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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.

Please note, if you wish to log into the member only area for one or more hubs, you need to have provided your username for that hub. For our newer hubs you would have done that upon sign up, however for our older hubs you will need to use the links below to send these details to our administrators.

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.

If you would like to join this hub mailing list, please sign up here.

If you are already a member of this hub and would like to request access to the secure member area please contact us here.

Member Login

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eDNA Hub


Dr Tina Summerfield is currently setting up an eDNA Hub.

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

Member Login

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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.
Purpose

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

 

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

Member Login

 

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 30 members spanning 6 different departments within the University of Otago in Dunedin and Christchurch.

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

If you would like to join this hub mailing list, please sign up here.

If you are already a member of this hub and would like to request access to the secure member area please contact us here.

Member Login

 

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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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). A workshop and symposium on this technology were held at the end of March. Following this feedback indicated that there was sufficient interest to start this new Hub.

If you would like to join this hub mailing list, please sign up 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 (and Hub leader) is Ryan Powell. If you have any comments, questions or suggestions for the Hub and its activities please contact him here.

If you would like to join this hub mailing list, please sign up here.

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Variant Analysis Hub


The purpose of this hub is to build a shared resource of tools and expertise for characterising potential disease-associated human variants and seek to advance this skill base within New Zealand.

If you would like to join this hub mailing list, please sign up 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.

If you would like to join this hub mailing list, please sign up here.

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