AMP 2017 Annual Meeting Presentations and Handouts - AMP - Online Learning by AMP

 

AMP is the leading organization in the field of molecular diagnostics, and the AMP Annual meeting is the premier gathering of molecular professionals. As technologies change and new challenges arise, members and non-members alike rely on the AMP meeting to obtain the critical information needed to ensure that their patients receive the best care and best results.

This collection contains downloadable PDF slides of many of the presentations given during the AMP 2017 Annual Meeting. See the "topics" tab for a list of all the presentations for which slides are available.

 

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Course Information
Course Date:
November 16, 2017
Click on a topic name to see details and purchase options.
Thursday November 16, 2017

AMP Annual Meeting 2017 - Program Book

AMP CYP2C19 PGx Variant Standardization Project
Victoria M. Pratt, PhD, Indiana University, Indianapolis, IN, USA speaker did not provide permission to share slides

 

PGx  Standardization Project
Steven A. Schichmann, MD, PhD, John L. McClellan Memorial Veterans Hospital, Little Rock, AR, USA

Utah Genome Project: Genetic Discovery Powered by Utah\\\'s Large Families and Population Database
Deborah Neklason, PhD, University of Utah, Salt Lake City, UT, USA

The Challenges of Development and Application of the NCI-MATCH NGS Assay

P. Mickey Williams, PhD, Frederick National Labs, Frederick, MD, USA

 

Pediatric Clinical Trial Networks, Pathologist\\\'s Perspective
Marian H. Harris, MD, PhD, Boston Children\\\'s Hospital, Boston, MA, USA

High Dimensional Imaging of Tumor Immune Infiltrates Using MIBI
Michael Angelo, MD, PhD, Stanford University, Palo Alto, CA, USA

Hypertetraploid Partial Molar Pregnancy Identified by Microarray and STR Analysis, with Subsequent Choriocarcinoma Diagnosis
Elizabeth Barrie, PhD, Nationwide Children\\\'s Hospital, Columbus, OH, USA

Research Whole Exome Sequencing Identifies a Novel SH2D1A Variant in a 51-Year-Old Patient with CNS Lymphocytic Vasculitis
Patrick Blackburn, PhD, Mayo Clinic, Rochester, MN, USA

Acute Liver Failure Due to Echovirus 9 Associated with Persistent B Cell Depletion from Rituximab
Alex Greninger, MD, PhD, University of Washington, Seattle, WA, USA

Pyrosequencing Solves the Case of the Conflicting Bacterial Isolates
Damon Olson, MD, Baylor College of Medicine, Houston, TX, USA

Andrew P. Feinberg, MD, MPH, Johns Hopkins University School of Medicine, Whiting School of Engineering, and Bloomberg School of Public Health, Baltimore, MD, USA

Precursor B-cell Neoplasms (ALL)
Charles G. Mullighan, MBBS (Hons), MSc, MD, St. Jude Children\\\'s Research Hospital, Memphis, TN, USA

 

Genetic and Epigenetic Drivers of Diffuse Large B Cell Lymphoma
Laura Pasqualucci, MD, Columbia University Medical Center, New York, NY, USA

A Clinical Trial to Improve Risk Assessment in Acute Myeloid Leukemia that Uses Enhanced Exome Sequencing to Detect Leukemia Clearance Following Therapy
David H. Spencer, MD, PhD, Washington University School of Medicine, St. Louis, MO, USA

 

Next-generation Sequencing for Detecting MRD in Acute Lymphoblastic Leukemia

David Wu, MD, PhD, University of Washington, Seattle, WA, USA

HPV and Head and Neck Cancer
Joseph A. Califano, MD, University of California, San Diego, CA, USA

 

Blood-based Assessment of EBV DNA as a Tumor Marker
Jennifer A. Kanakry, MD, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

Clinical Implementation of Pharmacogenomics: From Reactive Testing to Preemptive Testing
Ann M. Moyer, MD, PhD, Mayo Clinic, Rochester, MN, USA

 

