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Association for Molecular Pathology

Webinars in 2012


Learn How to Register with the NIH Genetic Testing Registry (GTR) and Migrate Your Data From GeneTests

December 11, 2012


Presenters: Wendy Rubinstein, MD, PhD; Brandi Kattman, MS; and Adriana Malheiro, MS

NIH Genetic Testing Registry, Bethesda, MD

Host: Rong Mao, MD, ARUP Laboratories, Salt Lake City, UT


GTR is a public resource that enables health care professionals to locate available tests from participating laboratories and provides detailed information about the scientific basis of genetic tests as voluntarily submitted by test providers. The GeneTests Laboratory Directory will be phased out in the first half of 2013. Laboratories that participate in GeneTests need to take specific action if they wish to maintain a public presence at NIH.
GTR supports several modes of data submission and facilitates migration of data contained in GeneTests to GTR. Laboratory and test registrations have been accepted by GTR since the spring of 2012. Submission formats include interactive Web-based forms, semi-automatic submission using a test spreadsheet, and completely automatic submission by uploading an XML file. Currently, U.S. laboratories with over 40% of the test content in GeneTests have already registered their laboratories in the GTR.
In this webinar, the GTR staff will provide background information about GTR and will discuss a timeline for the transition period between GTR and GeneTests. The focus of the discussion will be on migrating (copying) existing data in GeneTests to GTR and completing the registration process for laboratory and test information. We will discuss strategies for planning the submission process and organizing your work and will share helpful hints gained from previous submitters. The webinar will focus on the interactive submission website, which is the hub for registry participation.

Learning Objectives:

  • Describe the multiple submission formats available
  • Outline the steps to organize laboratory and test information prior to submission
  • Acknowledge how to get help during the submission process
  • Follow how to log into and navigate the GTR online submission site

The Epigenetic Basis of AML and MDS: Insights From Genome-wide DNA Methylation Studies

November 6, 2012


Presenter: Maria (Ken) Figueroa, MD, University of Michigan, Ann Arbor, MI

Host: Sara Taylor, PhD, Tarleton State University, Ft. Worth, TX


Aberrant DNA methylation is a hallmark of cancer, including acute leukemias, and epigenetic deregulation of gene expression through aberrant DNA methylation or histone modification plays an important role in the malignant transformation of hematopoietic cells. In the past years, novel mutations have been described in genes from the epigenetic machinery (TET2, DNMT3A and EZH2) as well as in metabolic genes (IDH1 and IDH2), which impact the epigenetic status of the leukemic blasts. However, up until recently, DNA methylation studies in cancer were limited to a handful of candidate genes, with no real insight into the true aberrant patterning of DNA methylation on a genome-wide basis. Using genome-wide DNA methylation studies we have profiled a large cohort of primary AML and MDS specimens. Through a combination of supervised and unsupervised approaches we were able to determine that: (a) DNA methylation in cancer is not randomly altered, but in fact distinct DNA methylation patterns characterize the different forms of both AML and MDS, (b) DNA methylation can identify previously unrecognized subtypes of the disease, (c) aberrant loss of promoter methylation is a much more common occurrence than previously thought, (d) secondary AML and MDS present more profound epigenetic abnormalities than de novo AML and (e) DNA methylation biomarkers can successfully predict clinical outcomes. Furthermore, both in MDS and AML we observed the existence of recurrent epigenetic lesions, predominantly hypermethylation, which affected almost all cases, irrespective of genetic or mutational subtype. These recurrent epigenetic lesions, which are never seen in normal hematopoietic progenitors are likely to play cooperative roles in malignant transformation.


Learning Objectives:

  • Investigate the nature of DNA methylation changes in AML and MDS.
  • Evaluate the role that mutations in epigenetic modifiers play in determining epigenetic patterns.
  • Assess the potential for novel diagnostic and therapeutic opportunities that epigenetic abnormalities afford us

HIV Diagnosis: Times They Are A Changing

October 9, 2012


Presenter:  Richard L. Hodinka, PhD, Children's Hospital of Philadelphia, Philadelphia, PA

Host: Paula A. Revell, PhD, Texas Children's Hospital, Houston, TX


Laboratory methods for the diagnosis of HIV infection are undergoing considerable change, as are testing policies and strategies in the U.S. Newer generations of HIV tests have been developed and licensed, leading to improved assay performance and earlier detection of HIV. With this webinar, the latest technologies and issues related to HIV diagnostic testing will be discussed, including 4th generation assays for the simultaneous detection of HIV antigen and antibody, rapid confirmation tests, qualitative molecular testing for HIV RNA, alternatives to the traditional testing algorithm, and topics involving routine and home testing for HIV.


Learning Objectives:

  • Describe the most recent changes in technology for the laboratory diagnosis of HIV
  • Select, apply and interpret laboratory tests for HIV diagnosis
  • Summarize and evaluate alternative testing algorithms for HIV diagnosis and confirmation
  • Discuss the latest recommendations for routine and home HIV testing

Bioinformatics for Next Generation Sequencing: Establishing a Pipeline for Candidate Gene Identification in Exome and Genome Sequencing Data

September 25, 2012


Presenter:  Karl Voelkerding, MD, ARUP Laboratories, Salt Lake City, UT

Host: Rong Mao, MD, ARUP Laboratories, Salt Lake City, UT


The application of exome and genome sequencing for candidate and presumptive causal gene identification in inherited disorders has begun to enter clinical practice. This webinar will present a bioinformatics pipeline for candidate gene discovery based on open-source and commercial softwares applied to Illumina sequencing data. Principles, approaches and assessment metrics for alignment, variant calling and annotation will be presented along with algorithms for candidate gene identification. Although focused on exome and genome scale sequencing data, the fundamental principles are applicable for analysis of multi-gene panels and other next-generation sequencing technologies.


