Friday 9th September 2022
The Changing Landscape of Genomics
Dr Joep de Ligt
Senior Science Lead, Bioinformatics and Genomics at ESR.
Through a combination of technological advancements, decreases in cost as well as smart wet-lab and bioinformatics procedures, genomics is becoming increasingly real-time and accessible to different users. In his talk, Joep gave practical examples from the work ESR is undertaking to illustrate how these things are changing – not only in how we utilise genomics but also how people are using sequencing to replace arrays and generate completely new tests.
Dr Joep de Ligt is the Senior Science Lead bioinformatics & genomics at ESR. He leads teams that cover both the Human and Infectious disease spaces ranging from wet-lab to data crunching. These teams demonstrated the capability and value of rapid whole genome sequencing in New Zealand’s COVID-19 response. Their current research focus is delivering on the health impact potential of sequencing-based technologies.
17-18 May 2022. GIM participated in a two-day workshop run by Murray Broom (DNAiTECH: Pictured in top right panel) and Zakiyya Mohammed (senior biology teacher at Tamaki College). Tamaki College students were the first school students in Tāmaki Makaurau / Auckland to use LAMP (loop mediated isothermal amplification). They applied this technique to assess the microbial content of streams at the foothills of the Hunua Ranges, using DNAiTECH’s E. coli kit, developed for use in schools. As an AIMHI consortium school (Achievement in Multicultural High Schools), students were able to use Kokako Lodge at the Hunua Falls as their base, obtaining and filtering samples and extracting DNA on the first day, then on the next running the LAMP assays, which allow real-time monitoring of DNA amplification using portable DNAiTECH devices connected to smartphones. The students learned a lot and enjoyed the experience of hands-on modern molecular biology. The data they each obtained was able to be used for their NCEA assessments (an example of data produced by students is shown in the bottom right panel). The success of DNAiTECH’s workshop sets the stage for similar LAMP and/or eDNA sequencing retreats for school students at Kokako Lodge in future years.
April 11th 2022 – The Daily Encourager is a charitable trust that seeks to enhance the education, health and spirit of people of Aotearoa/New Zealand. The Trust’s April 2022 online news features GIM’s SouthSci-funded school outreach project in which primary school students from the Glen Innes/Tamaki area sampled environmental DNA (eDNA) from their local awa.
May 27 2021 – Genomics Into Medicine hosted a visit from Tāmaki College senior biology students to the Faculty of Medicine and Health Sciences. The students were able to view lab spaces and visit the Medical Science Learning Centre. They also heard from established as well as up-and-coming Māori and Pacific doctors and researchers talking about their personal career paths in biomedical sciences and health care. Featured speakers included Drs Malakai Ofanoa, Kimiora Henare, James Opie, and two Maurice Wilkins Centre researchers, Dr Natalie Netzler and Doctoral student Christopher Puliuvea.
May 2021 – The New Zealand Association of Science Educators (NZASE) has published a resource for educators titled “Working With Scientists”. Mike Stone, NZASE Science Communicator, interviews teachers and scientists to explore the benefits and hurdles involved in establishing effective science outreach collaborations between schools and academia. This resource, which includes interviews with teachers involved in GIM’s SouthSci project, can be accessed here.
April 11th 2021 – GIM’s science outreach to primary schools students (see below) was the centrepiece of SouthSci’s first ever display at the MOTAT STEM fair. It was a great success with many youngsters interested in science enjoying the opportunity to hear about DNA sequencing and look at plant and animal tissues under the microscope. A video of interactions with children at SouthSci’s MOTAT display can be found here.
November 17-18 2020 – In collaboration with Kim Handley’s lab at the University of Auckland School of Biological Sciences, GIM’s SouthSci-funded science outreach project had Year 7/8 students conduct environmental DNA (eDNA) sampling. Four schools from the Glen Innes/Tamaki area of Auckland participated; St Pius X School, Glen Innes School, Point England School and Tamaki Primary School. Emilie Gios and Olivia Mosley, PhD. students from the Handley lab, showed primary school students how to collect water samples that were then put through a filtration device to capture microbes and eDNA for analysis. The students also collected individual samples that they took back to the classroom to look at under microscopes. Through this field trip, and with the permission of Ngāti Pāoa, primary school students were able to gain insights into the surprising range of species in and around the Omaru awa.
