> 6000 Mutations in Melanoma. Tests That Cay Be Employed. FISH for Additions/Deletions. Comparative Genomic Hybridization
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1 Winter Clinical 2017: The Assessment and Diagnosis of Melanoma Whitney A. High, MD, JD, MEng Associate Professor, Dermatology & Pathology Director of Dermatopathology (Dermatology) University of Colorado Health Sciences Center January 2017 Hawaii, Hawaii > 6000 Mutations in Melanoma Makes for Messy Model Tests That Cay Be Employed Comparative Genomic Hybridization (acgh) Fluorescent In Situ Hybridization (FISH) Gene Expression Profiling (GEP) Examines entire genome Comparative Genomic Hybridization Detects gains or losses in copy number Gains/losses exist in >95% of melanoma Performed on FFPE tx Bauer & Bastian,Derm Therapy, 2006; 19:40-9. FISH for Additions/Deletions (Am J Surg Pathol 2009;33: ) Best probe set 6p25 (RREB1) 11q13 (CCDN1) 6q23 (MYB) CEP6 86.7% sensitive 95.4% specific identified 6/6 metastasizing ambiguous lesions 1
2 Only 60% sensitivity and only 60% specificity in ambiguous lesions. Acknowledged that for difficult Spitzoid lesions the old probe set was probably only around 70% sensitive Proposes new probe set - 6p25, 9p21, 11q13, and 8q24 Particularly interesting is addition of loss of 9p21 (p16) Overall improvement in sensitivity reported to be 94% 23 Gene Expression Profiling qrt-pcr on FFPE that is microdissected Developed and validated on N=400+ nevi/mm No lab test works all the time DermTech Another GEP based test Uses tape stripping Set for high SENSITIVITY and lesser SPECIFICITY 2
3 What you really need to know about Genetics and Melanoma Prognosis Darrell S. Rigel, MD MS Clinical Professor of Dermatology New York University School of Medicine DISCLOSURE OF RELEVANT RELATIONSHIPS WITH INDUSTRY Darrell S, Rigel, MD Melanoma Management Challenge Castle A, H, I Other Cancers 1,584,500 Cancer USA Skin Cancer 2,900,000 Magnitude of the Problem DS Rigel 2010 More Skin Cancers than all other cancers combined Skin Cancer USA Melanoma - USA Melanoma 76,380 Lifetime Risk Invasive MM 1/74 1/65 1/54 1/40 NMSC (BCC SCC) 2,100,000 1/1500 1/600 1/250 1/150 1/ Projected DS Rigel 2010 DS Rigel 2010 Rigel et al, NYU Melanoma Cooperative Group,
4 Analysis of Trends in US Melanoma Incidence and Mortality Melanoma US 2016 US Annual Deaths From Melanoma Estimated number of annual deaths from melanoma in the United States from 2009 to present Invasive = 76,380 In-situ = 68,480 Glazer et al, JAMA Dermatol Analysis of Trends in US Melanoma Incidence and Mortality Lifetime Risk of Developing Invasive Melanoma in the United States Changes in the annual lifetime risk of developing invasive melanoma in the United States from 1930 to 2016 % Surviving Melanoma US 10 Year Survival 92 Localized Regional Distant Stage 12 Glazer et al, JAMA Dermatol Pollack et al, J AmerAcad Dermatol, 2011 Melanoma US by Disease Stage Invasive MM US Cases by Thickness SEER % 16% 11% 3% 72% 8% 4% Localized Regional Distant Pollack et al, J AmerAcad Dermatol, 2011 <1mm mm mm 4+mm Landow et al, SID poster,
