Molecular Genetics
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 Sanger sequencing service
Diagnostic Clinical Genetic Services
We accept clinical samples for level 1 confirmatory Sanger
Sequencing . 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 at the Australian BioResources
facility in Moss Vale and shuttled several times a week to Garvan,
where the amplification and analysis takes place. The mouse genotyping
service is accredited against the NATA ISO 17025 standard providing
controlled quality in an automated high throughput 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.
Methylation Quantification
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.