GenomeWebinars

Tue
Jun
5
11:00 am2018
Sponsored by
Linguamatics

Text Mining at Sanofi for Genotype-Phenotype Associations in Multiple Sclerosis

Genome Webinar

Associate Director, Translational Sciences,
Sanofi

Head of Life Science,
Linguamatics

This webinar will discuss how Sanofi used literature mining to annotate the association of human leukocyte antigen (HLA) alleles with diseases and drug hypersensitivity as part of a multiple sclerosis (MS) biomarker discovery project.

For any drug development project, it is important to have a comprehensive understanding of the genetic associations for the disease of interest. While public databases of genomic variants provide valuable information, there can be many gaps in the biological knowledge. For Sanofi’s internal MS biomarker project, they needed a comprehensive catalogue of annotations to HLA alleles and turned to Linguamatics I2E to text-mine the scientific literature.

The HLA region is the most polymorphic region of the human genome. HLA alleles have been associated with more than 40 different autoimmune diseases, various types of cancer, infectious disease, and drug adverse events. However, there are no known resources that systematically annotate the association of HLA alleles and diseases.

For the Sanofi MS project, a workflow was established for whole-exome sequencing-based HLA typing and analysis. This identified more than 400 HLA alleles. The Linguamatics I2E platform was used to search the literature to annotate the association of the HLA alleles with diseases and drug hypersensitivity. This project resulted in more than double the previous disease associations and the curated annotations were fed into a knowledge base for broad use within the Sanofi team.


What will you learn?

  • How natural language processing (NLP) text mining can extract structured data from unstructured text in scientific papers
  • How text mining is used at Sanofi to extract the most up-to-date published knowledge for a gene or group of genes, including information on diseases and specific allele variations
Sponsored by
Thu
Jun
14
11:00 am2018
Sponsored by
Sophia Genetics

Overcoming Challenges in Hematological Genomic Testing with Advanced AI

Genome Webinar

Assistant Professor, UNC School of Medicine

Clinical Application Product Manager, Sophia Genetics

This webinar will discuss an effort underway at the University of North Carolina Medical Center's to overcome limitations in the hematological genomic testing workflow with artificial intelligence (AI) from Sophia Genetics.

In the first part of this webinar, Dr. Nathan Montgomery of the UNC Medical Center will discuss the rigorous evaluation his lab performed to evaluate Sophia Genetics Myeloid Solution against the overall performance of other vendors' solutions.

The Myeloid Solution is a molecular application that bundles Sophia AI with a capture-based target enrichment kit and full access to Sophia DDM platform. The application is designed to accurately characterize the complex mutational landscape of relevant hematological disorders associated with leukemia, myelodysplastic syndromes, and myeloproliferative neoplasms.

Dr. Montgomery will first explain the limitations and challenges of the current myeloid test workflow, and the rationale for the group's decision to evaluate other solutions, including the need to perform orthogonal testing of genes with high GC content such as CEBPα. Then, he will lay out the strategy he and his group applied to objectively assess the overall strengths and weaknesses of each technology. Finally, Dr. Montgomery will present his team's conclusions and the reasons they decided to work with Sophia Genetics.

In the second part of this webinar, Dr. Montgomery will give an update on UNC Medical Center's progress with in-house validation and the lab's next steps.

In the last part of the webinar, Dr. Alexander Kurze of Sophia Genetics will briefly introduce a solution that will be soon available to test for gene fusions in hematological diseases.

Sponsored by
Tue
Jun
19
1:00 pm2018
Sponsored by
Advanced Cell Diagnostics

RNA in situ Hybridization: The Next Generation of Immunohistochemistry?

Genome Webinar

Director of Anatomic Pathology, Department of Laboratory Medicine,
Geisinger Health System

Chief Medical Officer,
Advanced Cell Diagnostics

This webinar will provide evidence for the use of RNA in situ hybridization (RNA ISH) as a replacement for immunohistochemistry (IHC) in cancer research and diagnostic applications.

IHC is the gold standard for many diagnostics, but the approach has some shortcomings, including low diagnostic sensitivity, background staining, unstable antibodies, no available antibodies and a multitude of staining protocols.

RNA ISH has the ability to overcome these problems with IHC and has the potential to address issues with other technologies, including molecular “grind and bind” methods such as PCR, next-generation sequencing and gene expression profiling. The RNAscope RNA ISH method from Advanced Cell Diagnostics uses a brightfield in situ hybridization-based assay to visualize cellular RNA in formalin-fixed, paraffin-embedded tissue sections. The highly sensitive assay shows promise for detecting biomarkers that are missed by other methods.

In this webinar, IHC expert Fan Lin of Geisinger Health System will review the common applications of RNA ISH in anatomic pathology, discuss how to interpret RNA ISH results and touch on the potential pitfalls of RNA ISH.

Sponsored by
Tue
Jun
26
12:00 pm2018
Sponsored by
Lexogen

The Landscape of Alternative Polyadenylation in the Lung Cancer Transcriptome

Genome Webinar

National Cancer Institute, Center for Cancer Research

This webinar outlines a study that sought to characterize the landscape of alternative polyadenylation (APA) in the lung cancer transcriptome in order to gain insight into the role of APA in cancer progression.

APA involves the selection of an alternate poly(A) site on the pre-mRNA that leads to generation of isoforms of various length. In cancer, APA is emerging as an alternative mechanism for proto-oncogene activation in the absence of somatic mutations. Recent studies show a correlation of APA profiles with cancer prognosis, suggesting that APA is an important mechanism of cancer progression. In addition, environmental exposures such as temperature and exogenous hormones can also induce APA as a stress-response mechanism.

In this webinar, Dr. Adriana Zingone of the National Cancer Institute, Center for Cancer Research will discuss her team's work to characterize APA in the lung cancer transcriptome and to test a hypothesis that smoking modulates differential usage of polyadenylation sites within mRNA transcripts.

Sponsored by
Thu
Jun
28
1:00 pm2018
Sponsored by
PerkinElmer

An Optimized NGS Workflow for Human Metagenomic Analysis

Genome Webinar

Senior Scientist, Genomic Applications Department, Illumina

This webinar will review a standardized, high-throughput, and fully automated library prep protocol for human metagenomic analysis. 

The human gastrointestinal tract hosts up to 100 trillion microbes with the greatest numbers residing in the distal gut. Given the vast presence of microbial genetic information, the ability to characterize communities from fecal material via next generation sequencing (NGS) has revolutionized the understanding of the human microbiome, and its influence on health. In order to gain further insight on these influences, the need for a standardized and scalable NGS metagenomics protocol is needed to minimize inconsistencies among existing methods (sample collection, sample storage conditions, experimental design, and scalability), which typically lead to data disparities and misrepresentation of the true state of the human microbiome.

In this webinar, Dr. Agata Czyz of Illumina's Genomic Applications Department will discuss a comparative metagenomics study that relied on a high-throughput and automated library prep protocol for stool. Dr. Czyz will discuss several parameters and methodologies that her team tested as well as the key findings of the study.

Sponsored by