IMPLEMENTING NEXT GENERATION SEQUENCING IN A PATHOLOGY LABORATORY
|
|
|
- Benedict York
- 5 years ago
- Views:
Transcription
1 Madrid, Spain IMPLEMENTING NEXT GENERATION SEQUENCING IN A PATHOLOGY LABORATORY Dr. JL Rodríguez Peralto
2 NGS
3
4
5
6
7
8
9
10
11 Ion Torrent Oncomine Focus Assay - Implementation experience for EGFR mutation detection at HOSPITAL 12 DE OCTUBRE For Research Use Only. Not for use in diagnostic procedures.
12 Oncomine Focus Assay (Thermo Fisher) Hotspot genes, n=35 Copy Number Variants, n=19 Fusion drivers, n=23 AKT1 ALK AR BRAF CDK4 CTNNB1 DDR2 EGFR ERBB2 ERBB3 ERBB4 ESR1 FGFR2 FGFR3 GNA11 GNAQ HRAS IDH1 IDH2 JAK1 JAK2 JAK3 KIT KRAS MAP2K1 MAP2K2 MET MTOR NRAS PDGFRA PIK3CA RAF1 RET ROS1 SMO ALK AR BRAF CCND1 CDK4 CDK6 EGFR ERBB2 FGFR1 FGFR2 FGFR3 FGFR4 KIT KRAS MET MYC MYCN PDGFRA PIK3CA ALK RET ROS1 NTRK1 NTRK2 NTRK3 FGFR1 FGFR2 FGFR3 MET BRAF RAF1 ERG ETV1 ETV4 ETV5 ABL1 AKT3 AXL EGFR ERBB2 PDGFRA PPARG DNA Panel 52 genes RNA Panel For Research Use Only. Not for use in diagnostic procedures.
13 Oncomine Focus Assay Workflow Tumor Sample Oncomine Assay* DNA/RNA Kit Ion PGM System* Next-generation Sequencing Ion Reporter Workflow* Automated analysis for SNVs, indels, CNVs and gene fusions Positive Variants Mutations Copy Number Variants Gene Fusions Ion 318 Select Chip* For Research Use Only. Not for use in diagnostic procedures.
14 NGS-DNA (41) - 31 adenocarcinomas (A) - 1 Large cell carcinoma (C) - 9 metastatic adenocarcinomas (M) Mutación CNV EGFR KRAS ALK BRAF AKT1 MTOR FGFR4 MET PIK3CA JAK ERBB3 BRACA1 APC GNAQ GNA11 KIT MYC A A A A A A A A A A A A A C A A A A M A A A A A M A A M A A A M A M A A M M M A M C5 C9 C12 C14 C15 C16 C22 C24 C25 C27 C11 C10 C21 C13 C1 C2 C18 C8 C33 C34 C36 C37 C26 C4 C39 C7 C32 C38 C19 C23 C28 C17 C3 C20 C29 C6 C30 C31 C35 C40 C41 Mutation HotSpot Mutación HotSpot for validation Amplification
15 NGS (41) EGFR Nº Cases % Cases WT 27 65,9 DEL ,2 L858R 6 14,6 L858R/V834L 1 2,4 INS20 1 2,4 DEL19/T790M 1 2,4 COBAS (40) EGFR Nº Cases % Cases WT 28 70,0 DEL ,5 L858R 6 15,0 INS20 1 2,5
16 DISCORDANT CASES 7,5%, 3/40 COBAS DEL19 WT L858R NGS DEL19-T790M L858R L858R-V834L
17 For Research Use Only. Not for use in diagnostic procedures. Oncomine Knowledgebase Reporter Software
18 NGS-RNA (37) - 27 adenocarcinomas (A) - 1 Large cell carcinoma (C) - 9 metastatic adenocarcinoma (M) Mutación CNV Fusion EGFR KRAS ALK BRAF AKT1 MTOR FGFR4 MET PIK3CA JAK ERBB3 BRACA1 APC GNAQ GNA11 KIT MYC ALK MET A A A A A A A A A A A A A C A A A A M A A A A A M A A M A A A M A M A A M M M A M C A A M A A A M C5 C9 C12 C14 C15 C16 C22 C24 C25 C27 C11 C10 C21 C13 C1 C2 C18 C8 C33 C34 C36 C37 C26 C4 C39 C7 C32 C38 C19 C23 C28 C17 C3 C20 C29 C6 C30 C31 C35 C40 C41 C42 C43 C44 C45 C46 C47 C48 C49 Mutation HotSpot Mutation HotSpot for validation Amplificaction Unvaluable Fusion - 1 ALK positive confirmed by FISH - 16 ROS1 negative IQ
19 For Research Use Only. Not for use in diagnostic procedures. Oncomine Knowledgebase Reporter Software
20 BEAR Project
21 BEAR Project - Participating Sites
22 BEAR Project - Samples 48 FFPE samples : each of the 8 sites provided 6 Samples : 4 samples for gene mutation analysis (DNA extraction) 2 samples for fusion transcript analysis (RNA extraction) Previously characterized samples: Colorectal adenocarcinoma Lung adenocarcinoma Melanoma Papillary thyroid carcinoma Pancreatic adenocarcinoma