Implementing and Assessing Outcomes with Genotype-Guided Therapy
Larisa H. Cavallari, PharmD, University of Florida, College of Pharmacy, Gainesville, FL, USA

Computational Dissection of Intra-tumor Genetic Heterogeneity and Applications to the Study of Cancer Treatment, Evolution, and Metastasis

Scott L. Carter, PhD, Dana-Farber Cancer Institute, Boston, MA, USA

 

Strategies and Challenges for Somatic Mutation Detection by Next-gen Sequencing
Daniel C. Koboldt, MSc, Institute for Genomic Medicine at Nationwide Children\\\'s Hospital, Columbus, OH, USA

Perspectives and Diagnostic Considerations in Spinal Muscular Atrophy
Thomas W. Prior, PhD, Ohio State University, Columbus, OH, USA

 

Genetics of ALS

Vivianna M. Van Deerlin, MD, PhD, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA

 

Microbial Anthropology
Maria G. Dominguez-Bello, PhD, BSc, MSc, New York University School of Medicine, New York, NY, USA speaker did not provide permission to share slides


A Collaborative Effort to End the Pandemic Era: The Global Virome Project
Jonna Mazet, DVM, MPVM, PhD, One Health Institute, University of California, Davis, CA, USA

 

Friday November 17, 2017

Gene Expression Profiling During Infection Using Digital Barcoded Probe Technology
Wenjie Xu, PhD, NanoString Technologies, Seattle, WA, USA

Implementation of a Diagnostic Device Syndromic Disease Network
Lindsay Meyers, BSc, BioFire Diagnostics, LLC, Salt Lake City, UT, USA

Introduction to Smarticles™ Technology: Potential Applications in Antimicrobial Stewardship
Michael Lewinski, PhD, Roche Molecular Systems, Inc., Pleasanton, CA, USA

Enabling Scientific Discovery Through Interactive Visual Data Analysis
Alexander Lex, PhD, University of Utah, Salt Lake City, UT, USA

Single Molecule Quantification of Rare DNA and RNA Variants in Heterogeneous Samples
Todd E. Druley, MD, PhD, Washington University School of Medicine, St. Louis, MO, USA

Panel DiscussionAaron D. Bossler, MD, PhD, University of Iowa, Iowa City, IA, USA

(EAC Vice-Chair New Codes Subcommittee)

 

Richard D. Press, MD, PhD, Oregon Health & Sciences University, Portland, OR, USA

(EAC Vice-Chair Coverage Subcommittee)

 

Anthony N. Sireci, MD, Columbia University Medical Center, New York, NY, USA  
(EAC Vice-Chair Pricing Subcommittee)

A Case of MSI-high Colorectal Cancer Responsive to Checkpoint Blockade Immunotherapy after Progression to Metastatic Disease
Maryam Shirazi, MD, Columbia University Medical Center, New York, NY, USA

RBM10-TFE3: A Potential Diagnostic Pitfall Due to Cryptic Intrachromosomal Xp11.2 Inversion Resulting in False-negative TFE3 FISH Renal Cell Carcinoma
Deepu Alex, MD, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

Not So Ancillary: A Case of Correction of Primary Diagnosis with Molecular Studies
Adam Wilberger, MD, University of Colorado Hospital, Aurora, CO, USA

Mutation Signature as a Diagnostic Clue in Lung Carcinoma
Navin Mahadevan, MD, PhD, Brigham and Women\\\'s Hospital, Boston, MA, USA

Molecular Point-of-Care Tests for Infectious Diseases: Opportunities and Challenges
Frederick S. Nolte, PhD, Medical University of South Carolina, Charleston, SC, USA

Molecular Pathology Informatics - Toolsets and Infrastructures for Supporting Clinical Trials
Mark Routbort, MD, PhD, University of Texas MD Anderson Cancer Center, Houston, TX, USA

Interpreting the Cancer Genome: Identifying Driver Alterations and Therapeutic Options
Nikolaus Schultz, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

G24 - Discovery of Unique Disease- and Gene-specific Peripheral Blood DNA Methylation Signatures Allows Molecular Diagnosis and VUS Classification in Hereditary Genetic Syndromes
Bekim Sadikovic, PhD, London Health Sciences Centre, Western University, Ontario, Canada

