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Apr 29, 2022

RPG Seminar (2022-04-29)

Date: Friday, 29 April 2022

Time: 5:00 p.m. - 6:00 p.m.

Via Zoom:

Meeting ID: 931 8903 9276

Password: 964752


5:00 p.m.

Presenter: Miss Rongting HUANG, PhD candidate
Primary Supervisor: Dr. Yuanhua HUANG
Presentation Title: XClone: Statistical modelling of copy number variations in single cells
Abstract: Somatic copy number variation (CNVs) are major mutations in various cancers for their development and clonal evolution. Analysing CNV in single-cell RNA-seq data is of critical importance for both detecting the CNV states in tumour cells and revealing its impact on transcriptional phenotypes. However, the intrinsic low coverage and high noise properties in scRNA-seq make it difficult to call the CNVs accurately. A few computational methods (inferCNV, CopyKAT, HoneyBADGER, CaSpER) have been recently proposed to analyse CNV from scRNA-seq data, but their accuracy and computational efficiency have not been well benchmarked. Here we present a statistical method, XClone, that integrates expression levels and allelic balance to enhance the detection of haplotype-aware CNVs from scRNA-seq data and the reconstruction of tumour clonal phylogeny. Compared to commonly used methods, XClone is found to be a promising tool for accurate CNV analysis across multiple data sets, including a well-characterized and verified gastric cancer sample that covers copy loss, gain, and loss of heterozygosity.


5:30 p.m.

Presenter: Mr. Jonathan Wai King KONG, MPhil candidate
Primary Supervisor: Dr. Sung Chul KWON
Presentation Title: Rapid identification of druggable siRNA sequences
Abstract: Since the discovery of RNA interference (RNAi), an endogenous post-transcriptional regulation pathway, efforts have been put into developing siRNA therapeutics. One strand of the 21-nt RNA duplex guides the RNA-mediated silencing complex (RISC) to a disease-associated mRNA and silences the protein expression through de-adenylation or slicing. In siRNA drug development, one of the bottlenecks is screening for druggable siRNA sequences by their efficiency and accuracy. A previously reported pipeline requires laborious and time-consuming synthetic siRNA delivery to cell lines and mice. Moreover, the previous method could not systematically examine the long-term side effects of the continuous siRNA treatment. Thus, we will develop a platform that can report both on- and off-target effects of all tiling siRNA candidates along the target mRNA. A recently approved siRNA drug target gene, PCSK9, will be used as a benchmark.


Should you have any enquiries, please feel free to contact Miss Cynthia Cheung at 3917 9748.