VCGS/MCRI Genomics Facility

Overview

The VCGS/MCRI Genomics Facility offers a diverse portfolio of sequencing services on a clinical and research basis. We offer DNA and RNA extraction, Next Generation Sequencing assays (including sample QCs, library preparation, library QC, and sequencing; but currently excluding bioinformatics). The laboratory is NATA accredited and operates in accordance with NPAAC and ISO15189 standards.

Capabilities

Genomics

Clinical Whole Genome Sequencing (human) Whole Genome Sequencing (other organisms) Clinical Whole Exome Sequencing (human) Whole Exome Sequencing (other commercially available organisms) Custom panels

SNP micro-array genotyping

Illumina GSA v3 Illumina GDA Illumina GDACyto Illumina EPIC

Microbiomics / Pathogen Genomics

16S V4/V5, shotgun sequencing, WGS (bacterial genomes), metagenomics

Amplicon sequencing

CFTRbrary: highly sensitive, versatile, and low cost assay that allows the detection of many more CF variants, including the Poly-T and TG tract Mitochondrial genome sequencing Custom assays

Sequencing of pre-made libraries

Illumina compatible libraries only

Transcriptomics

Bulk RNAseq (total RNA, mRNA, low input, fragmented RNA, etc.)

Single-Cell Omics

10x Genomics single-cell RNA-seq

DNA/RNA extraction

High throughput DNA extractions, RNA extractions (by agreement only)

Epigenomics

ATACseq, ChIPseq, Illumina EPIC (methylation) array

Other

ATACseq, ChIPseq, custom assays (by agreement only)

Plate Reader

ClarioSTAR (2x), TECAN Infinite Nano+, SpectraMax M2

Micro-array scanner

Illumina iScan

Liquid handling

Intergra biosciences VIAflo 96, Hamilton Starlet, Hamilton NGS STAR, Agilent BRAVO

Quality Control (QC) instrumentation

There are several options nucleic acid quantitation and quality control: •Qubit 2.0 and 3.0 for genomic DNA quantification or emPCR enrichment check, as examples •TapeStation 2200 and 4200, an automated alternative to traditional gel electrophoresis •E-Gel agarose for electrophoresis •QIAxcel

Equipment

Short-read sequencing

Illumina MiSeq (x2), Illumina NextSeq500 (x1), Illumina Novaseq6000 (x2)

Sanger (ABI) sequencing

Applied Biosystems™ 3730XL DNA Analyzer (2x)

Single-cell technologies

10x Genomics Chromium Controller

Real-time PCR / qPCR / Digital droplet PCR (ddPCR)

LightCycler® 480 Real-Time PCR System Bio-Rad's Droplet Digital PCR (ddPCR) System

Automated Liquid Handling

•Hamilton PCR STARlet assay ready workstation •Hamilton NGS STAR for Library Prep assay ready workstation •Agilent Bravo Automated Liquid Handling Platform

Access Information

For further information visit www.vcgs.org.au/tests

Contacts

General lab contact for extraction services
dna.extractions@vcgs.org.au

General lab contact for sequencing services
genomics@vcgs.edu.au

Dr Stefanie Eggers
Head of Nucleic Acid Extraction and Sequencing Technologies
stefanie.eggers@vcgs.org.au

Jessica Riseley
Deputy Head of Nucleic Acid Extraction and Sequencing Technologies
Jessica.riseley@vcgs.org.au

Team Members

Iwona Büttner | Team Leader of Nucleic acid Extraction and Sequencing Technologies - DNA Extraction | iwona.buettner@vcgs.org.au

Simone Rowley | Team Leader of Nucleic acid Extraction and Sequencing Technologies - Sequencing Platform | simone.rowley@vcgs.org.au

Justin Crockett | Team Leader of Nucleic acid Extraction and Sequencing Technologies - Sequencing Platform | justin.crockett@vcgs.org.au

Sandra Nicoletti | Project Officer | Sandra.nicoletti@vcgs.org.au

Matthew McLeod | Automation and Integration Specialist | matthew.mcleod@ vcgs.org.au