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Workshops and Trainee Events

 

 Education track

 Trainee track

 Clinical track

 

Unless otherwise indicated, you must register for the ASHG 2012 Annual Meeting and check the appropriate box on the registration form in order to participate in the workshops listed below.  Seating is limited, so please register early.


 

Undergraduate Faculty Genetics Education Workshop

Advance registration required.

Tuesday, November 6
8:00 am – 3:00 pm, Moscone Center, Room 300, Esplanade Level (South)

 

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This is a special session for undergraduate faculty organized by the ASHG Undergraduate Faculty Subcommittee before the commencement of the annual meeting. The workshop will cover human genetics content and pedagogies for undergraduate faculty teaching biology courses with significant genetics content. The overarching goal is to encourage effective teaching of human genetics so that it contributes to improving the genetic literacy of students.

 

The cost of the workshop is $25 USD. Breakfast and lunch will be served. Contact Katherine Lontok (klontok@ashg.org) for further information.

 


 

High School Workshop (for San Francisco students and teachers)

Advance registration required.
Tuesday, November 6
8:30 am – 2:30 pm, Moscone Center, Room 303/305, Esplanade Level (South)

 

 

 

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The High School Workshop is organized by the ASHG Information and Education Committee with ASHG member volunteers on the program. Students and teachers will interact with genetics researchers and learn about the field of human genetics. The workshop comprises several inquiry-oriented genetics lessons and plenary sessions. Attendance is limited to 150 participants. Breakfast and lunch will be served. Contact Michael Dougherty (mdougherty@ashg.org) to sign up and for further information.

 


 

Trainee-Mentor Luncheon

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Wednesday, November 7
12:45 pm – 2:15 pm, Moscone Center, Room 303/305, Esplanade Level (South)

 

 


The Trainee-Mentor Luncheon is a wonderful opportunity for trainees (graduate students, postdoctoral fellows and clinical fellows) in the field of human genetics to meet and talk informally with senior members of the Society about career options, goals, and professional opportunities. The luncheon is held at the beginning of the meeting so that trainees can continue their discussions with these mentors at other times during the course of the meeting. Please click here for the list of confirmed mentors.

The cost of a boxed lunch is included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.
 
NOTE: Mentors who are invited to participate should NOT order tickets for themselves when completing the online registration form.
 


 

Discovering Biological Data at NCBI

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Wednesday, November 7
12:45 pm – 2:15 pm, Moscone Center, Room 307, Esplanade Level (South)

 

 

This workshop is organized by Deanna Church and Eric Sayers from NIH. The presenter will be Peter Cooper from the NCBI. The National Center for Biotechnology Information (NCBI) is the premier repository for biological information in the U.S. and is the primary archive for submitter-provided data through resources such as the Sequence Read Archive (SRA), GenBank, GEO, dbSNP, dbVar and dbGaP. This workshop will provide both general strategies for finding data at the NCBI and an introduction to various tools for visualizing and analyzing sequence data, which can be especially valuable when trying to follow up regions of interest in a GWAS study or trying to understand how a novel variant could be affecting phenotype.

 

Resources at NCBI use the Entrez system to search various databases and display records. This workshop will give a basic introduction to using the Entrez system to perform searches and find related data starting with a list of reviewed human genes.  Specific tasks covered include finding reference sequences, mapping variations, identifying homologous genes, exploring expression studies, and using MyNCBI to save searches and manage data. For questions, contact Deanna Church via email at church@ncbi.nlm.nih.gov.

 

Lunch is included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.

 


 

Clinical Interpretation of Cytogenomic Arrays: Tools & Resources

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Wednesday, November 7
12:45 pm – 2:15 pm, Moscone Center, Room 304/306, Esplanade Level (South)

 

Workshop requirements: Registrants should be familiar with basic computer skills and Internet browsing. It is recommended that participants be familiar with accessing and configuring the databases covered in this session (see below). Registrants must bring a laptop to this session in order to participate. Laptops should have full battery power and must have a wireless card.

