8850 Stanford Blvd, Suite 2900 Columbia, MD 21045 PH. 443-535-4060 | www.nsh.org

Molecular PathologyTechnology & MethodsForum

NSH has partnered with Targos Inc and AKESOgen, Inc to design this unique three day forum focused on molecular pathology methods & techniques utilizing expert faculty from both the United States and Europe. In-situ hybridization, microarrays and next-generation sequencing techniques are indispensable tools in molecular pathology and clinical diagnostics.

The National Society for Histotechnology Proudly Presents The

October 26-28, 2015

Atlanta, Georgia

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Membership Status (check all that apply): Select Registration Type: Current NSH Member, my dues are paid Member ($399.00) New Member – I would like to join today ($80) Non Member ($499.00) No Thanks – not a member and I don’t wish to join Additional Registrant ($350.00)

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Cancellations and RefundsAll cancellations must be received in writing by October 12, 2015 to receive a full refund. Cancellations received after October 12, 2015 and no shows to the training are non-refundable. Substitutions are accepted at any time. We must receive your substitution request in writing. Individuals registering within two weeks of the start date will not be eligible for a refund.

Molecular PathologyTechnology & MethodsForum

Date: October 26-28, 2015Place: Emory Conference Center Hotel • Atlanta, Georgia

This forum 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.

The Emory Conference Center Hotel is situated on a 26 acre forest preserve tucked away in the heart of Atlanta. Registrants are responsible for hotel / travel arrangements. We have secured a small block of rooms at the discounted group rate of $159.00 plus applicable taxes. To secure the group rate attendees must make reservations online: https://aws.passkey.com/event/14059858/owner/10456513/home.

Lodging Emory Conference Center Hotel | 1615 Clifton Road NE | Atlanta, GA 30329

Who Should Attend?This course is directed toward practicing histotechnologists, pathology assistants and 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.

Registration Fees:NSH Member: $399.00Non Member: $499.00Group Registration: Additional registrants from same location will be charged $350.00 per person.

Registration Fees include: All training materials, NSH contact hour certificate, continental breakfast and lunch each day.

Registration Fees: Member: $399 | Non Member: $499

Registration Form 2015 Molecular Pathology Technology & Methods Forum

Course OutlineCourse Topics

DNA-RNA In-Situ Hybridization (ISH)• Course to cover details of materials and methods• Over-view of potential problems (Probe size, tissue preparation,

hybridization buffer, pH, etc.,).• Novel approaches in ISH (FISH and CISH) probe development • Pathology/oncology applications

Microarray• Explanation of terminologies (e.g., targets and probes)• Chemistry of hybridization. Target to probe• Steps required in a microarray experiment (workflow)• Differences between microarray platforms: affymetrix, Agilent

Technologies and illumina • affymetrix to show glass/silicon microarray and their instrumentation

to students through power point slides• Agilent Technologies to show glass/silicon microarray and their

instrumentation to students through power point slides.• illumina to show microscopic beads and their instrumentation to

students through power point slides• Advantages of the microarray technology over FISH, IHC and RT-PCR

Next-Generation Sequencing (NGS)• illumina sequencing and chemistry• 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

• Custom panel sequencing, ChIP-seq, Coverage, De novo assembly• Library Preparation, Adapters, Index/Barcode, Multiplexing, Target

Enrichment, Baits, In-Solution Capture, Amplicon Sequencing, Gene Panels, Library Complexity, Electropherogram

• Read, Single-End Reads, Paired-End Reads, Mate Pair Reads, Read lengths (short, medium, long)

• Whole genome, Exome, RNASeq (transcriptome), Targeted sequencing, Deep sequencing , Call, SNP/SNV, CNV’s, indels.

• Uniplex PCR, Mulitplex PCR• Variant detection, alignment processing, single nucleotide variant

detection• Depth of coverage and unformity, sensitivity, specificity• Validation, base calling, read mapping and coverage analysis• RNA-seq. Methylome sequencing• BLAST, FASTQ• Circos plot• 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

• NGS reference standards• Laboratory process, data generation and quality control• Discussion of output, reagent cost, accuracy, error rate, noise, read

stability, throughput and turnaround time

The three day forum will focus on DNA-RNA ISH, Microarrays and NGS.

