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Pathologist,
Moffitt Cancer Center

This webinar will discuss how Moffitt Cancer Center has implemented a new capture-based application to accurately assess myeloid malignancies by detecting complex variants in challenging genes in a single experiment.  

Molecular profiling by next-generation sequencing (NGS) of myeloid tumors has become a routine part of disease management. One of the difficulties and limitations of NGS technology has historically been the inability to reliably detect mutations in certain GC-rich gene regions (such as the CEBPA gene) and insertions/deletions in genes such as FLT3, NPM1, and CALR. 

Many labs have circumvented these limitations by performing parallel orthogonal testing, which is redundant, costly, and inefficient. Furthermore, in late 2018, the US Food and Drug Administration approved a targeted therapy for FLT3-mutated acute myeloid leukemia, making accurate and reproducible mutation detection of paramount importance for guiding treatment.

In this webinar, Dr. Mohammad Hussaini of the Moffitt Cancer Center will discuss development of a comprehensive solution that captures 98 genes noted to be of importance in myeloid disease. In particular, he will describe:     

  • The process of evaluating and implementing this new capture-based NGS solution 
  • The accurate detection of challenging genes such as FLT3, CALR, and CEBPA 
  • The global analytical performance of this solution

Associate Scientist & Professor, Department of Urology; Vattikuti Urology Institute, Henry Ford Health System

Application Scientist, Advanced Cell Diagnostics 

Pseudogenes are a class of non-coding RNA with unknown functions. While there have been anecdotal observations pseudogene candidates with distinct functional roles, the overall genome-wide expression of pseudogenes in cancer has not reported until recently, with the help of next-generation sequencing technology.

In this webinar, Nallasivam Palanisamy of the Henry Ford Health System will discuss an effort to understand the genome-wide expression of pseudogenes across several solid cancers, which revealed a novel gene fusion involving a pseudogene in prostate cancer.

The objectives of this seminar are:

  • to present an overview of pseudogene expression in cancer
  • to discuss a method for the analysis and discovery of cancer-specific pseudogenes
  • to outline the application of RNA in situ hybridization for the analysis of pseudogenes

Professor of Pathology,
University of Pittsburgh

This webinar will discuss a study that used long-read transcriptome sequencing to explore the distribution of isoforms in colon cancer samples and their metastasis counterparts. 

The complexity of mammalian gene expression involves the combinatorial use of exons during RNA splicing. The selective splicing process generates a plethora of isoforms per gene and accounts for what is arguably the largest source of variation in transcriptome diversity and adaptability. However, the quantification of the diversity of mammalian transcriptome is impeded by the lack of accurate, quantitative, and affordable long-read isoform sequencing.

Accurate analyses of the distribution of isoforms, fusion gene isoforms, and point mutation isoforms remains a huge challenge for human malignancies. In this webinar, Jianhua Luo of the University of Pittsburgh will discuss a study that used the ability to capture transcripts from user-defined sets of genes together with synthetic long-read sequencing of full-length mRNA to characterize the long-read transcriptomes from three pairs of colon cancers and their metastasis counterparts.

Dr. Luo will share how the study demonstrated a unique pattern of RNA isoform redistribution and enrichment for specific mutated isoforms and fusions in metastatic cancer cells in comparison with their primary cancer counterparts. The isoform switching and mutation-enriched isoforms are predicted to have subtle effects on protein structure, which may differentially impact protein signal transduction and response to drug treatment.

The results demonstrate that the use of probe capture and long-read sequencing provides focus and granularity that was previously inaccessible in transcriptome analysis. Full-length transcriptome analysis may be essential for our understanding of gene expression regulation in human cancers.