Upcoming events hosted by or involving Genetics Otago will be listed here. Please check back regularly for updates. A calendar of events that may be of interest to our members can be found at the bottom of this page and in the sidebar of other pages on this site, please note that this includes events hosted outside of Genetics Otago.
- VISG Seminar Series
- Variant Analysis Hub Workshop
- Postgraduate Retreat
- GO Symposium
- Calendar of Events
VISG Seminar Series
The Virtual Institute of Statistical Genetics (VISG) Hub is a key part of Genetics Otago, providing a platform for researchers to collaborate and exchange knowledge and expertise in statistical genetics. The VISG Hub hosts seminars, workshops, and other events to promote statistical genetics research and foster collaboration between researchers.
We’re excited to announce our monthly genetics research seminars, aimed at connecting researchers in the field. The seminars will commence in May 2023 and will be hosted by GO’s Virtual Institute of Statistical Genetics (VISG) Hub along with the Department of Mathematics and Statistics at the University of Otago. These seminars will be available in person or via Zoom, and all are welcome.
Date: 3rd Thursday of the month
Time: 11:00 am – 12:00 pm
- May: Associate Professor Phil Wilcox, University of Otago
- June: Professor Mik Black, University of Otago
- July: Dr Ludovic Dutoit, University of Otago
– please note that this seminar will be held on the 27th of July rather than the 20th due to ICG.
- August: Dr Setegn Alemu, AgResearch
- September: Ee Cheng Oi, Abacus Bio
- October: Franziska Weik, Beef + Lamb NZ Genetics
- November: Dr Jane Symonds and Dr Megan Scholtens, Cawthron
– please note that this seminar will be held on the 17th of November rather than the 16th due to the GO Annual Symposium.
If you would like the Zoom details for this event, please contact us.
The seminar will be held on the 21st of September, 11 am in St David Complex Seminar Room A G.02 and will be given by Dr Ee Cheng Ooi, AbacusBio.
Title: Using SNP effects to understand the underlying biological mechanisms linking traits: a study of milk yield and fertility in dairy cattle
Abstract: Fertility in dairy cattle has declined as an unintended consequence of single trait selection for high milk yield. The antagonistic genetic correlation between milk yield and fertility is now well-documented, however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified.
One of the clusters included variants that increase milk yield and decrease fertility, where the ‘archetypal’ variant (i.e., the one with the largest effect) was associated with the gene GC, while others were associated with TRIM32, LRRK2, and U6. These genes can be characterized by their effects on transcription and alternative splicing, suggesting that these processes are likely contributors to the antagonistic relationship between the two traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, affected milk yield but had little effect on fertility and are characterized by their effects on insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT affected fertility but not milk yield, and were characterized by their effects on GnRH neuronal migration, embryonic development, and/or ovarian function.
The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis-generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways which have been previously unexplored within the context of dairy production.
Biography: Ee Cheng Ooi is a cattle vet and consultant at AbacusBio, an agricultural science and technology company based in Dunedin. She is originally from Melbourne, Australia, but moved to New Zealand after completing her PhD in the genetic improvement of fertility in dairy cattle last year. After a decade of working for the Australian dairy industry, she decided to broaden her horizons by working across a variety of other countries and species, including beef and sheep. Her interests lie in agricultural extension, livestock production systems, veterinary epidemiology, and biostatistical analysis.
If you have any questions about this seminar series please contact us.
Variant Analysis Hub Workshop
Session 1 will start with an exploration of the core features of Nextflow and learning the fundamental commands and options for executing workflows. Next, we will learn the core features of nf-core and its tooling. This knowledge will then be applied as we learn the structure of an nf-core workflow and how customize its execution. Finally, we will learn about nf-core tooling for users and how it can help you execute your workflow.
The ideas and skills you learn during Session 1 will then be applied during Session 2 where we will explore the source code of the `nf-core/sarek` workflow. We will learn how to build a run command and then customize its execution. The session will finish by discussing how to execute Sarek at scale using full-size data.