Tuesday, October 27, 20157:00 AM - 8:00 AM Continental Breakfast8:00 AM - 8:30 AM Molecular Portraits of Human Breast Tumors Using

Complementary DNA Microarrays Presented by Sunil Badve, MBBS, FRCPath, Joshua Edwards Professor of Pathology & Laboratory Medicine, Departments of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN

8:45 AM - 9:30 AM Discovery of Recurrent Gene Fusions in Gastric Cancer Using aCGH Presented by Nallasivam Palanisamy, MSc., MPhil, PhD., Associate Scientist, Department of Urology, Henry Ford Health System, Adjunct Associate Professor,University of Michigan Centre for Translational Pathology, Detroit, MI

9:30 AM - 10:00 AM Break10:00 AM - 10:30 AM Introduction to Polymerase Chain Reaction (PCR),

Sanger and Next-Generation Sequencing (NGS) Presented by Nallasivam Palanisamy, MSc, MPhil, PhD, Associate Scientist, Department of Urology, Henry Ford Health System, Adjunct Associate Professor,University of Michigan Centre for Translational Pathology, Detroit, MI

10:30 AM - 11:00 AM A Pathologist’s View of Pre-analytical FFPE Sample Preparation Methods and Their Impact on Next-Generation Sequencing Presented by Hans-Ulrich Schildhaus, MD, Professor and Head of Molecular Tumor Pathology, Institute of Pathology. University Hospital Göttingen, Göttingen, Germany

11:00 AM - 11:30 AM DNA Repair in FFPE Tissues to Increase NGS Library Yields Presented by New England BioLabs Inc.

11:30 AM - 12:00 PM Nucleic Acid Extraction Methods from Clinical FFPE Samples using Adaptive Focused Acoustics ™ Technology Presented by Covaris, Inc.

12:00 PM - 1:00 PM Next-Generation Sequencing 101: An Overview of Workflow and Explanation of Terminologies Presented by illumina, Agilent Technologies, Horizon Discovery Group plc, New England BioLabs Inc.

1:00 PM - 2:00 PM Lunch2:00 PM - 6:30 PM Sample Preparation, cDNA Synthesis/Amplification

and Target Enrichment Methods for Next-Generation Sequencing Presented by Agilent Technologies and illumina

Wednesday, October 28, 20157:00 AM - 8:00 AM Continental Breakfast8:00 AM - 10:00 AM Technical Presentation: Sequencing Using the

illumina Platform Presented by illumina10:00 AM - 10:30 AM Break10:30 AM - 11:30 AM NGS Reference Standards Presented by Horizon

Discovery Group plc11:30 AM - 12:30 PM Clinical Next-Generation Sequencing of FFPE

Tumor Specimens: Standardization for Lung Adenocarcinoma Presented by Michael R. Rossi, PhD, FACMG, Assistant Professor, Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA

12:30 PM - 1:30 PM Lunch1:30 PM - 3:30 PM Pipeline and Tools for NGS Analysis – Genome and

Transcriptome Presented by Agilent Technologies-Cartagenia and illumina

3:30 PM - 4:00 PM Break4:00 PM - 5:00 PM An Oncologist’s 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 Presented by Brian Leyland-Jones, MBBS, PhD, Vice President of Molecular and Experimental Medicine. Avera Cancer Institute, Consulting Professor, Division of Oncology, Stanford University School of Medicine

5:00 PM - 6:30 PM Open Discussion and Q&A: Comparison of ISH, Microarray and NGS Moderated by Sunil Badve, MBBS, FRCPath, Joshua Edwards Professor of Pathology & Laboratory Medicine, Departments of Pathology and Laboratory Medicine, Indiana University, Indianapolis, IN

ALL RIGHTS RESERVEDNo 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

Monday, October 26, 20157:00 AM - 8:00 AM Continental Breakfast & Registration7:45 AM - 8:00 AM Opening Remarks Presented by George L Kumar

PhD, MBA, Targos, Inc. and Mark Bouzyk, PhD, AKESOgen, Inc.