5 Invasive MM US Deaths by Thickness SEER % 27% 17% 27% Clinical Issue in Early Stage Melanoma All newer therapies and regional interventions are effective in metastatic melanoma Within Stage IV use and resected Stage III disease, early intervention is consistently shown to be a (or in many cases the most) significant predictor of response 1, 2, 3, 4, 5, 6, 7 While AJCC clinicopathologic factors are good majority of deaths occur in early stage disease8, 9, 10 Prognostic accuracy needs to be Improved as it has direct implications on how we follow up our patients Stage at Diagnosis Excludes Stage IV Stage III Stage II 7% 13% Stage II 13% Stage I 80% Stage I 80% Deaths by Stage at Diagnosis Excludes Stage IV Stage III 24% Stage II 35% Stage I 41% 1 Del Vecchio et al., Future Oncology; 2 Hodi et al., NEJM; 3 Joseph et al., Jrnl Clin Onc; 4 Kaufman, et al., Jrnl <1mm mm mm 4+mm Landow et al, SID poster, 2016 Clin Onc (ASCO abstract); 5 Lyle et al., Jrnl Clin Onc (ASCO abstract); 6 Menzies et al., PLoS One; 7 Steinman el al., J Surg Onc.; 8 AJCC v7, (2010) Journal of Clinical Oncology; 9 SEER data 2012; 10 Morton, et al NEJM Page 20 What is DecisionDx-Melanoma Gene Expression Profile Test (GEP) Identifies a genomic profile, not genetic mutations Validated proprietary 31 gene expression profile test Uses in formalin fixed, paraffin embedded tissue specimen obtained from primary biopsy That is, no special processing on behalf of the dermatologist or dermatopathologist Cellular Functions of GEP Pull Out Genes Related to Recurrence Migration/chemotaxis/ metastasis Chemokine/secreted molecules Gap junction/cellular adhesion Extracellular matrix protein Transcription factor Gerami et al, Clin Cancer Res; 21(1), 2015 CXCL14 SPP1 CLCA2 S100A9 S100A8 BAP-1 CXCL14 MGP SPP1 GJA1 DSC1 PPL MGP ARG1 TRIM29 ID2 Differentiation/ proliferation Cell surface receptors Structural proteins Immune response Other CRABP2 SPRRIB BTG1 TACSTD2 CLCA2 ROBO1 CST6 KRT6B KRT14 LTA4H S100A8 S100A9 TYRP1 ARG1 CXCL14 SAP130 EIF1B AQP1 RBM23 GEP Test Workflow Primary melanoma tumor tissue RNA isolation cdna generation and amplification (14X) Microfluidics PCR gene card 28 discriminant gene targets and 3 control genes Analysis of GEP with a proprietary algorithm to determine class and metastatic risk Class 1 low metastatic risk Class 2 high metastatic risk What is DecisionDx-Melanoma Gene Expression Profile Test (GEP) Identifies a genomic profile, not genetic mutations Validated proprietary 31 gene expression profile test Uses in formalin fixed, paraffin embedded tissue specimen obtained from primary biopsy That is, no special processing on behalf of the dermatologist or dermatopathologist Validated binary algorithm identifies likelihood of developing recurrence / metastasis within 5 years: Low risk Class 1 profile or High risk Class 2 profile 3
6 DecisionDx-Melanoma Clinical Validation Studies Validation Study #1: Validation Set Characteristics Validation Set (n=104) Age, median yrs (range) 58 (18-94) Follow-up, median yrs (range) 5.7 ( ) Disease-Free Survival AJCC Stage n (%) 0 0 (0%) I 56 (54%) II 34 (33%) III 12 (11%) IV 2 (2%) Breslow Thickness Median mm (range) 1.4 ( ) 1mm 45 (43%) > 1mm 58 (56%) Mitotic Index 1/mm2 29 (28%) > 1/mm2 53 (51%) Ulceration Absent 65 (63%) Present 28 (27%) Growth Pattern Superficial spreading 56 (54%) Nodular 25 (24%) Desmoplastic/lentigo 10 (10%) maligna/ acral lentiginous 5-yr DFS Class 1 = 97% Class 2 = 31% Gerami et al, Clin Cancer Res; 21(1), 2015 DecisionDx-Melanoma Clinical Validation Studies GEP testing vs. Sentinel Lymph Node Biopsy Sentinel Lymph Node biopsy, when positive, generally indicates worse prognosis Staging, not therapeutic, procedure When negative, patients may still develop metastases Validation Study #2: DecisionDx-Melanoma Combined with SLNB Status Improves Prediction of Overall Survival GEP testing vs. AJCC Criteria OS Class 1/SLNB- Class 1/SLNB+ AJCC criteria best for Stage I (thin, skin localized lesions); not very good for Stage II (thicker, skin localized lesions) Class 2/SLNB- Class 2/SLNB+ Broad range of values n 5-yr OS # of events Class 1/SLNB % 7 Class 1/SLNB+ 9 77% 2 Class 2/SLNB % 37 Class 2/SLNB % 16 AJCC developed an on line predictor tool Data about melanoma and patient entered Prognostic value given Gerami et al, J Am Acad Dermatol 72(5):780-5.e3,