 

Darrel Waggoner, University of Chicago, and Christa Lese Martin, Emory University, will present this workshop, which is geared for clinical geneticists and residents, genetic counselors and genetic counseling students, laboratory directors, laboratory training fellows, and other laboratory personnel. This interactive session will cover basic information about the differences between the various array platforms and will discuss strategies for choosing the appropriate array platform for your patients, including issues related to repeating arrays utilizing different platforms. Through an interactive case-based format, participants will learn how to use current tools for cytogenomic array data analysis and how to apply these tools in the clinical setting.  The UCSC Genome Browser, Database of Genomic Variants, DECIPHER, ISCA and dbVar databases will be covered. Through active online participation, participants will search databases to collect information useful for clinical interpretation (normal population variant versus pathogenic change, gene, and other functional DNA elements) using specific cases of genomic imbalance detected by cytogenomic arrays.

 

This workshop will offer CME and CEU credits. For a fee, a tutorial for learning to configure the databases is available through the ACMG Web site. 

 

Seating is limited, so please register early. Lunch is included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.

 


 

UCSC Genome Browser Interactive Workshop (Intermediate/Advanced Users)

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Wednesday, November 7
7:00 pm – 8:30 pm, Moscone Center, Room 304/306, Esplanade Level (South)

 

 

Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card in order to participate.

 

Robert Kuhn and Pauline Fujita, University of California, Santa Cruz, Center for Biomolecular Science & Engineering, will present this interactive workshop on Web-based genomic tools. The workshop will cover intermediate-to-advanced use of UCSC tools, especially Custom Tracks, Sessions and the Table Browser.  Attendees should already be comfortable with basic Genome Browser navigation. 

 

The workshop will offer instruction on using the Table Browser to access the more than five terabytes of genomic data in the UCSC database.  Insight into methods for intersecting data between linked tables and filtering data to access specific subsets of large datasets will be offered.

 

Advanced features of the Custom Track utility can be used to visualize high-throughput DNA sequence data, via upload of bigBed, bigWig and BAM file types, the latter offering visualization of differences from the reference assembly (SNPs) in a user-uploaded alignment file.  User-hosted datasets (the Track Data Hub feature) will be demonstrated. The Track Hub feature allows users enhanced control of their data display, and an option to share it with the entire UCSC user community. Automated program-driven querying of data in the public MySQL database will also be demonstrated. For technical or content questions about the workshops, contact Robert Kuhn via email at kuhn@soe.ucsc.edu. Registration questions should be direct to ASHG at ashgmeetings@ashg.org.

 

Seating is limited, so please register early. Refreshments are included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.

 


 

Social Media + Scientists = Success: Strategies for Using Social Media to Benefit Your Research, Your Career, and Your Connections

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Wednesday, November 7
7:00 pm – 8:30 pm, Moscone Center, Room 310, Esplanade Level (South)

 

 

This workshop, which is moderated by Jonathan Gitlin, science policy analyst at NHGRI, will involve short presentations from panelists who have demonstrated a high degree of effectiveness using social media, followed by a highly interactive discussion with the audience. The panelists are drawn from a cross-section of the genomics community and include an early-stage researcher (Daniel MacArthur, Harvard University), a senior faculty investigator and former editor for Nature (Chris Gunter, HudsonAlpha), and an industry representative in the commercial sector (Shirley Wu, 23andMe).

This workshop will open with a brief introduction to the different social media platforms that will be discussed and an overview of their uses and benefits for scientists at any stage in their career. The session will also feature a brief “Social Media 101” tutorial that shows attendees how to actually use the particular social media tools that the speakers will be discussing in this workshop (either live online or as PowerPoint slides with screenshots). Attendees will leave the workshop armed with knowledge about effective ways to use social media in the context of their genetics/genomics work.

 

Seating is limited, so please register early. Refreshments are included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.

 


 

Diagnostic Challenges: Review and Discussion of Unique Cases (Rare & Unknown)

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Thursday, November 8
12:45 pm – 2:15 pm, Moscone Center, Room 303/305, Esplanade Level (South)

 

 

 

Diagnostic Challenges is organized and moderated by Karen W. Gripp, A. I. duPont Hospital for Children and Pedro Sanchez, Children’s Hospital Los Angeles/University of Southern California. The session provides an opportunity for registrants to bring and present cases (rare and unknown) to a panel of expert clinical geneticists (see below) for discussion of differential diagnosis, treatment and counseling options. The session provides a lively give-and-take discussion in an informal environment between the audience and the panel as each case is presented. Audience participation in suggesting diagnosis or testing is encouraged.

