaboration Cytocell: Kerry McKenna (Study Co-ordinator) Darleen Welford (Director of Regulatory Compliance) Steve Chatters (Senior Product Manager Pathology) Stewart Kennedy UMCU, Pathology: Roel de Weger Stefan Willems Ton Peeters Petra van der Weide Kevin van der Ven Manon Huibers TICO europe: Tessa Vermeer Marie-Christine Vierhout Shivanand Richardson

65 Molecular Pathology UMC Utrecht

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