Physical Poster + E-Poster Presentation 34th Lorne Cancer Conference 2022

Complementing whole genome sequencing with whole transcriptome sequencing in precision oncology (#245)

Leila N Varghese 1 , Jacek Marzec 1 , Sehrish Kanwal 1 , Stephen J Luen 2 3 , Stephen Fox 4 , Tran Pham 1 , Jayesh Desai 2 3 , Oliver Hofmann 1 , Sean Grimmond 1 , Joseph Vissers 1
  1. Centre for Cancer Research and Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
  2. Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
  3. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
  4. Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia

Background:

Next Generation Sequencing (NGS) techniques, such as Whole Genome Sequencing (WGS), are increasingly being applied in a clinical setting to provide diagnostic and prognostic insight, as well as to suggest targets for treatment and identify mechanisms of resistance to therapy. Whole genome analyses can identify genomic changes including single nucleotide variants, copy number change and structural variants, such as gene fusions. Interpreting the biological impact of these variants by WGS alone can present ambiguities, particularly in predicting the impact of structural and splice-site variants, where reading frame may be unclear.

Approach:

We applied Whole Transcriptome Sequencing (WTS) to complement our tumour and germline WGS pipeline. We utilized RNAsum (https://github.com/umccr/RNAsum), a pipeline developed in-house to post-process, report, and visualise RNAseq data.

Findings:

WTS provides quantitative additional evidence for genome curation with expression data:

  • Expression changes with respect to internal (UMCCR) and external (The Cancer Genome Atlas https://www.cancer.gov/tcga) data sets from 33 cancer types, or a Pan-Cancer data set, can support genomic evidence for amplifications, homozygous deletions, and loss of heterozygosity.

WTS also offers qualitative information on the effects of:

  • splice-site variants; for example, evidence of exon skipping, and intron retention.
  • fusion events; whether gene fusion is expressed, frame of fusion, and exons involved.

 Conclusions:

Analyses of tumour transcriptomes in parallel with genomic sequencing provide powerful information to aid our interpretation of cancer patient genomes. Our current pipeline now routinely includes sequencing of both patient genome and transcriptome to inform our curation decisions.