Genomics Core Research Facility
Facility Directors: Associate Professor Mark Watson, Associate Professor Abha Chopra
Murdoch University, Murdoch, Western Australia
Core research areas supported
Our translational facility aims to produce clinical practice-altering outcomes for patients with chronic and acute diseases through supporting technologies across our core research and domain areas. We work with researchers and industry groups to meet their advanced genomics needs.
Our nucleic acid sequencing platforms include the Illumina NovaSeq 6000, NextSeq and MiSeq platform (reads up to 2 x 300 bp). This includes whole genome sequencing, Exome sequencing, RNA-Seq and CITE-Seq, as well as myriad of other specialised bulk and single cell technologies such as TCR sequencing and targeted gene sequencing, including ASHI accredited HLA typing. We also have Oxford Nanopore sequencing for long range sequencing projects and scaffolding (reads can be typically 15kb but can be100Kb plus under special prep conditions.
We support medical researchers where immunology plays a pivotal role in disease with our ASHI accredited Human Leucocyte antigen genes (HLA) typing pipelines. Using our automation and custom LIMS system we have capacity to type large cohorts of samples to unambiguous, high resolution in a single pass. We offer Class 1 HLA A (Exon 2,3), B (Exon 2,3), C (Exon 2,3) and Class II DRB1,3,4,5 (Exon 2), DQB1 (Exon 2,3), DQA1 (Exon 2), DPB1 (Exon2) exon specific typing that resolves Alleles to four or more digit typing levels covering coding region allelic variation.
Single Cell TCR Assay
The single cell TCR assay employs a Smartseq approach to capture complete V(D)J variable regions of the TCR transcript using indexed primers which enable high throughput sequencing at low cost. The advantage of this assay is it can be combined with Single Cell 3’ RNAseq assay to gain additional information from the same cells. The workflow for the assay is underpinned by a custom LIMS system, advanced liquid handlers, alongside in-house developed tools for data analysis and visualization.
Bulk TCR Assay
The Bulk TCR assay is an adaptation of our single cell TCR assay, based on cell populations or total RNA . This assay is set up for large number of cells (5k-40k) cells directly sorted into our proprietry lysis buffer or from RNA extracted from PBMCs or sorted T cells of interest. The assay also utilises the Smartseq approach using special primers containing Unique Molecular Indexes (UMI’s) to account for PCR duplicates and amplification bias.
ERAP Genotyping Assay
Our lab delivers sequence-based typing using the Miseq Illumina platform to target single nucleotide polymorphisms (SNP) for Endoplasmic Reticulum Aminopeptidase 1 and 2 genes. For next-generation sequencing, multiple indexed amplicons are pooled together using our custom LIMS and advanced liquid handling systems, that allows sample tracking and maintains data integrity. Sequencing of the amplicons is followed by identification of the specific SNP variants using in-house developed data visualisation and analysis software.
We provide gene presence/absence typing for Killer-cell Immunoglobulin-like Receptors (KIR) genes and can also perform more in depth typing of KIR using next-generation sequencing. We have the capacity to type large cohorts of samples to high resolution for 14 gene loci, encoded within a 100-200 Kb region of the Leukocyte Receptor Complex.
Key Research Domains Supported
The key domain areas we support are headed by world leading clinical academic researchers working to translate research and produce clinical practice-altering outcomes for patients and drive the new innovations in the facilities core capabilities.
Viral sequencing and integration site analysis of HIV
Multiple sclerosis immunobiology
Bacterial genome sequencing
Viral genome sequencing
These domains are headed by research groups that have been instrumental in the development of the facility and its capabilities.
Associate Professor Mark Watson
Dr Watson is a molecular biologist with a longstanding research interest in virology, with a focus on molecular immunology and antivirals with more recent interest being in cancer immunology. He leads a team of postdoctoral scientists, postgraduate laboratory staff, bioinformaticians and software developers dedicated to genomics research that improves clinical outcomes for patients where immunology and infectious disease underpins their conditions.
Associate Professor Abha Chopra
Dr Chopra leads research and development for Murdoch’s Genomics Core Research Facility and has established a world class, state of the art accredited laboratory specializing in molecular genomics. She has an extensive track record in driving the development of novel, leading-edge techniques and analysis tools utilized by academic and industry collaborators throughout the world.