23 BEAR Project - Technical Approach - Total number of FFPE samples processed - DNA samples: 32 in triplicate - RNA samples: 16 in triplicate - Material sent from samples: - 3 sections from each sample to each processing laboratory - Laboratories that processed samples: - Hospital Ramon y Cajal Madrid - Hospital 12 de Octubre Madrid - Laboratorio de Dianas Terapeuticas Madrid - Technical support: - FAS: Andrea Verardi, Marco Morey - CAC: Francesco Acquadro
24 Oncomine Solid Tumour DNA and Fusion Transcript Kits Hotspot Genes n=22 Fusion Drivers n=4 EGFR ALK ERBB2 ERBB4 FGFR1 FGFR2 FGFR3 MET DDR2 KRAS PIK3CA BRAF AKT1 PTEN NRAS MAP2K1 STK11 NOTCH1 CTNNB1 SMAD4 FBXW7 TP53 ALK ROS1 RET NTRK1
25 BEAR Project - Results DNA 23 New Variants 30 Samples Oncomine Solid Tumor DNA CE-IVD General Filter BEAR 32 Previously characterized Variants Sensitivity: 100% (32/32) *In addition 23 potentially pathogenic variants not previously tested were found
26 BEAR Project - Results DNA WT BRAF mut EGFR mut KRAS mut NRAS TP53 P L1 LQ LQ L2 L3 LQ Wild type cases BRAF mut cases EGFR mut cases KRAS mut cases NRAS mut cases TP53 mut cases KRAS +TP53 mut cases BRAF + EGFR mut cases Low quality results P: previous characterization L1, L2, L3: results from the 3 labs performing Ion Torrent analysis LQ: low quality
27 BEAR Project Results DNA- Concordance L1 30 Samples 100% Concordance L2 30 Samples L1 26 Samples * 96% Concordance L2 26 Samples L3 26 Samples *1/26 bad quality samples didn't give results
28 BEAR Project Results DNA- Conclusions - NGS method used shows a very strong inter-laboratory concordance of results obtained - A total of 55 variants were identified in the 30 processed samples - All the expected variants (n=32) were identified (Sensitivity 100%) - 23 potentially pathogenic extra variants (not previously tested) were identified in the samples
29 Laboratorio de Dianas Terapeuticas Bárbara Angulo Carolina Dominguez Susana Hernández Fernando López Rios Hospital 12 de Octubre Jose Luis Rodríguez Peralto Yolanda Ruano Diana Cantero Hospital Ramon y Cajal José Palacios Tamara Caniego Almudena Santón Hospital Virgen del Rocio Michele Biscuola Enrique de Álava Fundación Jiménez Diaz Federico Rojo Cristina Chamizo Nerea Carvajal Hospital del Mar Beatriz Bellosillo Raquel Longaron Erica Torres Sergi Serrano Hospital Universitario Vall d Hebrón Javier Hernández Losa Roso Mares Rosa Somoza Hospital Universitario Marques de Valdecilla Javier Gómez Miguel Angel Piris Thermo Fisher Scientific and Technical support: Francesco Acquadro, CAC Andrea Verardi, FAS ; Marcos Morey, FAS
30 NGS strategies that we have tried for TMB: pros and cons Oncomine Tumor Mutation Load Assay TruSight Tumor 170 Qiaseq Comprehensive Cancer Panel Genes, Input sample and Technology 409 genes DNA RNA Amplicon-based 170 genes DNA RNA Hybridization capturebased 275 genes DNA RNA Hybridizationextension-based Detected alterations SNVs, CNVs, small InDels DNA: SNVs, CNVs, Indels RNA: Fusions, Splice Variants SNVs, CNVs, small Indels Horizontal coverage 1,75 Mb Mutational burden 0,52 Mb Mutational burden? 0,83 Mb Mutational burden? Data analysis Ion Reporter Software More artefacts Base Space Sequence Hub Software Data Less artefacts Insight Software Less artefacts (UMIs) Thermo Fisher Illumina Qiagen
31 TMB Mutations/Mb 32 NSCLCs from Hospital 12 de Octubre (Madrid) Oncomine Tumor Mutation Load Assay 9.3% High 44% Intermediate TMB Groups Mutations/Mb Low 1-5 Intermediate 6-19 High 20 Samples 46% Low For Research Use Only. Not for use in diagnostic procedures.
