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.
GO Annual Symposium
Genetics Otago has partnered with the Australasian Epigenetics Alliance to bring the AEpiA Conference to NZ for the first time, held 1st – 5th December 2024. The GO Symposium will begin with a shared session with the AEpiA delegates on the morning of the 5th of December and will then continue in its regular format for the remainder of the day.
As usual, the Symposium will highlight the fantastic research being done by GO members from around the country through presentations, posters and awards.
Date: Thursday 5th December 2024
Time: 9:00 am – 5:00 pm
Venue: Hutton Theatre, Otago Museum (for those joining from Christchurch and Wellington – a venue will be confirmed soon).
Programme
A draft programme will be available here soon.
Registration
Registration for this event is now open via the button below.
Abstract submission is part of the registration process, all abstracts must be submitted by no later than 5:00 pm on the 14th of November. Registration will close at 12:00 noon on Wednesday 20th November. Please keep the link provided at the end of your registration to make changes to your responses up until the closing date.
Registration Fee
Due to budget constraints, we will be charging a $50 per person registration fee for all attendees to subsidise the costs associated with the Symposium. We have received confirmation that this registration fee can be paid from S accounts, and if you are in a position to make a donation on top of this fee, we would gladly receive it. However, we do not want the payment to be a barrier to attendance, so if you are not in a position to make a payment, please contact us go@otago.ac.nz.
Payment Methods
Payments from an S account (or other University account) can be journaled to Genetics Otago account GL.10.LH.A14.2541 via your finance associate. Please include the surname(s) of the registrants that the payment covers in the narration.
If you need to make payment using funds from outside the University this can be arranged via the Cashier’s Office. Please contact us for details (go@otago.ac.nz).
Awards
The Annual Genetics Otago Awards including The Genetics Otago Award, Outstanding Mentor Awards, Student Supervisor Award, Publication Awards, Poster Awards and Science Communication Prize will be presented at the conclusion of the Symposium and nominations for these are now open.
Award nominations close at 12:00 noon on Wednesday 20th November (except for Poster and Science Communication Awards which are at 5 pm 14th of November) and should be submitted by email to go@otago.ac.nz.
Full details of the awards can be found here: Award Details.
Oxford Nanopore Technology Workshop
Join us at Ōtākou Whakaihu Waka, Dunedin, for a one day Oxford Nanopore Technology symposium. This event, jointly hosted by Genomics Aotearoa and the Genetics Otago ONT hub, will feature research talks highlighting different ONT use cases, a technical sequencing demonstration and an EPI2ME workshop.
This is an in-person event being held on Friday, December 6th at the Ōtākou Whakaihu Waka / University of Otago campus.
Registration for this event is free of charge.
This event is sponsored by ONT, and is supported by the Otago Genomics Facility.
Contact tyler.mcinnes@otago.ac.nz for any queries.
CRISPR Workshop
Details coming soon. Proposed date: 6th December.
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.
Join us from 24-26 July 2023 in either Auckland, Wellington or Dunedin for the PacBio HiFi Sequencing Experience Tour Roadshow Event. New Zealand is the ninth stop of the PacBio Asia Pacific HiFi Sequencing Experience Tour, to find out how HiFi sequencing is helping scientists find accurate and actionable genome-wide insights for the most important scientific discoveries.
Simply select one preferred location from the 3 locations in Auckland, Wellington, and Dunedin.
There will be presentations by industry-leading scientists and the opportunity for peer-to-peer discussions and networking during this event. Whether you have a single sample or a multi-genome project, complete and accurate long-read sequencing is designed to support your desire to make an impact.
Together with our partner, Millennium Science, we look forward to meeting you in person.
Highlights include:
The opportunity to connect with and hear from your peers
Immerse yourself in rich scientific content from across the Plant & Animal, Human, Rare & Inherited Diseases and Microbial genomics segments
Learn how to take full advantage of your samples and the PacBio HiFi advantage
See the website for more details.
