Course Directors George L Kumar PhD, MBA Vice President of Marketing and Scientific Affairs Targos Inc Bayhill Drive San Bruno, CA USA

Transcription

1 NSH Molecular Pathology Technology & Methods Forum: IN-SITU HYBRIDIZATION, MICROARRAY AND NEXT-GENERATION SEQUENCING IN CLINICAL DIAGNOSTICS October 2015, Location: Emory Conference Center. Atlanta, GA Course Directors George L Kumar PhD, MBA Vice President of Marketing and Scientific Affairs Targos Inc Bayhill Drive San Bruno, CA Mark Bouzyk, PhD Chief Scientific Officer AKESOgen, Inc Northwoods Place Norcross, GA Summary: In-situ hybridization, microarrays and next-generation sequencing techniques are indispensable tools in molecular pathology and clinical diagnostics. The course is designed to provide participants a theoretical foundation and practical application into the methods and technology involved in localizing DNA sequences and gene transcripts within the interphase nuclei or on whole chromosomes, as well as rapid gene sequencing and expression analyses of a large numbers of target genes simultaneously. Audience: This course is directed toward practicing medical technologists, both in academic and private practice institutions, as well as in the pharmaceutical industry, who wish to broaden and/or update their understanding of the technology and the methods involved. Accreditation Statement: NSH is an approved provider of continuing education eligible to meet your needs for the Certification Maintenance Program, Florida license continuing education and general employer education requirements. Academic Faculty Anthony Warford, PhD, FIBMS, CSci Senior Lecturer in Cellular Pathology, University of Westminster, London 309 Regent Street London W1B 2HW United Kingdom Professor and Head of Molecular Tumor Pathology Institute of Pathology. University Hospital Göttingen Robert-Koch-Straße 40 d Göttingen, Germany Nallasivam Palanisamy, MSc., MPhil, PhD. Associate Scientist: Department of Urology: Henry Ford Health System Adjunct Associate Professor: University of Michigan Centre for Translational Pathology One Ford Place, Room 2D26 Detroit, MI 48202, Brian Leyland-Jones, MBBS, PhD Vice President of Molecular and Experimental Medicine.Avera Cancer Institute Professor: Department of Internal Medicine: University of South Dakota, Sioux Falls,, Consulting Professor: Division of Oncology: Stanford University School of Medicine, Palo Alto, CA,. Michael R. Rossi, PhD, FACMG Assistant Professor, Department of Radiation Oncology Emory University School of Medicine C Clifton Road NE, Atlanta, GA Sunil Badve, MBBS, FRCPath Joshua Edwards Professor of Pathology & Laboratory Medicine Departments of Pathology and Laboratory Medicine, Indiana University Indiana University Health Pathology Laboratory 350 West 11th Street, Room 4050 Indianapolis, IN

2 NSH Molecular Pathology Technology & Methods Forum: IN-SITU HYBRIDIZATION, MICROARRAY AND NEXT-GENERATION SEQUENCING IN CLINICAL DIAGNOSTICS October 2015, Location: Emory Conference Center. Atlanta, GA Commercial Faculty Advanced Cell Diagnostics 3960 Point Eden Way, Hayward, CA Agilent Technologies 5301 Stevens Creek Blvd Santa Clara, CA affymetrix 3420 Central Expressway Santa Clara, CA Covaris, Inc. 14 Gill Street, Unit H Woburn, MA illumina Illumina Way San Diego, CA Horizon Discovery Group plc 7100 Cambridge Research Park Waterbeach, Cambridge CB25 9TL, United Kingdom New England BioLabs Inc. 240 County Road Ipswich, MA Course Schedule/ Provisional timetable Monday, October 26, 2015 Session: DNA-RNA In-Situ Hybridization (ISH) 7:45-8:00 Opening remarks George L Kumar PhD, MBA and Mark Bouzyk, PhD :30 Introduction to ISH technology and detection of microrna s by ISH Anthony Warford, PhD, FIBMS, CSci 9:30-10:30 Detection of gene fusions and non-coding RNA by ISH 10:30-11:00 Break 11:00-12:00 FISH and CISH probe construction for the detection of ALK rearrangements in the adenocarcinomas of the lung 12:00-12:30 FISH assay performance monitoring using reference standards Horizon Discovery Group plc, Cambridge, United Kingdom 12:30-13:00 Quantification of RNA in situ hybridization signals Advanced Cell Diagnostics, Hayward, CA 13:00-14:00 Break