7 Can DecisionDx-Melanoma Use Tumor Biology to Improve Risk Prediction Based on Clinical Factors? AJCC online tool: melanomaprognosis.org Using AJCC database, estimates an individual patient risk using additional clinical factors Study compared results from online tool risk prediction to DecisionDx Melanoma class determination 205 Stage I and II patients from ongoing DecisionDx Melanoma validation cohort had all criteria for web prediction tool Ferris et al. Abstract #2050, American Academy of Dermatology, March 2015 Using 31-GEP with AJCC On-line Tool Improves Prognostic Accuracy AJCC Online Alone Total events 50 AJCC low risk 20 40% AJCC high risk 30 60% High risk Cox Multivariate Analysis Distant metastasis Death from all causes Low risk Deaths High risk Low risk Variable HR 95% CI p value GEP Class 2/AJCC 79% AJCC 79% GEP Class 2/AJCC 79% AJCC 79% High risk by GEP or AJCC Online Total events 50 Low risk 9 18% High risk 41 82% DecisionDx-Melanoma Analysis Summary This analysis shows that both SLNB positive status and DecisionDx- Melanoma Class 2 are important predictors of DMFS and OS. SLNB identified ~30% of patients who died, but 70% of patients who died were SLNB negative. Performing the DecisionDx-Melanoma assay in the SLNB negative cohort identified over 80% of those SLNB negative patients who developed distant metastasis and died. 100% 75% 50% 25% 0% SLNB SLNB+ All Deaths n=62 Class 2 DecisionDx Melanoma Class 2 identified 80% of SLNB deaths Case Study Presentation Patient A Patient B Age Lesion site Extremity Extremity Tumor thickness Ulceration No No Stage: IB IB SLN Status: Negative Negative AJCC 5-year survival 95.7% 95.7% estimate 1 DecisionDx-Melanoma Test Result. 5-year estimate 2 Class 1 result: 97% chance metastasisfree Class 2 result: 31% chance metastasisfree Clinical Outcome: Metastasis-free at 10 years post-diagnosis Metastasized at 0.6 year post-diagnosis (lung) 1 and Balch et al. J Clin Oncol 27: , 2009; 2 Gerami et al, Clin Cancer Res; 21(1), 2015 Case Study Presentation Patient X Patient Y Age Lesion site Extremity Axial Tumor thickness Ulceration No No Stage: IIA IIA SLN Status: Negative Negative AJCC 5-year survival 73.5% 76.4% estimate 1 DecisionDx-Melanoma Test Result. 5-year estimate 2 Class 1 result: 97% chance metastasisfree Class 2 result: 31% chance metastasisfree Clinical Outcome: Metastasis-free at 4.4 years post-diagnosis Metastasized at 2 year post-diagnosis (lung) Summary: DecisionDx Melanoma: Prospectively planned, archival studies demonstrate consistent results: Evaluating tumor biology through the 31 GEP assay provides improved stratification of both low risk and high risk of recurrence over AJCC stage and SLN status Independently validated in a single center, prospective study from St. Louis University Patient Management: Guidelines recommend that follow up management be individualized according to a patient s risk of recurrence, including both follow up frequency and decisions for baseline and serial imaging studies 1 and Balch et al. J Clin Oncol 27: , 2009; 2 Lawson et al, J Clin Oncol 31(suppl; abstr 9022),
8 Impact of a Threshold on Sensitivity and Specificity On the horizon Conservative Dermpath Low FISH threshold Low proprietary threshold any test Cowboy Dermpath High FISH threshold High proprietary threshold any test 3
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