A Multi-Session Seminar on Massively Parallel (aka High Throughput) Sequencing
October 15, 2010
9:30AM - Noon
OHSU Main Campus, HRC 14D03 (Hatfield Building, 14th floor)
Massively Parallel Sequencing - Technology, Service and Support Options at OHSU, and Data Analysis Considerations
Event schedule (Attendees are welcomed to come and go as needed):
I. 9:30 - 9:35 (5min): Introduction to the Integrated Genomics Laboratory, Speaker Dr. Chris Harrington
II. 9:40 - 10:25 (45min): MPSSR: technology and services, Speaker Dr. Robert Searles
III. 10:30 - 10:55 (25min): Analysis considerations, Biostats services/support, Speaker Dr. Shannon McWeeney
IV. 11:00 - Noon (1hr): Data analysis workflow/output options using GeneSifter software with high throughput sequencing data, Speaker Dr. Hugh Arnold of Geospiza (www.geospiza.com)
GMSR Microarray User Forum: Assay and Service Developments from the Gene Microarray Shared Resource (GMSR) and the Massively Parallel Sequencing Shared Resource (MPSSR)
OHSU BICC 124 (main campus library) and West Campus VGTI library (via video conference)
The GMSR and MPSSR have been busy! All are welcomed to join this open forum to discuss recent technological and service/support offerings (i.e., updates on small sample processing, FFPE sample processing, much more) from two genomics shared resources (GMSR and MPSSR). Bring your study ideas and challenges and learn how the shared resource offerings will apply to your research.
Also, this is the first Forum session to include information regarding massively parallel sequencing (aka high throughput sequencing) and we will discuss with Dr. Bob Searles, director of the MPSSR, the technology implemented in the MPSSR and the overlap and differences between microarray and massively parallel sequencing applications.
We are also looking for input from the campus community on new assays and services related to genomic services for basic, translational, and clinical studies and for feedback regarding experiences and expectations of the Shared Resource User.
Affymetrix Microarray Core User Workshop – Expression Array Assays:
May 14 - CANCELLED
GMSR Microarray Users Forum: GeneChip Rhesus array annotation: issues and progress. GMSR Users working with expression profiling of Rhesus samples have expressed that better annotation of the probe sets on the Affymetrix Rhesus array is needed. To help support this cause, the GMSR has set-up a cross-site video conference between OHSU investigators and Dr. Rob Norgren, one of the developers of the Affy Rhesus array, of the University of Nebraska. Dr. Steve Kohama of the OHSU Primate Center will give an overview of annotation work and analysis strategies, as will Dr. Norgren.
All OHSU investigators and affiliates are welcomed to attend and participate in this investigator-driven discussion.
Please pass this "save the date" message along to your colleagues. If you have any questions/input to share, please e-mail Dr. Chris Harrington of the GMSR Affymetrix Microarray Core (firstname.lastname@example.org).
No events are currently planned for January 2010.
No events are currently planned for December 2009.
Affymetrix Technical Seminar on (1) working with FFPE clinical samples for expression profiling, (2) the Medical Genomics Research Program, and (3) DMET array technology – Nov. 4, 2009, 2-4PM, HRC 14D03 (Hatfield Research Center bldg of OHSU main campus). In this three-part seminar, an application seminar on successfully using formalin-fixed Paraffin-embedded (FFPE) clinical samples for whole-transcriptome microarray analysis will be presented by Dr. Elai Davicioni from GenomeDx. Also, Affymetrix scientific staff will discuss the Medical Genomics Research Program and the recently launched DMET (Drug Metabolism Enzymes and Transporters) array panel and assay including how the Marshfield Clinic used the panel to more accurately define Warfarin dosing. The DMET™ Plus panel can be used to discover new biomarker associations, determine drug responders vs. non-responders, optimize drug dosing, selectively recruit for clinical trials, and much more. Click here for a detailed description and breakdown of the event schedule.