32 Comparison study of technologies using Foundation One as gold standard Patient # TMB MS Mutations Found VUS Total Tissue origin Type of tumour Illumina TST170 AmpliSeq CCP QiaSeq CCP Thermo TML D00/MCBM Med 7/Mb Stable STK11, MYC, KEAP1, TP53 ATR, BRIP1, CEBPA, EP300, FAM123B, IRS2, SDHA, TGFBR2, WT1 13 Brain Unknown primary adenocarcinoma 8,5 D01/MEER High 62/Mb Stable ERBB2, NF1, STK11, ERRFI1, MYC, ASXL1, CDKN2A, SMARCA4, TET2, TP Soft tissue Unknown primary adenocarcinoma 54 D02/ERR D03/MPCR D04/ARA Low 2/Mb Low 1/Mb Low 4/Mb Stable MAP2K1, ARID1A, CDKN2A/B, KDM5C, KDM6A BRCA2, STAT2, MAP3K1, SYK, TNFAIP3, MLL2, NSD1 12 Soft tissue Stable BCOR, MYB AKT1, AR, CTNNA1, FAT1 6 Lung Stable MLL3 FANCA, WISP 3 Lung Unknown primary squamous cell carcinoma Lung adenoid cystic carcinoma Lung adenoid cystic carcinoma 4 D08/MTLC Med 15/Mb Stable STK11, CDKN2A/B, KEAP1, TP Lung Lung adenocarcinoma 7,5 D10/MARP Low 4/Mb Stable KRAS, PIK3CA, APC, ARID1A, FAM1234B, TP53 BRIP1, SMAD2, MAP3K1, SMAD3, NOTCH1, ZNF703, POLE, PTCH1, ROS1 15 Peritoneum Unknown primary adenocarcinoma y = 1.077x R² = TML Thermo FoM
33 Conclusions NGS platform must be previously tested before to implant in a pathology laboratory NGS with a specific platforms is an effective and efficient technology NGS is accurate, easily to implant, cheaper and saver tissue than sequential PCR NGS is an excellent and precise technology to detect actionable mutations Some platform reports ie. Oncomine Knowledgebase Reporter Software facilitate the selection of target drugs and the clinical trials available for these patients. Thermo Fisher Scientific and its affiliates are not endorsing, recommending, or promoting any use or application of Thermo Fisher Scientific products presented by third parties during this symposium. Information and materials presented or provided by third parties are provided as-is and without warranty of any kind, including regarding intellectual property rights and reported results. Parties presenting images, text and material represent they have the rights to do so.
Targeted Agent and Profiling Utilization Registry (TAPUR ) Study. February 2018
Targeted Agent and Profiling Utilization Registry (TAPUR ) Study February 2018 Precision Medicine Therapies designed to target the molecular alteration that aids cancer development 30 TARGET gene alterations
Liquid biopsy: the experience of real life case studies
Liquid biopsy: the experience of real life case studies 10 th September 2018 Beatriz Bellosillo Servicio de Anatomía Patológica Hospital del Mar, Barcelona Agenda Introduction Experience in colorectal
SureSelect Cancer All-In-One Custom and Catalog NGS Assays
SureSelect Cancer All-In-One Custom and Catalog NGS Assays Detect all cancer-relevant variants in a single SureSelect assay SNV Indel TL SNV Indel TL Single DNA input Single AIO assay Single data analysis
Carga mutacional tumoral como biomarcador predictivo en el contexto de la inmuno-oncología
Carga mutacional tumoral como biomarcador predictivo en el contexto de la inmuno-oncología Eva M Garrido-Martin, PhD Grupo de Investigación Clínica en Cancer de Pulmón H12O-CNIO Disclaimer The opinions
Oncomine Focus assay panel and Oncomine Knowledgebase Reporter.
Oncomine Focus assay panel and Oncomine Knowledgebase Reporter. How it can help to identify relevant alteration and early phase trials. Dr Isabelle SOUBEYRAN Dr Emmanuel KHALIFA Molecular Pathology Unit
Jennifer Hauenstein Oncology Cytogenetics Emory University Hospital Atlanta, GA
Comparison of Genomic Coverage using Affymetrix OncoScan Array and Illumina TruSight Tumor 170 NGS Panel for Detection of Copy Number Abnormalities in Clinical GBM Specimens Jennifer Hauenstein Oncology
Illumina s Cancer Research Portfolio and Dedicated Workflows
Illumina s Cancer Research Portfolio and Dedicated Workflows Michael Sohn Clinical Sales Specialist Spain&Italy 2017 2017 Illumina, Inc. All rights reserved. Illumina, 24sure, BaseSpace, BeadArray, BlueFish,
Dr David Guttery Senior PDRA Dept. of Cancer Studies and CRUK Leicester Centre University of Leicester
Dr David Guttery Senior PDRA Dept. of Cancer Studies and CRUK Leicester Centre University of Leicester dsg6@le.ac.uk CFDNA/CTDNA Circulating-free AS A LIQUID DNA BIOPSY (cfdna) Tumour Biopsy Liquid Biopsy
MET skipping mutation, EGFR
New NSCLC biomarkers in clinical research: detection of MET skipping mutation, EGFR T790M, and other important biomarkers Fernando López-Ríos Laboratorio de Dianas Terapéuticas Hospital Universitario HM
Personalised cancer care Information for Medical Specialists. A new way to unlock treatment options for your patients
Personalised cancer care Information for Medical Specialists A new way to unlock treatment options for your patients Contents Optimised for clinical benefit 4 Development history 4 Full FIND IT panel vs
Frequency(%) KRAS G12 KRAS G13 KRAS A146 KRAS Q61 KRAS K117N PIK3CA H1047 PIK3CA E545 PIK3CA E542K PIK3CA Q546. EGFR exon19 NFS-indel EGFR L858R
Frequency(%) 1 a b ALK FS-indel ALK R1Q HRAS Q61R HRAS G13R IDH R17K IDH R14Q MET exon14 SS-indel KIT D8Y KIT L76P KIT exon11 NFS-indel SMAD4 R361 IDH1 R13 CTNNB1 S37 CTNNB1 S4 AKT1 E17K ERBB D769H ERBB
Clinical Grade Genomic Profiling: The Time Has Come
Clinical Grade Genomic Profiling: The Time Has Come Gary Palmer, MD, JD, MBA, MPH Senior Vice President, Medical Affairs Foundation Medicine, Inc. Oct. 22, 2013 1 Why We Are Here A Shared Vision At Foundation
Fluxion Biosciences and Swift Biosciences Somatic variant detection from liquid biopsy samples using targeted NGS
APPLICATION NOTE Fluxion Biosciences and Swift Biosciences OVERVIEW This application note describes a robust method for detecting somatic mutations from liquid biopsy samples by combining circulating tumor
APPLICATIONS OF NEXT GENERATION SEQUENCING IN SOLID TUMORS - PATHOLOGIST PROSPECTIVE
AMP COMPANION MEETING SYMPOSIUM AT USCAP 2015 NEXT-GENERATION OF PATHOLOGY: ROLE OF PATHOLOGIST IN NGS-BASED PERSONALIZED MEDICINE APPLICATIONS OF NEXT GENERATION SEQUENCING IN SOLID TUMORS - PATHOLOGIST
Next Generation Sequencing in Clinical Practice: Impact on Therapeutic Decision Making
Next Generation Sequencing in Clinical Practice: Impact on Therapeutic Decision Making November 20, 2014 Capturing Value in Next Generation Sequencing Symposium Douglas Johnson MD, MSCI Vanderbilt-Ingram
What is the status of the technologies of "precision medicine?
