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Urminder Singh Ph.D. defense seminar — 'Pan-tissue pan-cancer characterization of novel human orphan genes via analysis of RNA-sequencing data'

Jul 2, 2021 - 10:00 AM
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Urminder Singh, GDCB graduate student

 

 

 

 


 

Genetics, Development and Cell Biology Ph.D. candidate: Urminder Singh

Major: Bioinformatics and Computational Biology

Major Professor: Eve Wurtle, GDCB professor

Title: "Pan-tissue pan-cancer characterization of novel human orphan genes via analysis of RNA-sequencing data"

Abstract: The recently emerged, young orphan genes provide an organism with a cadre of unique species-specific proteins. In a bid to decipher the “dark transcriptome”, a result of pervasive transcription, researchers are exploring high-throughput sequencing-based gene annotation methods. Recent studies have made efforts to compile a comprehensive human transcriptome using data from experimental approaches such as RNA-Seq, Ribo-Seq and proteomics. A number of these studies continue to ignore orphan genes because of their non-canonical features, such as short length, and the lack of introns.

There is a growing interest to catalog the unannotated novel transcripts and ORFs and understand their roles in context of human physiology and diseases like cancer. This dissertation presents methods and tools to efficiently process, and analyze large RNA-Seq datasets for the purpose of identifying and characterizing orphans and other yet unannotated genes. Using these tools and methods, a reproducible and scaleable pipeline for annotating the human “dark transcriptome” is proposed. Feeding terabytes of tumor and non-diseased RNA-Seq to the pipeline identified thousands of tissue- and tumor-specific transcripts coding for novel peptides. Phylostratigraphy and synteny analysis revealed majority of novel genes are orphans encoding a human-specific protein. Pan-cancer analysis of these novel genes reveals their differential expression and association with overall patient survival suggesting their potential to be utilized for novel diagnostic and therapeutic interventions.

Webex link:

https://iastate.webex.com/iastate/j.php?MTID=mc8734f6f2e81e95debdd33805c430039

Event number: 120 663 2846

Event password: mzGyuNtw748 (69498689 from phones)

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+1-312-535-8110 United States Toll (Chicago)

Access code: 120 663 2846