 

Panelists Areas of Expertise/Special Interest

Margaret Adam                      

Cynthia Curry

Bill Dobyns

Dian Donnai                          

Karen Gripp                           

Julie Hoover-Fong                 

Micheil Innes                         

Marilyn Jones                         

Stephen Kahler                      

Pedro Sanchez                       

Anne Slavotinek                    

Andrea Superti-Furga            

Alain Verloes                         

 

Dysmorphology/Teratology

Dysmorphology

Brain Malformation

Dysmorphology

Rasopathies/Dysmorphology

Skeletal Dysplasia

Dysmorphology

Craniofacial Anomalies

Metabolic Disorders

LDDB/Possum Database

Eye Malformation/Diaphragmatic Hernia

Skeletal Dysplasia

Dysmorphology

 

 

Call for Cases: Cases may be diagnostic dilemmas, or consultation may be sought for confirmation of a suspected diagnosis. We urge attendees to submit their rare and unknown cases to the organizers via e-mail (diagnostic.dilemmas@gmail.com) in advance of the session, no later than November 4th. You can submit more than one case, but second cases will only be presented if there is enough time.

 

Each case will be presented using PowerPoint, with a limit of six slides and three minutes per presentation. Best suited are “visuals” with plenty of images. Any slides depicting patient information or images must have the consent of the patient. It is each presenter’s responsibility to obtain consent prior to sharing identifiable information. The discussion by the expert panel will follow the presentation. Discussion will be limited to 5 minutes.

 

If you have questions about the workshop, contact Karen Gripp via e-mail at kgripp@nemours.org. Registration questions should be direct to ASHG at ashgmeetings@ashg.org.

 

Lunch is included in the $10 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.

 


 

Galaxy 101: Data Integration, Analysis and Sharing  

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Thursday, November 8
7:00 pm – 8:30 pm, Moscone Center, Room 304/306, Esplanade Level (South)

 

 

Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card in order to participate.

 

Jennifer Hillman-Jackson, Penn State University and Jeremy Goecks, Emory University will present this workshop is an introduction to Galaxy’s basic functionality. Galaxy is an analysis and data integration framework for accessible, reproducible, and transparent biomedical research, which is available as a free public Web site and as an open-source software package that can be installed locally or on a computer cloud. Galaxy enables researchers to perform complex bioinformatics analyses, experimenting with multiple options and parameter settings.  It supports integration of data from multiple data sources, including user-uploaded data and popular online resources such as UCSC, BioMart and InterMine.  Galaxy also supports saving analysis, converting them to reusable workflows, and sharing and publishing of workflows and analyses.

    

In this workshop, you will learn how to use the Galaxy Web server (http://usegalaxy.org/) to integrate and analyze biomedical data, including how to (1) load and integrate your own data with data from popular online resources; (2) perform common analysis/operations on genomic data; and (3) save, share, describe and publish your analysis and generated datasets.

 

Seating is limited, so please register early. Refreshments are included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.
 


 

Trainee Development Program and Networking Session

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Thursday, November 8 
7:00 pm – 9:30 pm, Moscone Center, Room 309, Esplanade Level (South)

 

 

 

This event, organized by the ASHG Professional Development Committee, which is composed of trainees, will be presented by Derek Scholes, Chief, Policy and Program Analysis Branch, NHGRI, and Tyrone Spady, Senior Science Policy Analyst, FASEB. The session will focus on why scientists should care about and become active in public policy involving science. Some policy issues are directly relevant to the career development of trainees, such as research funding and data sharing, and others are more general, such as public acceptance/rejection of consensus science. Come engage in the discussion and learn how policy is used to advance genomic research and medicine, genetics education, etc. A networking session follows the formal program.
 