Session 2: What is the status of the technologies of "precision medicine? Gideon Blumenthal, MD, Clinical Team Leader, Thoracic and Head/Neck Oncology, Center for Drug Evaluation and Research (CDER), U.S.
The linking of specific cancer genetic alterations to molecular targeted therapies is driving a new era of personalised medicine
The linking of specific cancer genetic alterations to molecular targeted therapies is driving a new era of personalised medicine Oncologica addresses this new era of precision medicine by exploiting state
Accel-Amplicon Panels
Accel-Amplicon Panels Amplicon sequencing has emerged as a reliable, cost-effective method for ultra-deep targeted sequencing. This highly adaptable approach is especially applicable for in-depth interrogation
The Center for PERSONALIZED DIAGNOSTICS
The Center for PERSONALIZED DIAGNOSTICS Precision Diagnostics for Personalized Medicine A joint initiative between The Department of Pathology and Laboratory Medicine & The Abramson Cancer Center The (CPD)
Illumina Trusight Myeloid Panel validation A R FHAN R A FIQ
Illumina Trusight Myeloid Panel validation A R FHAN R A FIQ G E NETIC T E CHNOLOGIST MEDICAL G E NETICS, CARDIFF To Cover Background to the project Choice of panel Validation process Genes on panel, Protocol
Clinically Useful Next Generation Sequencing and Molecular Testing in Gliomas MacLean P. Nasrallah, MD PhD
Clinically Useful Next Generation Sequencing and Molecular Testing in Gliomas MacLean P. Nasrallah, MD PhD Neuropathology Fellow Division of Neuropathology Center for Personalized Diagnosis (CPD) Glial
EXAMPLE. - Potentially responsive to PI3K/mTOR and MEK combination therapy or mtor/mek and PKC combination therapy. ratio (%)
Dr Kate Goodhealth Goodhealth Medical Clinic 123 Address Road SUBURBTOWN NSW 2000 Melanie Citizen Referring Doctor Your ref Address Dr John Medico 123 Main Street, SUBURBTOWN NSW 2000 Phone 02 9999 9999
IntelliGENSM. Integrated Oncology is making next generation sequencing faster and more accessible to the oncology community.
IntelliGENSM Integrated Oncology is making next generation sequencing faster and more accessible to the oncology community. NGS TRANSFORMS GENOMIC TESTING Background Cancers may emerge as a result of somatically
Next generation histopathological diagnosis for precision medicine in solid cancers
Next generation histopathological diagnosis for precision medicine in solid cancers from genomics to clinical application Aldo Scarpa ARC-NET Applied Research on Cancer Department of Pathology and Diagnostics
5 th July 2016 ACGS Dr Michelle Wood Laboratory Genetics, Cardiff
5 th July 2016 ACGS Dr Michelle Wood Laboratory Genetics, Cardiff National molecular screening of patients with lung cancer for a national trial of multiple novel agents. 2000 NSCLC patients/year (late
Genomic Medicine: What every pathologist needs to know
Genomic Medicine: What every pathologist needs to know Stephen P. Ethier, Ph.D. Professor, Department of Pathology and Laboratory Medicine, MUSC Director, MUSC Center for Genomic Medicine Genomics and
Plasma-Seq conducted with blood from male individuals without cancer.