GMSR Microarray Users Forum – Discussion title: microRNA array assay options and project design considerations: GMSR Microarray Users Forum – Nov. 11, 2009, 11AM-Noon, BICC 124 with video conferencing to VGTI, West Campus. The discussion will be lead by Dr. Chris Harrington, Affymetrix Microarray Core Director. Current users with microRNA data are also encouraged to attend to discuss strategies and challenges associated with the array data analysis. Meeting contact: Dr. Chris Harrington, AMC Director (email@example.com).
GeneSifter Hands-on Analysis Workshop using Microarray Expression Data– Nov. 13, 2009, 1:30 – 3:30PM, BICC 120, presented by GeneSifter Scientific Staff, Drs. Eric Olson and Hugh Arnold. Hands-on microarray analysis with your own data and/or sample data provided at the session (expression data from Affymetrix, Illumina and other platforms). GeneSifter includes options for statistical analyses, data reduction/filtering, data visualization, and integration of current biological annotation including pathway and functional information. The GMSR currently licenses GeneSifter as one of the downstream analysis options for core customers.
GMSR Microarray Users Forum – Discussion title: High speed flowcytometry cell sorting meet gene microarray - How to control tumor-induced regulatory CD4+CD25+ T cells and inhibit their suppressive function in a model of lymphopenic reconstitution and tumor vaccination– Oct. 14, 2009, 11AM-Noon, OHSU Main Campus Library BICC 124 with video conferencing to VGTI, West Campus. Dr. Christian Poehlein, MD, of the Laboratory for Molecular and Tumor Immunology at Providence Portland Medical Center, will describe his work on a melanoma vaccine model and lead a discussion of the experimental model, the use of efficient flow cell sorting to reach >99% purity for RNA isolation of the different cell subsets, and some of the markers identified by the results of the gene microarray analysis. Contact Michelle Garred, GMSR User Support (firstname.lastname@example.org), for further information.
Webinar: Gene Expression Profiling in Cancer Research: Microarrays, Tag Profiling and Whole Transcriptome Analysis– Oct. 21, 2009, 10AM. Using data drawn from the GEO data repository and the Short Read Archive gene expression in Melanoma will be examined using microarrays, massively parallel sequencing (aka next gen sequencing) tag profiling and massively parallel sequencing whole transcriptome analysis data. This presentation will provide an overview of the gene expression data analysis process for these applications with an emphasis on identification of differentially expressed genes, identification of novel transcripts and characterization of alternative splicing. Presented by Dr. Eric Olson, Geospiza VP of Product Dev. To register for the webinar, go to http://www.geospiza.com/News/events.shtml
Affymetrix Microarray Core User's Workshop:3' IVT expression arrays – Oct. 30, 2009, 10AM – Noon, OHSU CHH 14010 (Center for Health & Healing, 14th floor conference room). This 2-hour workshop will focus on the use of Affymetrix GeneChip arrays for gene expression analysis, including 3'IVT arrays, whole transcript Gene and Exon arrays, and microRNA arrays. We will cover array design, data formats, and Affymetrix expression analysis algorithms, data quality control procedures, and a brief overview of post-assay data analysis steps and software options. The analysis component of the workshop will largely focus on the 3'IVT array assay. The workshop is designed to assist investigators in understanding and interpreting the microarray data provided to them by the Core and is being presented by Dr. Chris Harrington, AMC Director and Michelle Garred, GMSR/AMC User Support Specialist.
GMSR Microarray Users Forum:
Identification of the Prostate Cancer Hypermethylome
Presented by Joshi Alumkal, MD, OHSU
Dr. Alumkal's lab used Illumina Golden Gate DNA methylation microarrays in order to more fully characterize the genes silenced by DNA methylation in both in vitro model systems of prostate cancer and human prostate cancer clinical samples. The goals were 1) discovery of novel putative tumor suppressor genes silenced by DNA methylation and 2) the discovery of novel DNA methylation diagnostic/prognostic biomarkers. Dr. Bob Searles, Director of the Illumina Microarray Core, will provide the introduction on the Illumina platform/arrays used in this study.
Wednesday, June 10, 2009
11AM – Noon
BICC 124, OHSU main campus, with video conferencing to VGTI library, OHSU West Campus