FAQs

General FAQs

What factors reduce my success in SNP genotyping?

Do you offer fine mapping?

Can non-human samples be analysed?

What is good quality DNA?

What DNA extraction method should I use?

Can AGRF extract my DNA? 

Can you analyse DNA from histology slides or mouthwashes?

When will you send my results?

Is my data confidential? 

 

Fragment Analysis and Microsatellite Genotyping

What fluorescent dyes can I use?

Can you recommend software to view/analyse my data?

What size standards can be used?

What material do I require for Microsatellite genotyping?

I’m designing my own primers for a microsatellite project, what amplification conditions do the AGRF use?

Can you design my primers for me?

There aren’t any primers published for my species, what can I do?

 

Illumina FAQs

What’s involved in the DNA QC assessment?

How do I know if the quality of my DNA is sufficient for the Infinum assay?

 

Infinium Genotyping Assay

What are the minimum DNA requirements for the Infinium Genotyping assay?

In what format will we receive the Infinium Genotyping data?


 

Infinium Methylation Assay

What are the minimum DNA requirements for the Infinium Methylation assay?

What bisulfite conversion kit do you use?

What is the minimum amount of DNA required to perform the bisulfite conversion?

Do you accept bisulfite converted DNA? When you perform the bisulfite reaction, which conditions do you use? In what volume do you elute? How much bisulfite converted DNA do you require for the illumina process?

Is bisulfite converted DNA stable enough to send through regular post?

In what format will we receive the Infinium Methylation data?

 

General FAQs

What factors reduce my success in SNP genotyping?

The most significant factor in reducing the success of SNP genotyping is the quality of DNA.  All platforms, whether it be sequencing or SNP genotyping rely on good quality DNA to produce high quality results.  Therefore, good quality DNA is expected to give a higher call rate and a greater accuracy per call than poor quality DNA. 

Do you offer fine mapping?

AGRF can fine map any region of any DNA. 

 Can non-human samples be analysed?

Genotyping can be performed on any sample of DNA. Studies have been conducted by AGRF using a broad range of DNA samples, including samples from:

human blood

other human tissues from histology sections

bovine blood and hair samples

ovine blood

wheat

barley

AGRF also offer a Nucleic Acid Extraction Service.  Please refer to the Nucleic Acid Extraction and Amplification service for further information.

What is good quality DNA?

Good quality DNA generally has an OD 260/280 ratio of 1.8.  Different platforms vary in the minimum quality of DNA they require.  However, high quality DNA will yield better quality results for all platforms. 

What DNA extraction method should I use?

There are a variety of kit based and in-house methods for DNA extraction that can be used.  For small numbers of samples the AGRF SNP service recommend commercially available column-based extraction systems. For further information on the most appropriate eluate material (e.g. Tris, EDTA or water), please refer to the Sample Submission Requirements. 

Can AGRF extract my DNA?

Yes.  The AGRF has a comprehensive nucleic acid extraction service for extraction of DNA from a broad range of sample types.  This service caters specifically to the requirements of any downstream AGRF services as well as other platform specifications if required.  Please refer to the Quote Request page to generate a quote for this service. 

Can you analyse DNA from histology slides or mouthwashes?

AGRF can analyse DNA from histology slides and other samples that contain very small amounts of DNA, including mouthwashes and virtually any biological sample, provided the DNA reaches a suitable quality for the required service.  However, AGRF does not offer DNA extraction from these trace samples. Please refer to the Sample Submission Requirements for further information.

When will you send my results?

Result turn around time is project and platform dependent  (i.e. sample number versus SNPs per sample to be processed).  Please contact us to obtain specific information regarding turn around times.

Is my data confidential?

Access to data is provided via a client login which is password protected. Please refer to the AGRF Policies page for further information.

Fragment Analysis and Microsatellite FAQs

What fluorescent dyes can I use?

Products labelled with FAM, NED, PET, VIC and HEX are routinely separated.  We can also calibrate for the dR110, dR6G, dTAMRA, dROX, fluorescein, TMR, JOE dyes.  Please contact us if you have another dye system in mind.

Can you recommend software to view/analyse my data?

There are free software packages available for viewing and analysing .fsa files.  If you would like further information please contact us.

What size standards can be used?