This online workshop is delivered by Genomics Aotearoa and NeSI, and will be taught from 10:00am-4:00pm NZT on Wednesday the 26th of July, 2023, and is for New Zealand researchers interested in learning to create and work with pangenome graphs.
This workshop will include:
– An introduction to pangenome graphs.
– Setup guide for using the tools and data in the workshop.
– Overview of the PGGB toolkit.
– Choosing parameters to construct a graph.
– QC
– Extracting variant data.
– Mapping short reads against a pangenome graph.
This workshop assumes some familiarity with Shell. You will need to be able to do the following tasks via command line:
– Navigating files and directories.
– An understanding on full versus relative paths.
– Working with files and directories (examining files, creating, copying, moving and removing).
– Use a command line-based text editor such as nano.
If you lack the above skills, you can use these sites as a refresher:
– Introduction to Command Line Carpentries lesson https://datacarpentry.org/shell-genomics/
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.
The material for this workshop can be previewed here.
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 tyler.mcinnes@otago.ac.nz.
Register for this workshop at Eventbrite here.
Dovetail Genomics is organising a webinar with the title of “What is 3D genomics and why it matters”on 2nd Aug. In this webinar, we explore the vital role of chromosome folding and spatial organisation in gene regulation, and its seamless integration with multi-omic strategies such as transcriptomics and epigenomics. Discover real-world applications of 3D Genomics in gene regulation and oncology, including oncogenic regulation in multiple myeloma and enhancer hijacking in prostate cancer. Plus, learn how to effectively incorporate 3D Genomics into your research.
What you’ll learn:
- How 3D Genomics fits into the multi-omic toolbox (including ChIP-seq & ATAC-seq).
- What information 3D Genomics uniquely unlocks.
- Why integrating 3D Genomics provides valuable insight into your research.
Speaker: Cory Padilla, Ph. D., Product Manager, Dovetail Genomics, part of Cantata Bio
Department of Zoology Friday Seminar: 4th August, 12:00pm, Zoom
Invasive species, and the secrets they can teach us about the genetics of local adaptation.
Katarina Stuart (School of Biological Sciences, University of Auckland)
Invasive species present an invaluable opportunity to explore how organisms may cope with dramatic environmental shifts. Invasive species are introduced to new ranges, and must quickly respond to the new selection pressures in a process termed ‘rapid adaptation.’ At the same time, invasive species often undergo a genetic bottlenecking during translocation, which may cause a reduction of diversity in the population due to a loss of rare genetic variants. By studying the genetic shifts invasive populations have undergone, we may begin to understand better how genetic diversity supports a population’s ability to survive. In particular, ongoing developments in sequencing and analytical tools are enabling more comprehensive characterization of diverse components of genetic diversity present in natural populations. Here, we examine the invasion story of a well known avian pest, the common myna (Acridotheres tristis). Using whole genome resequencing we explore the impacts of successive bottlenecks on genomics variation, comparing patterns across a diverse range of different genetic variants, which include single nucleotide polymorphisms, structural variants, and transposable elements. With such data, we hope to better understand how components of genetic variation contribute to adaptive potential in an invasive population, as this has important implications not just in invasive species management and forecasting, but also in conservation efforts focused on vulnerable and managed native species.
Friday 4th August, 12:00pm
In-person hub: Benham seminar room (B215)
Zoom link: https://otago.zoom.us/j/97890882533?pwd=R0l0SXowNy9nTE02T21RZWUybjVoQT09
Meeting ID: 978 9088 2533
Password: 798823
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:
https://otago.zoom.us/j/97097442106?pwd=RlczU3VCdFBmbmt4Yng4VW5OcHdSdz09
About Joseph
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.
Setup
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 tyler.mcinnes@otago.ac.nz.
Tyler McInnes
Training Coordinator, Genomics Aotearoa
www.genomics-aotearoa.org.nz
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.
https://www.indigidataaotearoa.com/
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.
