Course Outline

The three day forum will focus on DNA-RNA ISH, Microarrays and NGS.  Below is a summary of topics to be covered.  Scroll down to see the complete agenda with times.

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

Monday, October 26, 2015
7:00 AM - 8:00 AM Continental Breakfast & Registration
7:45 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 Break
11:00 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 Lunch
2:00 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 - 3:30 PM Technical Presentation: From Sample Preparation to Data Processing, Interpretation and Analysis
Presented by affymetrix
3:30 PM - 4:00 PM Technical Presentation: From Sample Preparation to Data Processing, Interpretation and Analysis
Presented by Agilent Technologies
4:00 PM - 4:30 PM Break
4:30 PM - 5:00 PM Technical Presentation: From Sample Preparation to Data Processing, Interpretation and Analysis
Presented by 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

Panel will consist of all academic and commercial faculty of the day's sessions
Tuesday, October 27, 2015
7:00 AM - 8:00 AM Continental Breakfast
8:00 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 Break
10:00 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 Lunch
2:00 PM - 4:00 PM Sample Preparation, cDNA Synthesis/Amplification and Target Enrichment Methods for Next-Generation Sequencing
Presented by Agilent Technologies and illumina
4:00 PM - 4:30 PM Break
4:30 PM - 6:30 PM Continued: Sample Preparation, cDNA Synthesis/Amplification and Target Enrichment Methods for Next-Generation Sequencing
Presented by Agilent Technologies and illumina
Wednesday, October 28, 2015
7:00 AM - 8:00 AM Continental Breakfast
8:00 AM - 10:00 AM Technical Presentation: Sequencing Using the illumina Platform
Presented by illumina
10:00 AM - 10:30 AM Break
10:30 AM - 11:30 AM NGS Reference Standards
Presented by Horizon Discovery Group plc
11:30 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 Lunch
1:30 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 Break
4:00 PM - 5:00 PM 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


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
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