 

Mock Study Section Workshop

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Friday, November 9
12:45 pm – 2:15 pm, Moscone Center, Room 303/305, Esplanade Level (South)

 


Did you ever wonder what really happens in study section meetings and how proposals get discussed? In this workshop, attendees will have the opportunity to work with NIH staff to learn about the proposal review process, including the typical dynamics of study section deliberations. The NIH streamlining process will be demonstrated, and the workshop will present examples of mistakes applicants commonly make. Ron Adkins and Barbara Thomas, from NIH's Center for Scientific Review, will lead the session.

Seating is limited, so please register early. Lunch is included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.
 


 

Galaxy Workshop: Working with High-Throughput Data and Data Visualization

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Friday, November 9
12:45 pm – 2:15 pm, Moscone Center, Room 304/306, Esplanade Level (South)

 

 

Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card in order to participate.

 

Jennifer Hillman-Jackson, Penn State University and Jeremy Goecks, Emory University will present this workshop which is an analysis and data integration framework for accessible, reproducible, and transparent biomedical research, which is available as a free public Web site and as an open-source software package that can be installed locally or on a computer cloud. Galaxy enables researchers to perform complex bioinformatics analyses, experimenting with multiple options and parameter settingsIt supports integration of data from multiple data sources, including user-uploaded data and popular online resources such as UCSC, BioMart and InterMine.  Galaxy also supports saving analysis, converting them to reusable workflows, and sharing and publishing of workflows and analyses.    

 

In this workshop, you will learn how to use the free public Galaxy Web server (http://usegalaxy.org/) to analyze and integrate next generation sequencing (NGS) data.  The public server includes a wealth of high-throughput sequencing tools, and this workshop will walk through examples of analyses using 1000 Genomes data using Galaxy to extract insight from “big data.”  The workshop will also demonstrate Galaxy’s visual analytics capabilities, showing how to use Galaxy visualization to iteratively guide analysis. This workshop builds on the Galaxy 101 workshop, and basic knowledge of Galaxy will be helpful.

 

Seating is limited, so please register early. Lunch is included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge. Tickets are non-refundable.
 


 

Ensembl Browser Interactive Workshop for Intermediate/Advanced Users

Separate advance registration required. Please check the appropriate box on the meeting registration form.
Friday, November 9
7:00 pm – 8:30 pm, Moscone Center, Room 304/306, Esplanade Level (South)

 

 

Workshop requirements: You must bring your laptop. Your laptop should have full battery power and must have a wireless card in order to participate.

 

Paul Flicek, Giulietta M. Spudich and Bert Overduin from the European Bioinformatics Institute will present an interactive workshop on the Ensembl genomic tools (www.ensembl.org). Ensembl provides an infrastructure for genomic information for over 60 species, from storage through to analysis and visualization. The workshop is tailored to intermediate/advanced users of the genome browser and other Ensembl tools including the Ensembl Variant Effect Predictor (VEP). Participants will be offered hands-on experience in the use of Ensembl, bringing advanced genome analysis methods closer to the community. Ensembl integrates information from other databases hosted at the European Bioinformatics Institute and elsewhere and provides access findings from international consortia such as the 1000 Genomes Project and ENCODE to produce and display integrated views of genome function.

 

This workshop introduces highlights and new ways of integrating information in the genome browser and analysis of variation data.  New gene regulation tracks based on integrated analysis of ENCODE and Human epigenome data will be explored. We will also demonstrate how to find phenotypes and population frequencies for sequence variation from sources like the 1000 Genomes Project, and new tools allowing quick analysis of sequence variants on proteins. We will also review data upload, allowing visual comparison of BAM files (e.g., sequence reads) to the reference genome, genes, SNPs, and regulatory features in the region and quick export of sequence and annotation for genomic regions.  We will show how to access up to date external data sources using DECIPHER as an example. The presenters will also provide some pointers to accessing Ensembl programmatically through the public MySQL instance and our Perl APIs. Participants will be given a DVD containing a virtual machine with the latest APIs installed and the programmatic environment tweaked to run several scripts to explore Ensembl resources beyond the browser. For questions about the workshop, contact Giulietta (gspudich@ebi.ac.uk).

 

Seating is limited, so please register early. Refreshments are included in the $25 USD registration fee. Seats may be reserved only by registering in advance. Tickets will be issued along with your meeting badge.  Tickets are non-refundable.

 


 

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