December 16th 2019 – GIM held an informal 1-hour mini-workshop for staff interested in visualisation technologies. This mini-workshop focused around a basic set of visualisation equipment coming into the medical school in 2020, potentially including VR, AR and ‘tilewall’ or other screen capability. The Centre for eResearch is taking a pivotal role in providing these technologies.
In the first weeks of November and December, twelve classes of Year 7 and Year 8 students from Auckland Normal Intermediate participated in the GIM-Auckland Museum co-developed programme on Unzipping DNA. Earlier in the year, on September 18th, Year 9 students from Kaipara College visited the Auckland Museum to participate in the programme.
October 30th 2019 – The three schools in the Genomics Into Medicine SouthSci project held a Genomics Hui at Point England School, holding competitions in which approximately 200 Year 7 and Year 8 students were able to show their enthusiasm and learning of information about the tree of life and the structure and function of cells and DNA
October 27th 2019 – Genomics Into Medicine’s SRIF stage-gate funding extension application was successful.
Key objectives over the next two years are to:
1) Maintain an active medical genomics academic environment between Auckland’s academic hospital clinicians and University.
2) Generate Long term sustainability for medical genomics research through international connections, engaging school students and participating in future planning.
3) Facilitate currently active UoA medical genomic research programs to achieve high impact outputs and additional funding.
4) Incorporate a cross-faculty data science component into Auckland’s medical genomics research programs.
GIM hosted additional Friday afternoon hacky hours on September 20th (Machine Learning), October 11th (epigenetics) and November 8th (Machine Learning).
August 16th 2019 – GIM’s Professor Cris Print delivered the opening keynote address at the 2019 Victorian Cancer Bioinformatics Symposium in Melbourne, Australia. His keynote was titled: Cancer Bioinformatics – How Hard Can It Be? (http://viccancerbioinfsymposium.org).
2019 Bioinformatics Hacky Hours
Seven hacky hours have been held to help researchers with bioinformatics and share expertise. If you are a local researcher and want to be placed on the hacky mailing list, contact GIM. Recent themes are illustrated by the flyers shown here (clockwise from top left, RNAseq held on 7th June, Variant Calling held on 12th July, Metagenomics held on 26th July, Data Representation held on 9th August and Machine Learning held on 20th Sept. (highlighting 2I/Borisov and best laid plans of machines & men.
GIM especially thank William Schierding, Peter Tsai, Ben Curran and Nicholas Knowlton for their expert contributions to these events.
26th July 2019 – GIM funded a workshop in Auckland to finalise bioinformatic pipelines involving the University of Auckland, ESR and the University of Otago. Over the course of 2018 and 2019 a series of containerised genomic analysis pipelines (B-pipe in Singularity and Docker) and visualisation protocols were developed for use by NZ translational researchers. This effort was funded by Genomics Aotearoa, with starting-point pipelines contributed by the Auckland NETwork! cancer genomics bioinformaticians and visualisation software contributed by ESR.
July 19th 2019 – GIM supported seminar in conjunction with Department of Molecular Medicine and Pathology
Meeting the Challenges of Teaching Pathology and Engaging Communities with Pathology in the 21st Century.
Assoc. Professor Diane Kenwright
Head of the Department of Pathology and Molecular Medicine and Associate Dean of Learning and Teaching at the University of Otago, Wellington.
Pathology is in a process of rapid transition as a consequence of modern genomics and application of machine learning to histological data. Professor Kenwright’s seminar focussed on how to meet the challenges of teaching pathology in the 21st century and the local solutions that have been developed to engage medical students in pathology components of the Otago Medical School MBChB degree. Additionally, she addressed the questions: Who are the communities that academic pathology interacts with and how can mutually beneficial relationships between academics, clinical colleagues and the wider community support learning of pathology. Professor Kenwright’s pathology education youtube channel can be accessed here (LINK).
June 26th 2019 – GIM supported seminar in conjunction with Department of Molecular Medicine and Pathology
The Supernatural History of Sex Changing Fish, Cryptic Female Choice, and Biodiversity Survey of the World’s Most Famous Loch.
Professor Neil Gemmell
Department of Anatomy, University of Otago.