We routinely use GeneScan  120LIZ, GeneScan 500LIZ, GeneScan  600LIZ, GeneScan 1200LIZ, and Promega Internal Lane Standard 600.  Please contact us if you require an alternative size standard.

What material do I require for Microsatellite genotyping?

To genotype one individual, the amount of DNA required is dependat on the number of markers to be screened.  Please refer to Sample Submission Requirements for further information including formulas to calculate the DNA concentrations required.

I’m designing my own primers for a microsatellite project, what amplification conditions do the AGRF use?

The AGRF aims to amplify microsatellite markers with annealing temperatures between 55°C and 60°C. 

Can you design my primers for me?

Yes, primers can be designed for any species where source sequence is available.

There aren’t any primers published for my species, what can I do?

Microsatellite discovery can be performed through next generation sequencing and primers can be designed from the resulting sequence.  Or you may wish to try published primers for a closely related species.

 

Illumina FAQs

What’s involved in the DNA QC assessment?

The AGRF DNA QC assessment for the Illumina Infinium service involves resolution on 0.8% agarose gel and nanodrop assessment. The quality of the DNA will be communicated to the client prior to the commencement of the illumina process.

How do I know if the quality of my DNA is sufficient for the Infinum assay?

For both the Infinum Genotyping and the Infinium Methylation assays, we recommend fragment sizes of at least 2kb.

Infinium Genotyping Assay

What are the minimum DNA requirements for the Infinium Genotyping assay?

The AGRF requests 1ug of DNA at 100ng/ul. If you have less than the 1ug of DNA required, we can accommodate this, so please let us know.

In what format will we receive the Infinium Genotyping data?

We perform a preliminary analysis to ensure that the assay has performed within our specifications. The files we provide as part of the service are listed below.

  • BeadChip file
  • Genome Studio Project file (.bsc format)
  • Sample Sheet (.csv format)
  • CNMetrics Report (.csv format) {Includes LogRDev values}   
  • DNA Report (.csv format) {Includes SNP call rate values}
  • Text File (.xlsx format) {Summary file of data}
  • Final Report (.txt format)
  •  Bead pool manifest and cluster file (.bpm and .egt format)

We can also export files in PLINK or MERLIN format if you are using software packages which accept these file formats.

Infinium Methylation Assay

What are the minimum DNA requirements for the Infinium Methylation assay?

The AGRF requests 1.5ug of DNA at 100ng/ul. If you have less than the 1.5ug of DNA required, we can accommodate this, so please let us know. 

What bisulfite conversion kit do you use?

The Illumina recommended conversion kit is the Zymo EZ DNA Methylation Kit.

What is the minimum amount of DNA required to perform the bisulfite conversion?

The sample input amount into the bisulfite conversion is ≥500ng.

Do you accept bisulfite converted DNA? When you perform the bisulfite reaction, which conditions do you use? In what volume do you elute? How much bisulfite converted DNA do you require for the illumina process?

We do accept bisulfite converted DNA. If you wish to replicate our conditions, we incubate the conversion reaction overnight at (95oC for 30 sec., 50oC for 60 min.) x 16 cycles, then ‘hold’ at 4oC. Following the clean-up, samples are eluted in 12ul of M-Elution Buffer. The illumina process requires 4ul of the converted product.

Please note, we do not perform the DNA QC assessment on bisulfite converted samples.

Is bisulfite converted DNA stable enough to send through regular post?

We would recommend sending your bisulfite converted samples on dry ice.

In what format will we receive the Infinium Methylation data?

We perform a preliminary analysis to ensure that the assay has performed within our specifications. The files we provide as part of the service are listed below.

  • BeadChip file
  • Genome Studio Project File (.bsc format)
  • Sample Sheet (.csv format)
  • Samples Table (.txt format)
  • Bead pool manifest file (.bpm format)

News

Aboriginal mitogenome analysis shows 50,000 years of connection to country

16 March 2017

Genomic analysis of hair samples collected from Australian Aboriginals across the nation have indicated that cultural connection to country has existed for as many as 50,000 years. 

The Aboriginal Heritage Project, led by the University of Adelaide’s Australian Centre for Ancient DNA recently published their findings in the journal Nature (online 8th March 2017).  AGRF is proud to be associated with the work as part of an ARC linkage grant, with the AGRF’s Operations Manager Dr John Stephen as a Partner Investigator.

Read more ›