Supplementary Figures Supplementary Figure 1 Plasma-Seq conducted with blood from male individuals without cancer. Copy number patterns established from plasma samples of male individuals without cancer
Click to edit Master /tle style
Click to edit Master /tle style Tel: (314) 747-7337 Toll Free: (866) 450-7697 Fax: (314) 747-7336 Email: gps@wustl.edu Website: gps.wustl.edu GENETIC TESTING IN CANCER Ka/nka Vigh-Conrad, PhD Genomics
Clinical Grade Biomarkers in the Genomic Era Observations & Challenges
Clinical Grade Biomarkers in the Genomic Era Observations & Challenges IOM Committee on Policy Issues in the Clinical Development & Use of Biomarkers for Molecularly Targeted Therapies March 31-April 1,
Predictive biomarker profiling of > 1,900 sarcomas: Identification of potential novel treatment modalities
Predictive biomarker profiling of > 1,900 sarcomas: Identification of potential novel treatment modalities Sujana Movva 1, Wenhsiang Wen 2, Wangjuh Chen 2, Sherri Z. Millis 2, Margaret von Mehren 1, Zoran
Transform genomic data into real-life results
CLINICAL SUMMARY Transform genomic data into real-life results Biomarker testing and targeted therapies can drive improved outcomes in clinical practice New FDA-Approved Broad Companion Diagnostic for
Enabling Personalized
Molecular Enabling Personalized Diagnostics Medicine- Targeted Sequencing: NGS-based solutions Silvia Dorn Roel Reinders- Andreas Diplas Friday, 19.06.2015 Company Overview Founded in April 2011 Development
Select analysis on the next pages. Sample request and sending address see last page. Institut für Pathologie und Molekularpathologie
Diagnostic Tumor Genome Analysis Schmelzbergstrasse 12 8091 Zürich Tel.: (+41) 044 255 3929 Fax.: (+41) 044 255 4416 Client (address, telephone number): ngs.pathologie@usz.ch www.pathologie.usz.ch Sample-Nr:
Jocelyn Chapman, MD Division of Gynecologic Oncology. Julie S. Mak, MS, MSc Genetic Counselor Hereditary Cancer Clinic
Jocelyn Chapman, MD Division of Gynecologic Oncology Julie S. Mak, MS, MSc Genetic Counselor Hereditary Cancer Clinic Genetics underlies all cancers Somatic or tumor genetics Germline or inherited genetics
Secuenciación masiva: papel en la toma de decisiones
Secuenciación masiva: papel en la toma de decisiones Cancer is a Genetic Disease Development of cancer is driven by the acquisition of somatic genetic alterations: Nonsynonymous point mutations: missense.
Diagnostica Molecolare!
Diagnostica Molecolare! Aldo Scarpa Unità Diagnostica Molecolare Azienda Ospedaliera Universitaria Integrata di Verona e ARC-NET Centro di Ricerca Applicata sul Cancro PDTA CARCINOMA POLMONARE - IL PAZIENTE
Tumor mutational burden and its transition towards the clinic
Tumor mutational burden and its transition towards the clinic G C C A T C A C Wolfram Jochum Institute of Pathology Kantonsspital St.Gallen CH-9007 St.Gallen wolfram.jochum@kssg.ch 30th European Congress
Out-Patient Billing CPT Codes
Out-Patient Billing CPT Codes Updated Date: August 3, 08 Client Billed Molecular Tests HPV DNA Tissue Testing 8764 No Medicare Billed - Molecular Tests NeoARRAY NeoARRAY SNP/Cytogenetic No 89 NeoLAB NeoLAB
Next generation diagnostics Bringing high-throughput sequencing into clinical application
Next generation diagnostics Bringing high-throughput sequencing into clinical application Leonardo A. Meza-Zepeda, PhD Translational Genomics Group Institute for Cancer Research Leonardo.Meza-Zepeda@rr-research.no
Identification and clinical detection of genetic alterations of pre-neoplastic lesions Time for the PML ome? David Sidransky MD Johns Hopkins
Identification and clinical detection of genetic alterations of pre-neoplastic lesions Time for the PML ome? David Sidransky MD Johns Hopkins February 3-5, 2016 Lansdowne Resort, Leesburg, VA Molecular
Detecting Oncogenic Mutations in Whole Blood
WHITE PAPER Detecting Oncogenic Mutations in Whole Blood Analytical validation of Cynvenio Biosystems LiquidBiopsy circulating tumor cell (CTC) capture and next-generation sequencing (NGS) September 2013
Dr Yvonne Wallis Consultant Clinical Scientist West Midlands Regional Genetics Laboratory
Dr Yvonne Wallis Consultant Clinical Scientist West Midlands Regional Genetics Laboratory Personalised Therapy/Precision Medicine Selection of a therapeutic drug based on the presence or absence of a specific
Patricia Aoun MD, MPH Professor and Vice-Chair for Clinical Affairs Medical Director, Clinical Laboratories Department of Pathology City of Hope
Patricia Aoun MD, MPH Professor and Vice-Chair for Clinical Affairs Medical Director, Clinical Laboratories Department of Pathology City of Hope National Medical Center Disclosures I have no disclosures
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION Frampton et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing Supplementary Figure 1A Base substitution detection
SUPPLEMENTARY INFORMATION
doi:10.1038/nature13898 Supplementary Information Table 1 Kras mutation status of carcinogen-induced mouse lung adenomas Tumour Treatment Strain Grade Genotype Kras status (WES)* Kras status (Sanger) 32T1
