Garvan's ACRF Facility for the Molecular Genetics of Cancer was established in 2004 through a donation from the Australian Cancer Research Foundation (ACRF). It was designed to facilitate the search for cancer susceptibility genes and has developed into Garvan Molecular Genetics, the Institute’s core facility for high throughput services covering the areas of Capillary Sequencing, Mouse Genotyping, SNP Genotyping, Methylation Quantification, Cell Line Identification, Gene Expression Analysis and DNA/RNA extraction.
A diversity of platforms is available within Garvan Molecular Genetics to enable research within Garvan and the wider St Vincent's Hospital precinct, as well as external clients. The goals of the facility are aimed at providing high-throughput, sensitive, accurate and cost effective services, which include the following:
Sanger Sequencing and Fragment Analysis (NATA accredited)
Our Sanger Sequencing Service is NATA ISO 17025 and ISO15189 certified and we can therefore accept clinical samples for capillary sequencing. We offer several Sanger sequencing modules for this sequencing service. We can design primers, PCR amplify genes or exons and Sanger sequence the PCR product for you. Or we take the analysis through to a clinical report signed by a genetic pathologist. You choose the level of service you need. Alternatively, you can just submit premixed DNA and primer samples using our cost effective premix module which is competitive with international Sanger sequencing service providers both in price and quality. We employ the latest state of Sanger sequencing instrumentation and achieve average read-lengths of 1000+ Basepairs. Our Sanger Sequencing Service staff has many years of experience and can help in primer design, data interpretation or troubleshooting difficult templates. Services include:
- Standard Capillary Sequencing & Fragment Analysis
- Microsatellite Analysis
- NGS cross validation sequencing
- PCR product, plasmid, genomic DNA, SNPs
Clinical Diagnostic Sequencing Service
We accept clinical samples for level 1 confirmatory Sanger Sequencing and / or Human Copy Number Analysis. This service is NATA ISO 15189 certified. Please find more information here.
Mouse Genotyping (NATA accredited)
Our mouse genotyping service was established in 2007 and since then has developed into a national provider for high-throughput mouse genotyping. DNA is extracted via high throughput robotic platforms. PCR is set-up with in-house developed programming software that controls automatic liquid handling stations. Results are generated using High Resolution Meltcurve (HRM) Analysis and quantitative PCR data. This service is accredited against NATA ISO 17025 standard providing reliable results with cost effective technology in a quality controlled environment. Our mouse genotyping service is used by clients from numerous universities and research facilities around Australia and we have special expertise in copy number analysis and SNP detection. The Mouse Genotyping Service include:
- High-throughput Meltcurve Genotyping
- Copy number analysis for heterozygous-homozygous differentiation
- Routine SNP Genotyping for genetic monitoring of mouse inbred strains
Cell Line Identification
As per new requirements for acceptance of research publications in peer-reviewed journals, as well as the need to exclude misidentified or cross-contaminated cell lines from research, we offer a microsatellite based cell line identification service. The technology is built on the Powerplex 18D kit which uses the following 18 markers (seventeen STR loci and Amelogenin): D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, Amelogenin, vWA, D8S1179, TPOX, FGA, D19S433 and D2S1338.
Identification and re-identifiaction is achieved by comparison to reference samples via Garvan’s cell-line identification database. An analysis certificate is provided. We also test for mycoplasma via PCR.
Custom SNP Genotyping
Our custom SNP genotyping service uses a MassARRAY platform from Sequenom (now called Agena Bioscience) for high-throughput single nucleotide polymorphism (SNP) calling. The assay design allows the detection of 384 samples with up to 35 SNPs per well on one chip, bringing the cost per SNP down to a few cents.
This technology is an ideal validation system for next generation sequencing results. Our staff can advise on the assay setup, and performs all steps from assay design to data analysis.
Analysis of bisulfite treated DNA for quantitative methylation detection has become an indispensable tool for epigenetics research. With our Sequenom MassARRAY platform we offer a methylation quantification service for methylated CpG sites with an unmatched sensitivity of up to 5%.
Clients can choose either personalised custom methylation quantification projects or run preconfigured gene sets, so called EpiPanels, for cancer specific genes (~40 genes), human imprinted genes or mouse imprinted genes. Our staff can advise on the assay setup and performs all steps from assay design to data analysis with the EpiTyper software.
DNA & RNA Extraction and Quantification
We offer a high-throughput DNA & RNA and extraction service, which gives column-cleaned DNA via the QiaSymphony. Several high sensitive imaging systems are available, including the Vilber Fusion FX7 and the Licor Odyssey CLx as well as the gold standard for RNA analysis, the Agilent 2100 system.
High throughput sequencing, genotyping and methylation analysis
Instruments: Sequenom MassARRAY System, ABI 3130X, ABI 3500XL
Instruments: ABI Prism7900 HT, Lightcycler 480, Quantstudio3, Quantstudio6
Liquid Handling Robotics
Instruments: epMotion 5075, epMotion 5070, JANUS Varispan
DNA and RNA extraction and analysis
Instruments: Li-COR Odyssey, Vilber Fusion, Agilent Bioanalyzer 2100, Qiacub
For further information please contact Garvan Molecular Genetics Facility Manager Pavel Bitter at firstname.lastname@example.org or call (02) 9295 8384.