G44 - Runs of Homozygosity (ROH) Reveal that Segmental-UPD Occurs as a Result of Recombination Mediated Repair of Genomic Imbalance
Andrea L. Penton, PhD, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

G30 - Improved Screening for Cancer Predisposition Mutations in Patients with Advanced Solid Tumors Enabled by Tumor-normal Sequencing
Diana Mandelker, MD, PhD, Memorial Sloan Kettering Cancer Center, New York, NY, USA

G28 - Short Tandem Repeat Analysis Reveals a High Rate of Partial Hydatidiform Moles in Triploid Conceptions Identified by Prenatal Chromosome Microarray
Xuemei Wu, MD, PhD, Oregon Health & Science University, Portland, OR, USA

H28 - Haplotype Counting for Sensitive AML Relapse Detection
Marija Debeljak, BSc, Johns Hopkins University, Baltimore, MD, USA

H60 - Comparison of Clinical Digital Karyotyping by Comprehensive Next Generation Sequencing with Standard Cytogenetic Analysis in Pediatric Leukemia
Elizabeth M. Azzato, MD, PhD, St. Jude Children\\\'s Research Hospital, Memphis, TN, USA

H68 - Diagnostic Yield of Somatic Mutation Detection in Hematologic Malignancies Does Not Increase with Additional Mutation Analysis, and Supports More Focused Disease-specific Testing Models
Szabolcs Szelinger, PhD, University of California, Los Angeles, CA, USA

H34 - Implementation Considerations: Designing and Medically Vetting a Targeted Gene Panel for Hematologic Malignancies
Michelle Grant, DO, University of Vermont Medical Center, Burlington, VT, USA

ID74 - Detection of Resistance-Associated Substitutions in the Hepatitis C Viral Genome using the Sentosa SQ Hepatitis C Virus Genotyping Next-Generation Sequencing Assay
Jonas Pettersson, PhD, University of Southern California, Los Angeles, CA, USA

ID02 - Pathogen Detection by Metagenomic Next Generation Sequencing of Purulent Body Fluids
Wei Gu, MD, PhD, University of California, San Francisco, CA, USA

ID34 - Challenges Associated with Developing Rapid Molecular Diagnostics for Detection of Antibiotic Resistance
Megan Stonebraker, Diatherix Laboratories, Huntsville, AL, USA

ID60 - Extreme One-Step RT-PCR: Potential for Point-of-Care Viral Detection
Jessica A. Houskeeper, MRes, University of Utah, Salt Lake City, UT, USA

I06 - A New Allele-centric VCF File for Variants in ClinVar
Melissa J. Landrum, PhD, National Center for Biotechnology, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

I16 - Homopolymer Compression Improves Reference-Free, Kmer Based Whole Genome Strain Comparison for IonTorrent Data
Keith E. Simmon, PhD, ARUP Laboratories, Salt Lake City, UT, USA

I20 - Redesigning the Molecular Pathology Clinical Report for the Next-generation Genomic Era: The MSKCC Experience with the MSK-IMPACT Assay
Aijazuddin Syed, MSc, Memorial Sloan Kettering Cancer Center, New York, NY, USA

I28 - An Interlaboratory Assessment of Complex Variant Detection Using Multiplexed Positive Controls
Stephen Lincoln, Invitae, San Francisco, CA, USA

ST52 - Clinical Cancer Whole Exome and Transcriptome Sequencing of Pediatric Tumors at Columbia University Medical Center: Laboratory Perspective at Three Years
Susan J. Hsiao, MD, PhD, Columbia University Medical Center, New York City, NY, USA

ST56 - Clinical Utility of Large Scale Genomic Sequencing of Solid Tumors at a Large Academic Medical Center
Noah A. Brown, MD, University of Michigan, Ann Arbor, MI, USA

ST114 - Identification of Germline Variants in Tumor Genomic Sequencing Assays: Usefulness of Variant Allele Fraction and Population Variant Databases
Nathan D. Montgomery, MD, PhD, University of North Carolina, Chapel Hill, NC, USA