August 17, Dear Valued Client:
August 7, 08 Re: CMS Announces 6-Month Period of Enforcement Discretion for Laboratory Date of Service Exception Policy Under the Medicare Clinical Laboratory Fee Schedule (the 4 Day Rule ) Dear Valued
Evolución Clonal de los Tumores y Biopsia Líquida en Cáncer de Pulmón
Evolución Clonal de los Tumores y Biopsia Líquida en Cáncer de Pulmón Ignacio I. Wistuba, M.D. Professor and Chair Department of Translational Molecular Pathology The University of Texas M. D. Anderson
Pathologists role Ancillary Studies in Cytology Challenges. Pre-analytical issues. LUNG CYTOLOGY Predictive markers and molecular tests
Pathologists role LUNG CYTOLOGY Predictive markers and molecular tests Prof. Fernando Schmitt Department of Pathology and Oncology, Medical Faculty of Porto University Head of Pathology Unit, IPATIMUP
Liquid biopsy in lung cancer: The EGFR paradigm
Liquid biopsy in lung cancer: The EGFR paradigm Lynette M. Sholl, M.D. Brigham and Women s Hospital Dana Farber Cancer Institute Department of Pathology Boston, MA Disclosure of Relevant Financial Relationships
Karl Kashofer, Phd Institut für Pathologie Medizinische Universität Graz
Expanding on WHO guideline compliant molecular testing of central nervous system tumors by low density whole genome sequencing. Karl Kashofer, Phd Institut für Pathologie Medizinische Universität Graz
Precision Oncology: Experience at UW
Precision Oncology: Experience at UW Colin Pritchard MD, PhD University of Washington, Department of Lab Medicine WSMOS Meeting November 1, 2013 Conflict of Interest Disclosures I declare the following,
Assessing the Economics of Genomic Medicine. Kenneth Offit, MD MPH Chief, Clinical Genetics Service Memorial Sloan-Kettering Cancer Center
Assessing the Economics of Genomic Medicine Kenneth Offit, MD MPH Chief, Clinical Genetics Service Memorial Sloan-Kettering Cancer Center DISCLOSURES No conflicts Patents unenforced Consultancies unpaid
NeoTYPE Cancer Profiles
NeoTYPE Cancer Profiles 30+ Multimethod Assays for Hematologic Diseases and Solid Tumors Molecular FISH Anatomic Pathology The next generation of diagnostic, prognostic, and therapeutic assessment What
RNA Extraction from Formalin Fixed Paraffin Embedded (FFPE) Tissue Enabling Next Generation Detection of Gene Fusions
RNA Extraction from Formalin Fixed Paraffin Embedded (FFPE) Tissue Enabling Next Generation Detection of Gene Fusions William M. Rehrauer, PhD Associate Professor University of Wisconsin School of Medicine
Corporate Medical Policy
Corporate Medical Policy Molecular Panel Testing of Cancers to Identify Targeted Therapies File Name: Origination: Last CAP Review: Next CAP Review: Last Review: molecular_panel_testing_of_cancers_to_identify_targeted_therapies
Table S1. Demographics of patients and tumor characteristics.
Supplemental Tables for: A Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers Kim Hirshfield et al. Table S1. Demographics of patients and tumor characteristics.
Next Generation Sequencing in Haematological Malignancy: A European Perspective. Wolfgang Kern, Munich Leukemia Laboratory
Next Generation Sequencing in Haematological Malignancy: A European Perspective Wolfgang Kern, Munich Leukemia Laboratory Diagnostic Methods Cytomorphology Cytogenetics Immunophenotype Histology FISH Molecular
The International Association for the Study of Lung Cancer (IASLC) Lung Cancer Staging Project, Data Elements
Page 1 Contents 1.1. Registration... 2 1.2. Patient Characteristics... 3 1.3. Laboratory Values at Diagnosis... 5 1.4. Lung Cancers with Multiple Lesions... 8 1.5. Primary Tumour Description... 10 1.6.
Targeted Molecular Diagnostics for Targeted Therapies in Hematological Disorders
Targeted Molecular Diagnostics for Targeted Therapies in Hematological Disorders Richard D. Press, MD, PhD Dept of Pathology Knight Cancer Institute Knight Diagnostic Labs Oregon Health & Science University
Webinar Series. Characterizing cancers from liquid biopsies and FFPE samples: The rise of targeted sequencing panels. Participating experts
Characterizing cancers from liquid biopsies and FFPE samples: The rise of targeted sequencing panels April 13, 2016 Webinar Series Brought to you by the Science/ AAAS Custom Publishing Office Participating
Protein Domain-Centric Approach to Study Cancer Somatic Mutations from High-throughput Sequencing Studies
Protein Domain-Centric Approach to Study Cancer Somatic Mutations from High-throughput Sequencing Studies Dr. Maricel G. Kann Assistant Professor Dept of Biological Sciences UMBC 2 The term protein domain
NeoTYPE Cancer Profiles
NeoTYPE Cancer Profiles Multimethod Analysis of 25+ Hematologic Diseases and Solid Tumors Anatomic Pathology FISH Molecular The next generation of diagnostic, prognostic, and therapeutic assessment NeoTYPE
Supplementary Figure 1. Copy Number Alterations TP53 Mutation Type. C-class TP53 WT. TP53 mut. Nature Genetics: doi: /ng.
