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Tech Hubs

To help foster the unrivalled genetics research conducted by our members, Genetics Otago supports the establishment and running of several Technical Hubs focused on different technologies and techniques. These hubs are run by members of Genetics Otago and are open for all members to join. These groups provide a platform for collaboration and informal discussion between members in different areas but with similar research themes. Regular meetings, workshops and symposia are also held.

For more information on, or to join one of the existing Genetics Otago Tech Hubs, see the links below:

If you are working with a technique or technology that is not covered by one of these Hubs and you are interested in establishing a group, please contact us.

CRISPR Hub

The CRISPR Hub provides a forum for CRISPR users to share ideas, advice, resources, and expertise. We would also like to identify areas where additional input (e.g. training workshops etc.) are wanted or needed.

Purpose

CRISPR and related gene-editing technologies are becoming an increasingly popular and important tool for molecular biology and genetic studies, but to date research groups across various Departments have been working largely in isolation. The purpose of a CRISPR hub would be to provide a forum for those using/intending to use CRISPR to share ideas, tools and knowledge, and to develop a core of expertise within the University to support and extend the use of this technology. Our current membership covers all levels of expertise and experience, ranging from groups that are routinely carrying out CRISPR work to individuals who want to know more about how it might advance their work in the future.

Initial Goals
  • To compile a list of current CRISPR and proposed research.
  • To create a repository of IBSC approved projects to streamline the process for people applying for permission to use gene editing in the future.
  • To identify pre-existing expertise and tools within the University, and areas that would benefit from external input (eg inviting speakers/arranging training workshops).
  • To arrange regular forums for people to seek advice/share ideas etc.
  • Develop best-practice protocols for post-editing validation.

CRISPR Hub leaders are Dr Cushla McKinney (cushla.mckinney@otago.ac.nz) and Dr Indranil Basak (indranil.basak@otago.ac.nz).

If you would like to join this hub mailing list, please contact us here.

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eDNA Hub

The leaders of this Hub are Associate Professor Tina Summerfield (tina.summerfield@otago.ac.nz), Dr Eddy Dowle (eddy.dowle@otago.ac.nz) and Dr Gert-jan Jeunen (gert-jan.jeunen@otago.ac.nz).

If you would like to join this hub mailing list, please contact us here.

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ELSC Hub

The ethical, legal, social and cultural considerations (ELSC) Hub provides a forum to share ideas, advice, resources, and expertise for best-practice use of genomic medicine in our health care.

The implementation of genomic medicine into our health care will need careful and continued oversight of the (many and complex) ELSC considerations….who has access to our DNA health information, familial level confidentiality, disclosure, insurance, risk for stigmatising and racial profiling, to name but a few.

Taken broadly, there are commonalities in ELSC considerations with genomic medicine but each new genetic test or screen will have its own unique set of ELSC considerations. The molecular technology side of genomic medicine moves at a much faster pace than the ELSC solutions, and some would argue that the “horse has bolted” – and that we are never going to catch up….

Purpose

The purpose of this forum is to establish a network that connects people working in the different facets of genomic medicine – from the bench scientist to those working in the field of ELSC – working to the ethos that genomic medicine needs to improve health inequities, and not compound them.

Initial Goals
  • To compile a living database of researchers and other professionals working in the ELSC fields
  • To arrange regular forums for people to seek advice/share ideas etc.
  • Develop best-practice protocols for implementation research activities and evaluation of new molecular technology development

Leaders of the ELSC Hub are Associate Professor Sara Filoche (sara.filoche@otago.ac.nz) and Dr Josephine Johnston (josephine.johnston@otago.ac.nz).

 

If you would like to join this hub mailing list, please contact us here.

 

Epigenetics Users Group (EUG) Hub

The Epigenetics User Group (EUG) was founded in March 2017. Epigenetics is an important field of biomedical science and its application and use are rapidly increasing worldwide. The aim of EUG is to collectively address critical/technical problems, share resources, provide constructive peer review, provide academic consultancy in epigenetics and improve our collaborations. The group currently meets monthly and is actively expanding its membership. At the moment EUG has over 50 members spanning 6 different departments within the University of Otago in Dunedin and Christchurch.

EUG leader: Associate Professor Aniruddha Chatterjee (aniruddha.chatterjee@otago.ac.nz)

If you would like to join this hub mailing list, please contact us here.

