Page 54 - Hormel Institute Annual Report 2021-22

Rendong Yang, PhD
“Identifying specific subtypes of prostate cancer and the distinct pattern of mutations associated
with them will enhance development of
precise diagnostic tools that detect specific genetic aberrations, allowing doctors to reliably predict a patient’s outcome and prescribe
personalized treatment.”
Rendong Yang
54 | THE HORMEL INSTITUTE // UNIVERSITY OF MINNESOTA Computational Cancer Genomics
ASSISTANT PROFESSOR
Developing novel algorithms for indel
detection.
Our most recent work has been in the development of clinical genomic variant detection pipelines
for our customized oncology gene panels in the University of Minnesota Molecular Diagnostic Lab. We developed a new algorithm named ScanIndel to accurately detect insertion and deletion (indel) mutations in the human genome from next gener- ation sequencing data. In particular, ScanIndel re- liably detects medium-size and large indels. With this method, indels contribute to the pathogenesis of constitutional and somatic diseases can be identified quickly and accurately, which is import- ant for targeted therapy or patient prognosis.
Detecting gene rearrangement, splicing and epigenetic regulator of AR in prostate cancer.
We developed an integrated pipeline to detect structural rearrangements in the AR gene, which encodes the androgen receptor. Through this work, we identified diverse genomic-dependent
and genomic-independent AR splicing variants expressed in prostate cancer. Additionally, our early work focuses on prostate cancer epigenomic studies by analyzing the ChIP-seq data of AR and BRD4 in prostate cancer VCaP cell line. Our study revealed the crosstalk between AR and BRD4 signaling in prostate cancer progression.
Developing algorithms for detecting
cancer biomarkers.
We have been developing an Egonet algorithm by integrating gene expression micro-array data and protein interaction networks to identify network modules that can distinguish different breast cancer subtypes.
Detecting novel indels from prostate
cancer genome
We developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-