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.
Species-wide genomics of kākāpō provides transformational tools to accelerate recovery
A reminder about our Genomics Aotearoa seminar, online this Friday, August 4 at 3pm.
We welcome Dr Joseph Guhlin (University of Otago) to talk about Species-wide genomics of kākāpō provides transformational tools to accelerate recovery.
Please invite colleagues to join our genomics community and take part in this seminar. Look forward to seeing you there. Questions and discussions are welcome.
Join from PC, Mac, iOS, or Android:
Dr Joseph Guhlin graduated with a PhD in Plant & Microbial Sciences from the University of Minnesota.
Based at the University of Otago, he is working in the Genomics Aotearoa High Quality Genomes and Population Genomics programme. A programmer by trade, he is interested in small pop genomics, high-performance computing, gene family expansion and contractions, and applying machine learning to small populations and genetics.
This in-person workshop is delivered by Genomics Aotearoa and NeSI, and will be taught over two consecutive days on 9-10 August 2023 from 10am-4pm NZT. It is for New Zealand researchers interested in signals of selection in genomes.
Sign up to this workshop at Eventbrite.
The focus of this workshop is on identifying signals of selection in an example genome using the outlier analysis method. Outlier analysis assumes that the majority of the genome is under neutral selection and some loci will appear as outliers relative to this background.
This lesson assumes learner has no prior experience with the tools covered in the workshop. However, learners are expected to have some familiarity with biological concepts, including the concept of selection. You are expected to have some familiarity with both the R programming language and with basic command line (bash). If you need to refresh, please revise the material in our previous workshops on R and bash.
We encourage you to bring your own data! For participants who do not have their own data, a group dataset is available and will be used by the instructors during the examples.
During this workshop you will:
Download example genomic data (or prepare your own).
Use the PCAdapt tool to identify outlier loci within a genome.
Use VCFtools to identify outlier SNPS in population comparisons.
Use Bayescan to identify outlier SNPS based on allele frequencies.
Relate identified SNPS to phenotypic variation.
Compare the results of the different methods and discuss the results.
This is an in-person, hands-on workshop. 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.
Participants must have their own laptops and plan to participate actively. You will require a working web browser.
If you have any questions about these workshops, including whether they are suitable for you, please contact firstname.lastname@example.org.
Training Coordinator, Genomics Aotearoa
Webinar: 3D Genomics Experimental Considerations
Aug 10, 2023 3:00 PM (Auckland)
Join us for an insightful talk on 3D Genomics, where we will walk you through what is involved in designing and running a 3D Genomics experiment in the lab, sharing tips and best practices. We will also highlight how to QC the library, and what resources are available to navigate data processing. There will also be an opportunity to ask questions to our expert scientist.
What you’ll learn:
- How to design a 3D Genomics experiment.
- What is involved in running a 3D Genomics experiment in the lab.
- How to navigate data processing and QC analysis.
Speaker: Myriam El Khawand, Ph.D.
Senior Customer Success Scientist
Dovetail Genomics, part of Cantata Bio
There are 20 fully funded positions available on the program.
The program is open to Māori (tauira, kaitiaki, kaipakihi) who want to better understand the opportunities and challenges associated with māori data science, māori data sovereignty, as well as key technical, cultural and ethical issues.
Applications will be considered from university students in any discipline as well as people with strong iwi, community or business background.
Applications will close Sunday 16 July 2023.
Unravelling Gene Regulation with the Dovetail Pan Promoter Panel
Advancements in genomics have revolutionized our understanding of gene regulation, paving the way for ground-breaking discoveries in various fields, from developmental biology to disease research. At the forefront of this transformative landscape is the Dovetail Pan Promoter Panel, a genomics tool designed to unravel the intricacies of gene regulation.
In this seminar, we invite you to embark on a journey into the world of regulatory genomics and explore the power of the Dovetail Pan Promoter Panel. Led by renowned experts in the field, this seminar will delve into the unparalleled capabilities of the panel and its potential to unlock the hidden secrets of gene expression.