Supplementary Figure a Copy Number Alterations in M-class b TP53 Mutation Type Recurrent Copy Number Alterations 8 6 4 2 TP53 WT TP53 mut TP53-mutated samples (%) 7 6 5 4 3 2 Missense Truncating M-class
Sample Metrics. Allele Frequency (%) Read Depth Ploidy. Gene CDS Effect Protein Effect. LN Metastasis Tumor Purity Computational Pathology 80% 60%
Supplemental Table 1: Estimated tumor purity, allele frequency, and independent read depth for all gene mutations classified as either potentially pathogenic or VUS in the metatastic and primary tumor
Clinical, Pathologic and Molecular Updates
Colorectal Cancer: Clinical, Pathologic and Molecular Updates Joanna A. Gibson, M.D./Ph.D. Yale University School of Medicine/Yale New Haven Hospital, Department of Pathology Gastrointestinal, Pancreaticobiliary
ECMC cfdna consensus meeting
ECMC cfdna consensus meeting State of the art for cfdna technologies 24 th November 2014 Applications of ctdna analysis for drug development Potential of ctdna analysis to: Identify the right patients
AVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits
AVENIO family of NGS oncology assays ctdna and Tumor Tissue Analysis Kits Accelerating clinical research Next-generation sequencing (NGS) has the ability to interrogate many different genes and detect
Implementation of BRCA Oncomine panel for germline and somatic variant analysis
Tagliafico ESHG 2017.pptm 3.2% 03/03/2017 Implementation of BRCA Oncomine panel for germline and somatic variant analysis Enrico Tagliafico MD, PhD, Modena, Italy Center for Genome Research University
Changing the Culture of Cancer Care II. Eric Holland Fred Hutchinson Cancer Research Center University of Washington Seattle
Changing the Culture of Cancer Care II Eric Holland Fred Hutchinson Cancer Research Center University of Washington Seattle Transforming Cancer Therapy Eric Holland Fred Hutchinson Cancer Research Center
Oncofocus. Patient Test Report
Oncofocus Patient Test Report Oncofocus Patient Test Report Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL www.oncologica.com - Tel: +44 (0)1223 785327
ACTIVITY 2: EXAMINING CANCER PATIENT DATA
OVERVIEW Refer to the Overview of Cancer Discovery Activities for Key Concepts and Learning Objectives, Curriculum Connections, and Prior Knowledge, as well as background information, references, and additional
Lukas Bubendorf Pathologie. Liquid biopsies
Lukas Bubendorf Pathologie Liquid biopsies Liquid biopsies 1. Circulating cell-free tumor-dna (ctdna) 2. Circulating tumor cells (CTC) Source: Sysmex CTCs ctdna ctrna exosomes Quantification Protein RNA
The Next Generation in Cancer Diagnostics.
The Next Generation in Cancer Diagnostics. OncoTarget was created specifically for cancer patients. Every patient s cancer is unique, which is why discovering what makes it unique can be essential for
# 1 India s Best Selling Cancer Genomics Test Precision treatment for every Cancer Patient Patient Guide
# 1 India s Best Selling Cancer Genomics Test Precision treatment for every Cancer Patient Patient Guide PositiveSelect is India s widely used Cancer Genomics test with every 8 out of 10 patients opting
Targeted next-generation sequencing of 50 cancer-related genes in Japanese patients with oral squamous cell carcinoma
Original Article Targeted next-generation sequencing of 50 cancer-related genes in Japanese patients with oral squamous cell carcinoma Tumor Biology September 2018: 1 9 Ó The Author(s) 2018 Article reuse
MEDICAL POLICY. SUBJECT: MOLECULAR PANEL TESTING OF CANCERS TO IDENTIFY TARGETED THERAPIES (Excluding NSCLC and CRC) EFFECTIVE DATE: 12/21/17
MEDICAL POLICY SUBJECT: MOLECULAR PANEL TESTING OF PAGE: 1 OF: 5 If a product excludes coverage for a service, it is not covered, and medical policy criteria do not apply. If a commercial product, including
CentoCancer STRIVE FOR THE MOST COMPLETE INFORMATION
CentoCancer STRIVE FOR THE MOST COMPLETE INFORMATION CentoCancer our most comprehensive oncogenetics panel for hereditary mutations Hereditary pathogenic variants confer an increased risk of developing
Importancia del patólogo en los tumores de origen desconocido
Importancia del patólogo en los tumores de origen desconocido Dr. Federico Rojo Fundación Jiménez Díaz, Madrid IMIM-Hospital del Mar, Barcelona Cancer unknown primary 3-5 % of diagnosed cancers Variability
What is Precision Medicine?
Precision Medicine and the Treatment of Cancer Carlos L. Arteaga, MD Center for Cancer Targeted Therapies VICC Breast Cancer Program Vanderbilt-Ingram Cancer Center (VICC) Departments of Medicine and Cancer
NCCN Non-Small Cell Lung Cancer V Meeting June 15, 2018
Guideline Page and Request Illumina Inc. requesting to replace Testing should be conducted as part of broad molecular profiling with Consider NGS-based assays that include EGFR, ALK, ROS1, and BRAF as
Supplementary Figure 1. Cytoscape bioinformatics toolset was used to create the network of protein-protein interactions between the product of each
Supplementary Figure 1. Cytoscape bioinformatics toolset was used to create the network of protein-protein interactions between the product of each mutated gene and the panel of 125 cancer-driving genes
MEDICAL POLICY Genetic Testing for Breast and Ovarian Cancers
POLICY: PG0067 ORIGINAL EFFECTIVE: 07/30/02 LAST REVIEW: 01/25/18 MEDICAL POLICY Genetic Testing for Breast and Ovarian Cancers GUIDELINES This policy does not certify benefits or authorization of benefits,
Characterisation of structural variation in breast. cancer genomes using paired-end sequencing on. the Illumina Genome Analyser
Characterisation of structural variation in breast cancer genomes using paired-end sequencing on the Illumina Genome Analyser Phil Stephens Cancer Genome Project Why is it important to study cancer? Why
SALSA MLPA probemix P175-A3 Tumour Gain Lot A3-0714: As compared to the previous version A2 (lot A2-0411), nine probes have a small change in length.
