ACRF Cancer Genomics Facility

Profile

The ACRF Cancer Genomics Facility is South Australia’s premier facility for genomics services and has a strong reputation for reliability, high quality, cost-effectiveness  and customer loyalty. Its central location ensures it can be easily accessed by  Adelaide’s research and diagnostic communities.

 

Description

South Australia’s premier genomics facility.

In 2009, an Australian Cancer Research Foundation (ACRF) grant was awarded  to investigators from the Centre for Cancer Biology, SA Pathology and the University of South Australia to establish a premier cancer genomics facility in South Australia.

 

Products and services

The ACRF Cancer Genomics Facility provides a complete range of genomics and  bioinformatics services to the South Australian research community and gives  researchers streamlined, affordable access to powerful technologies that include:

  • Next-Generation Sequencing – Illumina, Ion Torrent, Roche/454
  • Microarrays – Affymetrix, Illumina
  • Bioinformatics Services

 

 

Type Manufacturer Model Technical Specifications
NGS Illumina HiSeq 2500 High output next generation sequencer, can generate up to 600Gb of sequence per run with 2 x 100 bp reads
NGS Illumina NextSeq 500 Larger benchtop sequencer, can sequence up to 120 Gb per run with 2x150bp reads in ~3 days
NGS Illumina MiSeq Fully integrated benchtop sequencer, can sequence up to 15Gb per run with 2 x 300bp reads
NGS Ion Torrent Proton Light independent next generation sequencer, measures pH (release of a H+) as confirmation of base integration, generates up to 10 Gb of sequence
NGS Ion Torrent PGM Light independent next generation sequencer, measures pH (release of a H+) as confirmation of base integration, generates up to 1Gb of sequence
Microarrays Illumina HiScan Scanner for Illumina’s high-multiplex BeadChips, Illumina’s BeadArray offerings include Genotyping, Linkage Analysis, Cytogenetic Analysis, Methylation and Gene Expression
Microarrays Affymetrix GeneChip Scanner & Fluidics Stations For processing SNP genotyping, cytogenetic and expression arrays
Sanger Sequencing Applied Biosystems 3730 & 3730XL 48 and 96 capillary electrophoresis systems
MALDI-TOF Sequenom (Agena) MassArray Highly sensitive SNP detection, can process 384 samples on a single chip
qPCR Fluidigm BioMarkHD High-throughput qPCR for gene expression and genotyping, 2304 or 9216 reactions per chip
qPCR Applied Biosystems ViAA 7 384 well qPCR system
Sample QC Agilent Bioanalyzer Digital electrophoresis sytem for RNA, DNA and NGS library quality control
Sample QC Shimadzu MultiNA Digital electrophoresis sytem for amplicon and NGS library quality control
Sample QC Invitrogen Qubit Picogreen based assays for determinging concentration of dsDNA, ssDNA and RNA
Library Prep Fluidigm Access Array High throughput PCR for generating amplicons to sequence via NGS
Library Prep Covaris S2 Ultrasonicator DNA and chromatin shearing
Library Prep Sage Pippin Prep Automated gel-based size selection
Single Cell Preps Fluidigm C1 Isolates up to 96 individual cells for downstream qPCR, RNA sequencing or DNA sequencing
Name Description Application
Next-generation sequencing Illumina or Ion Torrent sequencing  
mRNA Sequencing Library prep and sequencing of polyA fraction of RNA transcripts Differential expression, detect gene fusions, confirm coding variants
Stranded Whole Transcriptome Sequencing Library prep and sequencing of all transcripts except rRNA, libraries retain strand information with reads mapping back to the DNA template strand In addition to mRNA also detects lncRNAs, eRNAs, antisense RNAs, etc
Small RNA Sequencing Library prep and targeted sequencing of miRNAs and piRNAs Differential expression, miRNA discovery
DNA sequencing Library prep and sequencing of gDNA Detect variants, In/Dels, copy number variation, translocations, De novo assembly
Whole Exome Sequencing* Library prep, enrichment and sequencing of the protein coding portion of the human genome Detect variants, In/Dels
Amplicon Sequencing Amplicon generation and targeted custom panel sequencing Detect variants, In/Dels
ChIP Sequencing Library prep and sequencing of immunoprecipitated DNA Detect protien-DNA interactions of transcription factors and histone modifications
Single Cell Applications Isolation of 80 – 96 single cells for further downstream analysis qPCR, RNAseq, DNAseq
Expression Microarrays Hybridization based detection of expressed transcripts, Illumina and Affymetrix arrays Differential expression
miRNA Arrays Affymetrix array Detection of expressed microRNAs
Cytogenetic Arrays* SNP arrays from Illumina and Affymetrix For detection of copy number variation and LOH
qPCR High-throughput qPCR with Fluidigm, 2304 or 9216 reactions per run Gene expression and Genotyping
MassArrays* Sequenom (Agena) MassSpec for nucleic acid applications Genotyping, Mutation screening, Somatic Mutation detection, Epityper

* indicates NATA accredited assays

Contact

 Joel Geoghegan

Manager
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Location

Centre for Cancer Biology
IMVS Pathology
Frome Rd
Adelaide SA 5000