Attend the BIOBASE Satellite Workshop:

Saturday 8 June 2013
Time: 11.45 to 13.15 hrs

Meeting Room: 202/203 – Level 2
Speakers: Julien Philippe, CNRS, Institut Pasteur and Frank Schacherer, BIOBASE GmbH

Title: Identification of causal variants in type 2 diabetes (T2D) and obesity using NGS and BIOBASE’s HGMD^® Professional

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Learn how others are utilizing HGMD^® and Genome Trax™ in their research and what they were able to discover.

For more detailed information including agenda and speakers click here.

Space is limited. Reservations will be granted on a first come, first serve basis.

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As you can imagine this type of information is very difficult to obtain, unless you have a tool for upstream analysis of differential gene expression such as BIOBASE’s ExPlain™. With ExPlain analysis tool you can identify differentially expressed genes and regulatory network key nodes responsible for this change in just a few mouse clicks.  All you need is just a list of genes, preferably with fold change information, which is kindly provided by Hu et al as supplementary information to their publication. So what are you waiting for?

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The committee identified several roadblocks we face today, varying from difficulty in calling certain variants, to a need for a database that “represents an accurately curated compendium of known pathogenic variants.”  We at BIOBASE work to address the latter issue, particularly with The Human Gene Mutation Database (HGMD®),  as HGMD®  has historically curated to the standards that the ACMG has set for reporting variants that are inherited, and consisting mostly of SNPs/Insertions/Deletions from constitutional (non-tumor) tissue, that are likely pathogenic in nature.  BIOBASE’s Genome Trax™ tool already provides users with the ability to quickly annotate a genome with these HGMD® associations (along with transcription factor binding sites and other powerful annotations, for researchers), and even filter down to the ACMG suggested list of genes.  This includes the power to search for “variants that have been previously reported and are a recognized cause of the disorder,” according to HGMD®, as well as “previously unreported,” non-synonymous variants that fall within ACMG’s table of disease genes.

This report was exciting for me personally; as a strong believer in genomics and the impact it can have at the individual patient level, I have always felt it was a shame that so much potentially useful data has been thrown away, due not only to a lack of “clinical grade” confidence in genotype to phenotype associations, but also because of our fear of how a patient may respond to news concerning their health.  I am hopeful that the content and tools that we provide at BIOBASE will assist clinical researchers in continuing to expand the list of actionable data through hypothesis forming and confirmation.

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PRESENTATION

Genome Trax: whole genome variant analysis for diagnostics and medical research
Tuesday, March 19th at 3:15 pm (PT), Rivera room

Interpretation of human whole genome sequence data is emerging as the fundamental bioinformatics challenge of the 21st century.  We describe Genome Trax, an essential annotation source for identifying disease-related variants and for understanding the effect of variants in a medical context, and show how relevant variants can be discovered in a sample patient.

Functional Genomics Short Course
Monday, March 18th 9:00 am – Noon, Marseilles room

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Come by for a live demonstration of the Human Gene Mutation Database (HGMD®) and Genome Trax^TM.

Short Course 1:  Next Generation Sequencing From a Clinical Perspective: What are You Getting and What Does it Mean
March 19 12-5:00 pm
Course Director:  Darrel Waggoner, MD, FACMG, University of Chicago, Chicago, IL

Course Description: 
Diagnostic next-generation sequencing expands the scope of genetic data available, but also brings new challenges to clinical interpretation.  This short course will help those in clinical practice (physicians, clinical geneticists, genetic counselors and fellows) get the most out of their diagnostic next-generation sequencing results.  The format of the short course will be a workshop, utilizing a series of clinical case results to explore the interpretation and clinical implications of sequencing results.  The cases will address the following: 1) Using additional phenotypic information to aid in the interpretation of genetic results. 2) Using internet-based tools to aid in the interpretation of variants of uncertain significance by considering such information as population frequencies, predicted effects on the protein or RNA transcript, and evolutionary conservation.  3) Understanding the background technologies sufficiently to recognize the limitations of detection, and the possible reasons for incomplete results. The cases will point out the dynamic nature of the bioinformatics utilized in the interpretation, differences in the way clinical labs might implement next-generation technology through panels, whole exomes, and whole genomes, and how these differences influence the results that will be available.  Given the rapid pace of research and development of next-generation sequencing technology, this course will provide useful experiences to help practitioners translate findings more effectively to the clinical setting.

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Booth #2043

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