Learning Objectives:

  • Describe principles and process steps of next-generation sequencing data alignment, variant calling and annotation
  • Discuss metrics that can be monitored for assessment of data quality during bioinformatics process steps
  • Relate key concepts of algorithms and tools used for identification and ranking of candidate genes


New Mutations and the Genetic Basis of Autism and Intellectual Disability

July 11, 2012


Presenter:  Evan E. Eichler, PhD, University of Washington, Seattle, WA

Host: Amrik Sahota, PhD, Rutgers University, Piscataway, NJ


Despite high heritability, the genetic basis of autism and more broadly neurodevelopmental disease has remained largely elusive.  Studies of common variation have confirmed few genes that have withstood replication.

Studies of rare copy-number variants, however, have suggested that large deletions or duplications of genetic material involving multiple genes contribute to approximately 10% of disease etiology. These findings have suggested a new model where rare or private genetic variation at many different genes underlies neurodevelopmental diseases.  Recent advances in sequencing technology have now made it cost-effective to screen patients for rare or sporadic mutations identifying novel genes and pathways important in autism and intellectual disability.


Learning Objectives:.

    * Discuss the role of recurrent copy number variants in intellectual disability and autism

    * Summarize recent findings searching for de novo point mutations from exome sequencing

    * Present a model of the genetic architecture for autism and prospects moving forward


The 2012 Joint ACS/ASCCP/ASCP Guidelines for Cervical Cancer Screening: What you need to know

May 22, 2012

Support generously provided by


Presenter:   Mark H. Stoler, MD, University of Virginia Health System, Charlottesville,VA

Host:  Melinda Poulter, PhD, University of Virginia Health System, Charlottesville,VA


"A Pap smear every year"; that simple recommendation used to be all anyone needed to know about cervical cancer screening. New guidelines just released by the American Cancer Society, the American Society for Colposcopy and Cervical Pathology and the American Society for Clinical Pathology indicate that cervical cancer screening can begin later, be performed less often, and stop earlier than previously recommended. By doing so, the new guidelines ensure that we're doing the right tests at the right time - which is better for our patients, striking a balance between the benefits of the life-saving screening tests and the harms of over-testing, which can include unnecessary invasive procedures and worry.

Learning Objectives:

  • Review for the participant the latest data on cervical neoplasia that form the biological basis of these guidelines.
  • Facilitate the participant's understanding of the concepts of clinical validation of diagnostic tests and the need to balance the benefits and harms of screening.
  • Apply these concepts to review the new guidelines and place them in context relative to prior guidelines and the guidelines developed by other organizations.

Confused? You are not Alone. Molecular CPT Codes in 2012 and Beyond.  
A Webinar Presented by the AMP Economic Affairs Committee
April 16, 2012



Support generously provided by

Panelists: Jeffrey A Kant MD PhD, Roger D Klein MD JD, Elaine Lyon PhD, Paul Raslavicus MD MHA
Level of Instruction: Intermediate
Contact Hours: 1.0

Current coding for molecular assays will be reviewed to include the new molecular pathology section of the 2012 AMA CPT book. Current understanding of instructions from the Center for Medicare and Medicaid Services (CMS) regarding how providers should code molecular assays in 2012 will also be reviewed, since the new codes have not yet been accepted for payment. Participants will have an opportunity to submit questions as well as local experiences with CMS contractors or private payers during the first 3 months of 2012 in advance of the webinar for response by panelists

Learning Objectives:

Analyze current issues around fee schedule placement of new CPT codes and implications for various provider groups
Explain the rationale and structure of the new molecular pathology CPT codes for 2012

Apply current CMS instructions for coding molecular pathology assays in 2012
Identify perspectives on likely and potential changes as well as problems for molecular CPT coding in 2013 and beyond


Using RefSeq Gene: Identifying the HGVS Position in Genomic, cDNA, and Protein Coordinate System
A Webinar Presented by the AMP Clinical Practice Committee's Mutation Nomenclature Working Group
March 01, 2012


Presenter: Donna R. Maglott, PhD, National Center for Biotechnology Information, National Institutes of Health
Host: Janina A. Longtine, MD, The Mount Sinai Medical Center
Chair, AMP Clinical Practice Committee

Dr. Maglott will explain how to use tools at NCBI to identify the location of sequence variations, with an emphasis on RefSeqGene records (http://www.ncbi.nlm.nih.gov/refseq/rsg) . This will assist AMP members in identifying the correct nomenclature for gene mutation clinical reporting.

Dr. Maglott has been at NCBI since 1998, where she developed the databases supporting reference sequences (RefSeq), Gene, STS markers, Conserved CoDing Sequences (CCDS), and Map Viewer. She played a lead role in developing the functions to track and identify genes in NCBI's annotation pipeline. In recent years, she took the lead in introducing use of the HGVS standard to dbSNP's submission processing and to displays in multiple NCBI tools. .She currently manages the Gene (http://www.ncbi.nlm.nih.gov/gene), RefSeqGene (http://www.ncbi.nlm.nih.gov/refseq/rsg) and ClinVar (http://ncbi.nlm.nih.gov/clinvar/) projects and supervises technical support for the Genetic Testing Registry (GTR).