ST62 - Integrated Molecular Diagnostic Call Criteria for MET Exon 14 Skipping in Lung Cancer
Ryan J. Schmidt, MD, PhD, Harvard Medical School, Boston, MA, USA

Solid Tumor Genotyping: Technical and Clinical Validation with a Focus on Fusions
A. John Iafrate, MD, PhD, Massachusetts General Hospital, Boston, MA, USA

Intersection of Germline and Somatic Cancer Variants and New Areas of Clinical Utility
Colin C. Pritchard, MD, PhD, University of Washington, Seattle, WA, USA

Panel Discussion - there were no slides presented in this session.
Gregory A. Storch, MD, Washington University School of Medicine, St. Louis, MO, USA

Kimberly Hanson, MD, MHS, University of Utah, Salt Lake City, UT, USA

Correlation of AML and MDS Mutation Burdens and Response to Decitabine in the Peripheral Blood and Bone Marrow
John S. Welch, MD, PhD, Washington University School of Medicine, St. Louis, MO, USA

Dynamic Monitoring of Lymphoma Genome Evolution
Ash A. Alizadeh, MD, PhD, Stanford University School of Medicine, Stanford, CA, USA

Phenotype to Genotype: How Traditional Techniques Pave the Way to Targeted Testing and Individualized Medicine
Joseph J. Maleszewski, MD, Mayo Clinic, Rochester, MN, USA

From Genes to Genomes: Evolution of Molecular Testing for Inherited Cardiomyopathies

Birgit Funke, PhD, Veritas Genetics, Danvers, MA, USA
Harvard Medical School, Boston, MA, USA

Saturday November 18, 2017

The Role of Biobanks in Precision Medicine Research and Care
Nazneen Aziz, PhD, Kaiser Permanente Research Bank, Oakland, CA, USA

The "All of Us" Research Program- Precision Medicine Initiative: One Million Cohort

Mine S. Cicek, PhD, Mayo Clinic, MN, USA

AMP Bioinformatics Pipeline Validation Working Group: Development of Guidelines
Somak Roy, MD, University of Pittsburgh Medical Center, Pittsburgh, PA, USA

New AMP Guidelines on Validating Next Generation Sequencing Bioinformatics Pipelines
Alexis B. Carter, MD, Children's Healthcare of Atlanta, Atlanta, GA, USA

Molecular Diagnostic Testing for the Detection of Early Pancreatobiliary Neoplasms
Aatur Singhi, MD, PhD, University of Pittsburgh Medical Center Presbyterian, Pittsburgh, PA, USA

TT92 - Successful Extraction of RNA from Archived Bone Marrow Aspirate Smears for Use in Targeted RNA Sequencing
Tamara Restrepo, BSc, Boston Children's Hospital, Boston, MA, USA

TT82 - High Performance Detection of Cancer Mutations from Circulating DNA Using Single Color Digital PCR
Christina Wood-Bouwens, Standford School of Medicine, Department of Oncology, Stanford, CA, USA

TT24 - Screening Circulating Nucleic Acids of Pancreatic Ductal Adenocarcinoma Using a Plasmonic Nanosensor
Amogha Tadimety, Dartmouth College, Hanover, NH, USA

TT76 - Engineering of Isogenic Cell Lines Using the CRISPR/Cas9 Technology and Precise Characterization of Low Allelic Frequency FFPE Cell Line Blocks for Use as Molecular Reference Standards
Andrew Hilmer, PhD, Applied Stem Cell, Milpitas, CA, USA

Inv(16) Incidentally Detected by Leukemia Translocation Panel Screen in a Patient with Therapy-related Acute Myeloid Leukemia
Andres E. Quesada, MD, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA

A Confounding Case of Polycythemia Vera
Aaron Atkinson, PhD, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA

Identifying Patients at Risk for Myelodysplastic Syndrome through Next Generation Sequencing of Cytopenias with Equivocal or Absent Morphologic Dysplasia
Patrick Mann, MD, Washington University, St. Louis, MO, USA