SALSA MLPA probemix P175-A3 Tumour Gain Lot A3-0714: As compared to the previous version A2 (lot A2-0411), nine probes have a small change in length. This SALSA probemix is for basic research only! This
Looking Beyond the Standard-of- Care : The Clinical Trial Option
1 Looking Beyond the Standard-of- Care : The Clinical Trial Option Terry Mamounas, M.D., M.P.H., F.A.C.S. Medical Director, Comprehensive Breast Program UF Health Cancer Center at Orlando Health Professor
Whole Genome and Transcriptome Analysis of Anaplastic Meningioma. Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute
Whole Genome and Transcriptome Analysis of Anaplastic Meningioma Patrick Tarpey Cancer Genome Project Wellcome Trust Sanger Institute Outline Anaplastic meningioma compared to other cancers Whole genomes
Exons from 137 genes were targeted for hybrid selection and massively parallel sequencing.
SUPPLEMENTARY TABLES Supplementary Table 1. Targeted Genes ABL1 ABL2 AKT1 AKT2 AKT3 ALK APC ATM AURKA BCL2 BRAF BRCA1 BRCA2 CCND1 CCNE1 CDC73 CDH1 CDK4 CDK6 CDK8 CDKN1A CDKN2A CEBPA CHEK1 CHEK2 CREBBP
Development of Circulating Tumor DNA
Development of Circulating Tumor DNA Title of presentation Arial Bold 30pt in White Biomarkers Secondary title 22pt using Arial Next in White Generation Sequencing Brian Dougherty PhD, MBA Translational
Enterprise Interest Thermo Fisher Scientific / Employee
Enterprise Interest Thermo Fisher Scientific / Employee A next-generation sequencing assay to estimate tumor mutation load from FFPE research samples Fiona Hyland. Director of R&D, Bioinformatics Clinical
Next-generation sequencing based clinical testing for lung cancer in Japan
Review Article Next-generation sequencing based clinical testing for lung cancer in Japan Masayuki Takeda 1, Kazuko Sakai 2, Kazuhiko Nakagawa 1, Kazuto Nishio 2 1 Department of Medical Oncology, 2 Department
Fusion Analysis of Solid Tumors Reveals Novel Rearrangements in Breast Carcinomas
Fusion Analysis of Solid Tumors Reveals Novel Rearrangements in Breast Carcinomas Igor Astsaturov Philip Ellis Jeff Swensen Zoran Gatalica David Arguello Sandeep Reddy Wafik El-Deiry Disclaimers Dr. Igor
QIAGEN Complete Solutions for Liquid Biopsy Molecular Testing
QIAGEN Complete Solutions for Liquid Biopsy Molecular Testing Christopher Swagell, PhD Market Development Manager, Advanced Molecular Pathology QIAGEN 1 Agenda QIAGEN Solid Tumor Testing and Liquid Biopsy
Diagnostic application of SNParrays to brain cancers
Diagnostic application of SNParrays to brain cancers Adriana Olar 4/17/2018 No disclosures 55 yo M, focal motor seizure T2 T1-post C DIAGNOSIS BRAIN, LEFT FRONTAL LOBE, BIOPSY: - DIFFUSE GLIOMA, OLIGODENDROGLIAL
Result: POSITIVE Mutations Detected: EGFR-T790M, EGFR-L858R
11427 Reed Hartman Hwy Cincinnati, OH 45241 PATIENT INFO SAMPLE Name: John Smith DOB: 4/22/1973 Age: 43 Sex: Male Address: 126 Corporate Blvd. South Plainfield, NJ 07080 Date Collected: 12/22/2015 Date
EBUS-TBNA Diagnosis and Staging of Lung Cancer
EBUS-TBNA Diagnosis and Staging of Lung Cancer Nirag Jhala MD, MIAC Professor of Pathology and Lab Med. Director of Anatomic Pathology and Cytopathology Lewis Katz School of Medicine@ Temple University
Clinical molecular profiling of archival tumor tissue and cell-free DNA from patients with Erdheim-Chester disease
ECD International Medical Symposium New York City October 26, 2017 Clinical molecular profiling of archival tumor tissue and cell-free DNA from patients with Erdheim-Chester disease Filip Janku, Eli Diamond,
Utility of liquid biopsies EQA Program Naples, IT Sidney A. Scudder, MD Director, Clinical Science 13 May, 2017
Utility of liquid biopsies EQA Program Naples, IT Sidney A. Scudder, MD Director, Clinical Science 13 May, 2017 picture placeholder Agenda cobas EGFR Mutation Test v2 Ring Trial SQI Semi Quantitative Index
Diagnostic test Suggested website label Description Hospitals available
Diagnostic test Suggested website label Description Hospitals available Abbott Molecular Inc, PATHVYSION HER-2 DNA Probe Kit (FISH) PathVysion kit A diagnostic tool used to determine whether a particular
Comprehensive Analyses of Circulating Cell- Free Tumor DNA
Comprehensive Analyses of Circulating Cell- Free Tumor DNA Boston, MA June 28th, 2016 Derek Murphy, Ph.D. Scientist, Research and Development Personal Genome Diagnostics Acquisition of Somatic Alterations