3 Session: Microarray 14:00-15:00 Introduction to DNA/RNA microarrays and arraycgh 15:00-15:30 Technical presentation: affymetrix 15:30-16:00 Technical presentation: Agilent Technologies 16:00-16:30 Break 16:30-17:00 Technical presentation: illumina 17:00: 18:00 Software for microarray data analysis affymetrix, Agilent Technologies and illumina 18:00-18:30 Advantages/disadvantages of the microarray technology over IHC and FISH Q&A: Session moderated by Anthony Warford, PhD, FIBMS, CSci All academic and commercial faculty to participate 18:30 Adjourn Tuesday, October 27, 2015 Session: Microarray and Next-Generation Sequencing (NGS) :45 Molecular portraits of human breast tumors using complementary DNA microarrays Sunil Badve, MBBS, FRCPath :30 Discovery of recurrent gene fusions in gastric cancer using acgh 09:30-10:00 Break 10:00-10:30 10:30-11:00 11:00-11:30 11:30-12:00 Introduction to polymerase chain reaction (PCR), Sanger and Next-Generation Sequencing (NGS) A pathologist s view of pre-analytical FFPE sample preparation methods and their impact on next-generation sequencing DNA repair in FFPE tissues to increase NGS library yields New England BioLabs Inc. Nucleic Acid Extraction methods from clinical FFPE samples using Adaptive Focused Acoustics technology Covaris, Inc. 12:00-13:00 Next-Generation Sequencing 101 (Over-view of work-flow and explanation of terminologies) illumina, Agilent Technologies, Horizon Discovery Group plc, New England BioLabs Inc.

4 13:00-14:00 Break 14:00-15:00 Sample preparation, cdna synthesis/amplification and target enrichment methods for next-generation sequencing Agilent Technologies and illumina 15:00-15:30 Break 15:30-18:30 Continued: Sample preparation, cdna synthesis/amplification and target enrichment methods for next-generation sequencing Agilent Technologies and illumina 18:30 Adjourn Wednesday, October 28, 2015 Session: Next-Generation Sequencing (NGS) :00 Sequencing using the illumina platform Technical presentation by illumina 10:00-10:30 Break 10:30-11:30 NGS reference standards Horizon Discovery Group plc, Cambridge, United Kingdom 11:30-12:30 Clinical next-generation sequencing of FFPE tumor specimens: Standardization for lung adenocarcinoma Michael R. Rossi, PhD, FACMG 12:30-13:30 Break 13:30-15:30 Pipeline and tools for NGS analysis Genome and Transcriptome Agilent Technologies-Cartagenia and illumina 15:30-16:00 Break 16:00-17:00 An oncologists view of sequencing applications in the clinic: Interpretation and implementation issues involved in treating cancer patients using next-generation sequencing data: a health network experience of the first 300 cases Brian Leyland-Jones, MB BS, PhD 17:00-18:30 Open Discussion and Q&A: Comparison of ISH, Microarray and NGS 18:30 End of course Moderated by Sunil Badve, MBBS, FRCPath 19:30-22:00 Course dinner and informal networking opportunities

5 Session details DNA-RNA In-Situ Hybridization (ISH) o Course to cover details of materials and methods o Over-view of potential problems (Probe size, tissue preparation, hybridization buffer, ph, etc.,). o Novel approaches in ISH (FISH and CISH) probe development o Pathology/oncology applications Microarray o Explanation of terminologies (e.g., targets and probes) o Chemistry of hybridization. Target to probe o Steps required in a microarray experiment (workflow) o Differences between microarray platforms: affymetrix, Agilent Technologies and illumina o affymetrix to show glass/silicon microarray and their instrumentation to students through power point slides o Agilent Technologies to show glass/silicon microarray and their instrumentation to students through power point slides. o illumina to show microscopic beads and their instrumentation to students through power point slides o Advantages of the microarray technology over FISH, IHC and RT-PCR Next-Generation Sequencing (NGS) o illumina sequencing and chemistry o Comparison between (a) paired-end and (b) mate-pair sequencing library-construction processes, Pre-Capture Library, Post-Capture Library, Mapping alignment characteristics, gapped versus ungapped alignment, Contig assembly o Custom panel sequencing, ChIP-seq, Coverage, De novo assembly o Library Preparation, Adapters, Index/Barcode, Multiplexing, Target Enrichment, Baits, In-Solution Capture, Amplicon Sequencing, Gene Panels, Library Complexity, Electropherogram o Read, Single-End Reads, Paired-End Reads, Mate Pair Reads, Read lengths (short, medium, long) o Whole genome, Exome, RNASeq (transcriptome), Targeted sequencing, Deep sequencing, Call, SNP/SNV, CNV s, indels. o Uniplex PCR, Mulitplex PCR o Variant detection, alignment processing, single nucleotide variant detection o Depth of coverage and unformity, sensitivity, specificity o Validation, base calling, read mapping and coverage analysis o RNA-seq. Methylome sequencing o BLAST, FASTQ o Circos plot o Experiment Design, Sample Collection and Sample Input (Example: Lung Vs. Breast); Sample Preparation (Example: Lung Vs. Prostrate), Library Construction, Sequencing; Pre-Processing, Assembly, Post-Assembly Analysis and data management and analysis o NGS reference standards o Laboratory process, data generation and quality control o Discussion of output, reagent cost, accuracy, error rate, noise, read stability, throughput and turnaround time ALL RIGHTS RESERVED No part of this document or course outline may be reproduced in any form by digital or mechanical means or resold without prior written permission of the authors or National Society for Histotechnology