Detection of the Controversial ASXL1 c.1934dupG (p.G646Wfs*12) Insertion Variant From Targeted Next-generation Sequencing (NGS) Data
Michael Alberti, MD, PhD, Washington University, St. Louis, MO, USA

Passing the Baton: Keys to Successful Implementation of Laboratory Developed Tests (LDTs) and FDA-cleared Tests

Melissa R. Johnson, BSc, ARUP Laboratories, Salt Lake City, UT, USA

Jeff Stevenson, PhD, ARUP Laboratories, Salt Lake City, UT, USA

Jeffrey Chumley, MSc, MLS(ASCP)CM, ARUP Laboratories, Salt Lake City, UT, USA

Overview of Mitochondrial Disease and Nuclear Genetic Causes
Marni J. Falk, MD, Children's Hospital of Philadelphia, Philadelphia, PA
University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA

Mitochondrial DNA Disease: Etiology, Diagnosis, and Prevention
Sir Doug Turnbull, MBBS, MD, PhD, Newcastle University, Newcastle, UK

Development and Validation of a Whole-exome Sequencing Test for Simultaneous Detection of Point Mutations, Indels and Copy-number Alterations for Precision Cancer Care
Oliver Elemento, PhD, Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA

 

Integrated Genomic Profile Using Clinical Whole Genome and Transcriptome Sequencing to Enable Precision Oncology
Vaidehi Jobanputra, PhD, New York Genome Center, New York, NY, USA

ClinGen and ClinVar: Building Resources to Support Gene and Variant Interpretation

Heidi L. Rehm, PhD, Harvard Medical School, Boston, MA, USA

CIViC: A Curation Portal and Knowledgebase for Cancer Variant Interpretation

Obi L. Griffith, PhD, Washington University School of Medicine, St. Louis, MO, USA

Bacterial Resistance:  Detection with Molecular Methods
Robert A. Bonomo, MD, Louis Stokes VA Medical Center, Cleveland, OH, USA

 

Deep Sequencing for HIV-1 Clinical Management
Maria Casadellà, PhD, IrsiCaixa AIDS Research Institute, Barcelona, Spain

AMP/CAP Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels

Lawrence J. Jennings, MD, PhD, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA

 

AMP/ASCO/CAP Standards and Guidelines of Somatic Variant Interpretation and Reporting
Marilyn M. Li, MD, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA

 

Implementation of NGS Somatic Variant Guidelines into Clinical Practice
Marina N. Nikiforova, MD, University of Pittsburgh Medical Center, Pittsburgh, PA, USA

Panel Discussion

John D. Pfeifer, MD, PhD, Washington University School of Medicine, St. Louis, MO, USA

Robert Cook-Deegan, Arizona State University, Washington, DC, USA

Wayne W. Grody, MD, PhD, UCLA School of Medicince, Los Angeles, CA, USA

Jamie McDonald, MSc, University of Utah, Salt Lake City, UT, USA

Elaine Lyon, PhD, ARUP Laboratories, Salt Lake City, UT, USA and Past AMP President

Diagnosis of Clostridium difficile Infections: The Benefits of Molecular Testing
Ferric C. Fang, MD, University of Washington, School of Medicine, Seattle, WA, USA

Diagnosis of Clostridium difficile Infections: Why Toxin Tests Still Matter
Christopher R. Polage, MD, MAS, University of California, Davis School of Medicine, Sacramento, CA, USA

Mate-Pair Sequencing in Cytogenetics
Nicole L. Hoppman, PhD, Mayo Clinic, Rochester, MN, USA

Digital Karyotyping and Complex Rearrangement Analysis with Sequencing at Single Molecule Resolution
Hanlee P. Ji, MD, Stanford University School of Medicine, Stanford, CA, USA

Genome Editing with CRISPR-Cas Nucleases
J. Keith Joung, MD, PhD, Massachusetts General Hospital, Charlestown, MA, USA

Accelerating Prediction of Tumor Vulnerabilities Using Next-generation Cancer Models
Jesse S. Boehm, PhD, Broad Institute, Cambridge, MA, USA

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