Working With Us

We offer a complete genotyping-by-sequencing service — processing client supplied DNA into SNP markers. We work very closely with our clients from first contact to project completion — developing a collaborative relationship. When you bring your research to The Elshire Group, you work directly with the principal scientists and can leverage their expertise with ease. We consider every project with care. This is a better way to do science.

Please note that we do not take any projects on human or CITES listed species.

The XTen Advantage

The Illumina XTen was built specifically to drive down the cost of human genome resequencing. Always looking for ways to add value for our clients, The Elshire Group trialled the XTen platform with GBS as soon as there was an opportunity. The results were phenomenal and we switched to the XTen for all of our projects. It allows us to provide twice as many reads as the HiSeq 2500 without an increase in pricing to our clients. Additionally, the longer paired end reads offer more flexibility for downstream analyses, increasing accuracy and possibilities. Keep this in mind when comparing our service to others.

Genotyping-by-Sequencing Service

Project Setup & Consultation

Because genotyping-by-sequencing can be applied to many different species and research questions, we work directly with our clients to provide a customised project plan. This process starts with an email to us. See our contact us page for details.

Species / Enzyme Combination Optimisation or Validation

This step is necessary for each species / enzyme combination that we have not done before in house. It is necessary to have the right ratio of adapter molecules to sample DNA fragments to generate a quality GBS library. This step is a minor part of the process in terms of time and cost, but important for success.

GBS Library Preparation

Our standard laboratory method differs from the original GBS method in that we use combinatorial barcodes and paired end sequencing. We provide our clients with clear instructions for all steps of the process. Below, we provide information on the enzymes and multiplexing levels that we offer. If you require something different, please let us know and we will look at the options together.

Enzymes

  • ApeKI
  • PstI
  • EcoT22I

Multiplexing

Multiplexing is the number of samples that are put together into one library. We offer a number of levels of multiplexing. Our most popular are 94 plex and 188 plex.

Size Selection

Our standard library preparation does not involve a size selection step. We do offer it as an option for those whose needs include fewer marker sites and deeper sequence coverage per site or want to combine the paired end reads into longer reads. The size selection step is performed on a pippin prep after library amplification.

DNA Sequencing

DNA sequencing is performed on an Illumina HiSeq XTen with 2 x 150bp paired end reads. Typical yields are 400 to 500 million read pairs per lane of sequencing (over 800 million total reads). This equates to an average of 4.2 million read pairs per sample for a 94 plex or 2.1 million read pairs per sample for a 188 plex.

SNP Calling

Currently, we provide SNP calling using either the reference based SNP calling pipeline in TASSEL or the denovo SNP calling pipeline TASSEL-UNEAK. We are aware of a number of other pipelines and will offer them in the future. If you would like us to perform SNP calling using a specific pipeline, let us know.

Timing

We typically are able to provide you with a quote within 4 working days. We provide our services on a first come first served basis, unless otherwise agreed. Turn around time is dependent on our work queue. Please inquire to find out the current status of the queue.

Team Interactions

Students

Many of the projects we do include working with graduate students. We enjoy the opportunity to play a small part in their training. We have extensive experience in guiding students through the process of setting up GBS experiments.

Laboratory Staff

The quality of submitted DNA is key to generating excellent GBS data. We work directly with the client’s laboratory staff to help ensure success. Our clear protocols for DNA quality assurance and rapid response to any questions or concerns allow the wet lab staff to do their part with confidence.

Bioinformaticians

A portion of our projects are carried through to DNA sequencing and the clients conduct the SNP calling themselves. It has been our experience that genomics experiments are best conducted with the bioinformatician involved from the beginning. We encourage our clients to have an analysis plan from the outset and we provide information to detail exactly what was done to generate the sequence data. Through our stewardship of the Biospectra-by-Sequencing project, we are generating resources and opportunities for the evaluation of various SNP calling pipelines and a community of support.

Additional Services

While we focus on genotyping-by-sequencing as a service, we are passionate scientists with a range of interests and expertise. From time to time we consider picking up other interesting work. If there are projects beyond GBS that you would like collaborate with us on, please check out our individual team pages and contact us.