Date: 11th and 12th October 2023
Time: 9:00 am – 12:00 pm
Venue: Online (Dunedin Hub for attendees is Hunter Centre Computer Lab 1.15)
Registration for this event is via Eventbrite, please use the button below to be redirected to the registration page.
This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants
Genetics Otago would like to thank the below contributors to this event:
The biennial Genetics Otago Postgraduate Retreat is happening in 2023! This event is open to all PGDipSci, Hons, MSc and PhD students who are using genetics as part of their research – you do not need to be enrolled as a GENE major.
Date: Friday 27th of October 2023
Time: 8:30 am – 4:30 pm
Location: Gallery Room, Staff Club
The day will begin with tea and coffee before the formal programme begins at 9:00 am. They day will include sessions on science communication, Māori language, careers, wellbeing and ethics and will be fully catered. A full programme will be posted here once it is finalised.
Please register for this event using the button below
The Genetics Otago Annual Symposium is expanding in 2023! We will be holding a three day event, with two days of Hub workshops followed by the full day symposium. Posters will be on display for the three days and we hope to get as many members as possible involved in this free event!
Date: 14th – 16th November 2023
Time: 9:00 am – 5:00 pm
Venue: St David Lecture Theatre Complex (and Genetics 300-level teaching Lab)
Genetics Otago Hubs will host workshops on the 14th and 15th of November. You will be able to register for these when you register for the main Symposium. Full details on these workshops are still to come but we plan to host the following:
- eDNA Hub: workshop to cover analysis and processing of environmental DNA data.
- CRISPR Hub: workshop to cover gRNA design and optimisation, CRISPR screens and data analysis.
- Oxford Nanopore Sequencing Hub: a combo wet lab/computational workshop covering nanopore sequencing and small group data analysis.
- Ethical Legal and Societal Considerations (ELSC) Hub: a panel-focused workshop to stimulate discussion around National Academies of Sciences, Engineering, and Medicine (NASEM) report
- Outreach Hub: media training plus tips for increasing visibility for your own research
- Outreach Hub: teacher training on newly developed resource kits.
- Variant Analysis Hub: nf-core pipeline data analysis workshop overflow (for those who missed out in October)
We will add more details as they come in, so stay tuned.
The main Symposium will take place on the 16th of November in the St David lecture theatre. This will feature invited speakers as well as selected abstracts. At the conclusion of the Symposium the 2023 GO Award winners will be announced (more details below).
Confirmed invited speakers:
- Dr Nathan Kenny, Ngāi Tahu and Te Ātiawa (Department of Biochemistry)
- Associate Professor Sara Filoche (Department of Obstetrics, Gynaecology and Women’s Health – Wellington)
- Dr George Wiggins (Department of Pathology and Biomedical Science – Christchurch)
Genetics Otago presents annual awards as part of the Symposium programme. In 2023 we will be presenting awards in the following categories:
- The Genetics Otago Award
- Senior and Peer Mentor Awards
- Student Supervisor Award
- Student and ECR Publication Awards
- Student and ECR Poster Awards
- Science Communication Award
Nominations and entries for these awards are now open and will close at 5:00 pm on the 27th of October 2023. Full details of the awards and how to enter can be found here.
The programme of events will be posted here once finalised.
Registration for this event will open soon. Abstract submission will be part of the registration process, all abstracts must be submitted by no later than 5:00 pm on the 27th of October 2023.
Calendar of Events
The below is a calendar of events hosted by GO as well as events hosted by others that may be of interest to our members. If you have an event you would like us to include please contact us here.
Hosted at the University of Otago, the Bioinformatics Spring School 2023 is a week long training event for researchers, supported by Genomics Aotearoa and the New Zealand eScience Infrastructure (NeSI). This event is primarily targeted at researchers and students based in Aotearoa New Zealand. International applications will be considered but will need to be able to attend in-person.
Expressions of interest applications are now open and will close midnight, Friday 29th September 2023.
Full Details: https://otagobioinformaticsspringschool.github.io/2023/