 

Methods and Platforms
  • RRBS, WGBS and Bioinformatic/Statistical Analysis
  • EWAS
  • Targeted bisulphate sequencing
  • ATAC-seq and ChIP-seq
  • Chromatin interactions/4C-seq
  • CRISPR methylation

 

Fields of interest
Emerging Epigenetic Technologies

This field is focused on the development of bioinformatics tools and statistical methods to accurately analyse large epigenomic datasets produced by genome-wide sequencing technologies.

Key contacts

 

Cancer Epigenetics

This field is focused on documenting the epigenetic alterations (such as DNA methylation, miRNA, etc) that occur in cancer and the usefulness of epigenetic marks as predictors of cancer and cancer progression/metastasis. It also aims to determine the functional consequences of cancer-associated epigenetic changes in the laboratory.

Key contacts

 

Disease and Population Epigenetics

This field is focused on how epigenetic variants and environmental factors contribute to disease. Epigenetic association studies are being used to uncover relationships between phenotypes and epigenetic modifications such as DNA methylation.

Key contacts

 

Epigenetics of Model Organisms and Toolsets

Model Organisms: This field uses model organism to investigate the consequences that epigenetic alterations have on health and disease and also to understand the epigenetic mechanisms of trans-generational inheritance.

Toolsets:This field is focused on devising computational tools to support the processing, analysis and management of large-scale data sets generated from genome-wide sequencing methods.

Key contacts

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Outreach Hub

The intention of the Outreach Hub is to support the science curriculum in Aotearoa and make research and scientific careers more accessible to school students and teachers. The aim of this hub is to curate a list of volunteers who are happy to go into high schools, or attend Genetics outreach events, and talk about their research. The Hub will hopefully go beyond this and support a range of school-based outreach and resources around Dunedin, and beyond.

If you are interested in knowing more about this Hub please contact leaders Dr Emma Wade (emma.wade@otago.ac.nz) and Dr Nic Rawlence (nic.rawlence@otago.ac.nz)

If you would like to join this hub mailing list, please contact us here.

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Oxford Nanopore Hub

The purpose of this Technical Hub is to provide a core of expertise (and potentially some equipment access) based around the nanopore sequencing platform developed by Oxford Nanopore Technology Ltd (UK).

Hub Leaders: Dr Robert Day (robert.day@otago.ac.nz) and Dr Augustine Chen (augustine.chen@otago.ac.nz)

If you would like to join this hub mailing list, please contact us here.

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Postgraduate Students Hub

With no physical Department of Genetics our Postgraduate students are spread across several departments within the University and often don’t have a chance to interact with one another. Our Postgraduate Student Hub exists as a means to capture these students and offer them both assistance in their genetics based studies and a collegial environment to meet other Genetics students completing PhDs, MScs or BSc(Hons).

The current Genetics Otago Postgraduate Students representative is Amy Jones (amygjones98@gmail.com) who co-leads this hub with Meghan Mulligan (meghan.mulligan@postgrad.otago.ac.nz). If you have any comments, questions or suggestions for the Hub and its activities please contact them.

If you would like to join this hub mailing list, please contact us here.

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Single Cell Sequencing Hub

This hub is run by Dr Nathan Kenny (Biochemistry) and Dr Michael Meier (Pathology) and aims to popularise and advocate for the use of single cell approaches. We regularly organise meetings to chat about results and share new methods, as well as provide dedicated training. We also provide a platform to troubleshoot techniques and work on new and exciting applications of single-cell sequencing methods (broadly defined).

If you would like to join this hub mailing list, please contact us here.

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Variant Analysis Hub

The Variant Analysis (VA) Hub provides a platform to support researchers working with genomic variant data within the University. The VA Hub is focused on facilitating collaboration through the sharing of ideas, tools, and expertise across research groups and campuses. In addition, the VA Hub aims to identify areas of need within its community and organise workshops to address these issues.

VA Hub co-leaders: Dr George Wiggins (george.wiggins@otago.ac.nz) and Dr Ben Halliday (benjamin.halliday@otago.ac.nz)

If you would like to join this hub mailing list, please contact us here.

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Virtual Institute of Statistical Genetics Hub

A New Zealand-wide collaboration for developing new statistical tools and analytical pipelines for application in NZ contexts.

Hub Leaders: Dr Jie Kang (Jie.Kang@blnzgenetics.com) and Associate Professor Phil Wilcox (phillip.wilcox@otago.ac.nz).

If you would like to join this hub mailing list, please contact us here.

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