Date: 30th August, 2023
Time:3:00 PM – 5:00 PM (Auckland, NZ)
Speaker 1: Professor Yasuhiro Murakawa
Kyoto University Institute for Advanced Study (KUIAS)
Dissecting human disease pathways using high-resolution chromatin contact maps
Large-scale genome-wide association studies (GWAS) have yielded an increasing number of disease-associated genomic loci. However, the functional interpretation still largely remains unclear. Recently, it has become apparent that disease-associated genetic variants are often found within enhancers. Enhances act to strongly enhance the expression of their target genes in a cell-type specific fashion, by physically associating with their promoters. We have developed a 5’-end single-cell RNA sequencing approach to comprehensively map active enhancers from heterogeneous helper T cells. By integrating with GWAS datasets, we identified hundreds of human enhancers associated with autoimmune diseases. To gain important clues to human disease pathways, here we used Micro-C as well as promoter-capture Micro-C, methods that can analyze chromatin interactions with super-high resolution. We systematically identified target genes of these enhancers, revealing novel human disease molecular mechanisms. In sum, we provide a general framework to investigate molecular mechanisms underlying human diseases.
Speaker 2: Myriam Elkhawand, Customer Success Manager, Dovetail Genomics
Setting up the Dovetail® Pan Promoter Assay in the lab
In this second talk, Myriam will delve into the details of Dovetail Pan Promoter protocol and library quality control measures that play a pivotal role in assessing the success of the assay. She will discuss best practices in carry out the assay, library QC, emphasizing the importance of stringent quality standards for reliable data analysis. She will also share the analysis pipeline for Dovetail Pan Promoter panels.
Nanopore Day, Queenstown 2023
Date: Thursday 31st August 2023
Venue: Queenstown, New Zealand
Time: 9:00 – 17:00
Hear about the latest technical updates for Oxford Nanopore Technologies as well as talks from local scientists about their latest work using nanopore technology.
There will also be an opportunity to submit questions throughout the talks, which will be answered in the Q&A sessions following each presentation.
Please note that this is an in-person event.
There is no delegate fee for this event, but registration is required at https://nanoporetech.com/event/NanoporeDayQueenstown
Your place at this event will be confirmed via email from email@example.com.
Schedule available here: https://nanoporetech.com/event/NanoporeDayQueenstown
The Environmental Microbiomes team at Genomics Aotearoa is hosting the annual Metagenomics Summer School once more.
This practical, hands-on workshop focuses on prokaryotic metagenomics. It aims to guide learners through the process of analysing metagenomic sequence data, from metagenomic read sequences to curated metagenome-assembled genomes paired with downstream data analyses and visualisation in R. It also includes the following lessons:
Introduction to Bash shell and scripting (pre-workshop session)
Pragmatic considerations during experiment/sampling planning and decision-making (e.g., how much sequence data do I need? What are the approaches to analysing the data I have?)
Best practices in handling and processing metagenomic data
Viral genome prediction from metagenomic assemblies
This in-person workshop will be held at the University of Auckland, City Campus, from 5th to 8th September 2023. See our Metagenomics Summer School poster.
We invite learners of all bioinformatics skill levels to register their interest here.
Jian Sheng Boey
Genomics Aotearoa Bioinformatics Training Coordinator
Join the Malacological Society of Australasia on September 7th, from 12 to 1:40pm (New Zealand time) for an enlightening open online symposium on molecular tools applied to molluscs! We will hear from AP Claudio González Wevar, AP Felipe Aguilera, and DP Hamish Spencer on the application of these tools to very different aspects of malacology. The symposium is free of change, just RSVP to receive a Zoom link. More information can be found on our website.
This online workshop is hosted by Genomics Aotearoa and NeSI and is for New Zealand researchers interested in progressing their skills with the R programming language.
This is an intermediate workshop, please check you meet the prerequisites: Attendees must have introductory knowledge of R and be well versed in tidyverse (Intro to R + supplementary materials in that workshop). We expect that you will either have completed our Introduction to R workshop or have sufficient experience of your own.
Some of the topics covered in the workshop are:
- Introduction to relational data and the join function.
- Working with regular expressions and functions from the stringr package.
- Writing custom functions, working with conditional statements.
- ‘Defensive programming’.
- Iterations – for loops, and map_*() functions.
- The importance of data structure in R.
Setup: This is a fully online, hands-on workshop. 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.
Participants must have their own laptops and plan to participate actively. You will require a working web browser.