8:00 AM - 9:30 AM Introduction to ISH Technology and Detection of microRNA’s by ISH Presented by Anthony Warford, PhD, FIBMS, CSci, Senior Lecturer in Cellular Pathology, University of Westminster, London, United Kingdom

9:30 AM - 10:30 AM Detection of Gene Fusions and Non-coding RNA by ISH Presented by Nallasivam Palanisamy, MSc., MPhil, PhD. Associate Scientist: Department of Urology: Henry Ford Health System; Adjunct Associate Professor: University of Michigan Centre for Translational Pathology, Detroit, MI

10:30 AM - 11:00 AM Break11:00 AM - 12:00 PM FISH and CISH Probe Construction for the Detection

of ALK Rearrangements in the Adenocarcinomas of the Lung Presented by Hans-Ulrich Schildhaus, MD, Professor and Head of Molecular Tumor Pathology, Institute of Pathology. University Hospital Göttingen, Göttingen, Germany

12:00 PM - 12:30 PM FISH Assay Performance Monitoring Using Reference Standards Presented by Horizon Discovery Group plc, Cambridge, United Kingdom

12:30 PM - 1:00 PM Quantification of RNA In Situ Hybridization Signals Presented by Advanced Cell Diagnostics, Hayward, CA

1:00 PM - 2:00 PM Lunch2:00 PM - 3:00 PM Introduction to DNA/RNA Microarrays and arrayCGH

Presented by Nallasivam Palanisamy, MSc, MPhil, PhD, Associate Scientist: Department of Urology: Henry Ford Health System, Adjunct Associate Professor: University of Michigan Centre for Translational Pathology, Detroit, MI

3:00 PM - 5:00 PM Technical Presentation: From Sample Preparation to Data Processing, Interpretation and Analysis Presented by affymetrix, Agilent Technologies and illumina

5:00 PM - 6:00 PM Software for Microarray Data Analysis Presented by affymetrix, Agilent Technologies and illumina

6:00 PM - 6:30 PM Q&A Panel: Advantages/Disadvantages of the Microarray Technology over IHC and FISH Moderated by Anthony Warford, PhD, FIBMS, CSci, Senior Lecturer in Cellular Pathology, University of Westminster, London. United Kingdom

Forum FacultyForum Faculty

Advanced Cell Diagnostics3960 Point Eden Way,Hayward, CA 94545USA

affymetrix3420 Central ExpresswaySanta Clara, CA 95051USA

Agilent Technologies5301 Stevens Creek BlvdSanta Clara, CA 95051USA

Covaris, Inc.14 Gill Street, Unit H Woburn, MA 01801USA

Horizon Discovery Group plc 7100 Cambridge Research ParkWaterbeach, Cambridge CB25 9TL, United Kingdom

illuminaIllumina WaySan Diego, CA 92122USA

New England BioLabs Inc.240 County RoadIpswich, MA 01938USA

Academic Commercial

Anthony Warford, PhD, FIBMS, CSciSenior Lecturer in Cellular PathologyUniversity of Westminster, London309 Regent StreetLondon W1B 2HW, United Kingdom

Brian Leyland-Jones, MBBS, PhDVice President of Molecular and Experimental MedicineAvera Cancer Institute Consulting Professor: Division of Oncology: Stanford University School of Medicine, Palo Alto, CA, USA

Hans-Ulrich Schildhaus, MDProfessor and Head of Molecular Tumor PathologyInstitute of PathologyUniversity Hospital Göttingen Robert-Koch-Straße 40 d-37075 Göttingen, Germany

Michael R. Rossi, PhD, FACMG Assistant Professor, Department of Radiation OncologyEmory University School of Medicine.1365-C Clifton Road NE, Atlanta, GA 30322

Nallasivam Palanisamy, MSc., MPhil, PhD.Associate Scientist: Department of Urology: Henry Ford Health SystemAdjunct Associate Professor:University of Michigan Centre for Translational PathologyOne Ford Place, Room 2D26Detroit, MI 48202, USA

Sunil Badve, MBBS, FRCPathJoshua Edwards Professor of Pathology & Laboratory MedicineDepartments of Pathology and Laboratory Medicine, Indiana University Indiana University Health Pathology Laboratory350 West 11th Street, Room 4050Indianapolis, IN 46202. USA

George L Kumar PhD, MBAVice President of Marketing and Scientific AffairsTargos Inc.1001 Bayhill DriveSan Bruno, CA 94066, USA

Mark Bouzyk, PhDChief Scientific OfficerAKESOgen, Inc.3155 Northwoods PlaceNorcross, GA 30071, USA

Course Directors