Secrets of biology are often revealed by an astute choice of animal model, exemplified by pioneering studies on the squid giant axon. Professor Gemmell gave an informative and entertaining seminar on a sampling of his eclectic research. Fundamental questions remain unresolved about mechanisms of sexual differentiation and Gemmell presented new findings on sex change in fish (including the familiar New Zealand Spotty), covering work that identified a new form of post-mating sexual selection. He finished up with a rollicking tale of monster hunting, leaving the audience hanging with several teasers about environmental DNA (eDNA) findings from Loch Ness. Professor Gemmell can be viewed discussing the eDNA search for Nessie in this Time magazine piece (LINK).
1st June 2019 – Members of the GIM team – Kimiora Henare, Ben Lawrence and Cris Print published a paper in Lancet Oncology, titled: Mapping a Route to Indigenous Engagement in Cancer Genomic Research (Henare et al., 2019). Their paper is a clarion call to cancer researchers worldwide to fully engage with indigenous peoples in all parts of cancer research – as research participants, in research leadership, and in research governance. Exemplifying this approach, they describe a precision oncology research roadmap which seeks to reflect the values of Māori through ongoing dialogue, Māori leadership, agreed kawa (guiding principles) and tikanga (cultural protocols).
29th March 2019 – Dr Thierry Lints on behalf of the GIM initiative received $20,000 from the SouthSci Curious Minds fund for a project involving DNA sequencing by school students, using the Oxford Nanopore minION sequencing platform. This work is a collaboration with researchers in the University of Auckland School of Biological Sciences and Auckland Council. Students in a group of schools centered around Tāmaki College (Glen Innes Primary, Glenbrae School and Point England School) will undertake DNA sequencing of their local waterway, Omaru Creek, as it runs through Maungakiekie-Tāmaki into Wai o Taiki Bay, gathering genomic data to learn about genomics and the links between the environment and human health.
24th March 2019 – Professor Cristin Print and colleagues held a genomics plenary session followed by a 5-speaker workshop/discussion in the Goodfellow Symposium for general practitioners. If you attended this meeting your registration will allow you to download material at this link. The programme for the 2020 Goodfellow Symposium may be viewed here.
March 8th 2019 – GIM supported seminar in conjunction with the Maurice Wilkins Centre
Breast Cancer and New Aspects of Glutamine Metabolism: Metformin, Exosomes, Hormone Resistance and Repurposed Drugs.
Professor Adrian Harris
Professor of Medical Oncology. University of Oxford, UK. Director of Cancer Research Molecular Oncology Laboratories at the Weatherall Institute of Molecular Medicine.
Professor Harris described recent findings from his laboratory, which has a focus on the role of hypoxia in breast tumour biology. He discussed the links between the metabolic response to hypoxia and hypoxia-induced cell death, as well as the role of interferon signalling and tumour angiogenesis. His talk also provided some vignettes on predictive and prognostic studies in breast cancer his lab has conducted and discussed early exploratory phase trials in new drug development, covering also some of the molecular pathology and biomarkers used to develop new agents with pharmacodynamics monitoring for proof of target engagement. More information on Professor Harris’s research can be found here (LINK).
December 14th 2018 – GIM supported seminar in conjunction with Genomics Aotearoa
Delivering a National Genomics Medicine Service.
Dr Joo-Wook Ahn
Co-Chair of the United Kingdom’s Association for Clinical Genomic Science.
Dr Ahn described the structures put in place to launch a new genomics medical service (GMS) in the NHS in England, building on success of the 100,000 genomes project and transitioning clinical genetics laboratories into a networked service delivering a repertoire of tests that now include next-generation sequencing methods. He discussed the need for a national variant database to act as a central repository of variant interpretation activity and to allow genomics laboratories to benefit from each other’s experience and expertise. Dr Ahn also emphasised the importance of several education and training initiatives to facilitate the rapid uptake and mainstreaming of genomic methods in the wider NHS healthcare system, including a new state-registered profession for clinical bioinformaticians. Dr Ahn’s visit to New Zealand to help inform our national clinical genomics development is discussed here (LINK).
10th December 2018 – The GIM program, along with Genomics Aotearoa, brought Dr Wook Ahn (a national clinical bioinformatics leader from Genome England) to NZ for a month-long visit. The purpose of his visit was for New Zealand clinicians and researchers to: (i) gain insight into how research and clinical genomics could be scaled up in NZ, and (ii) raise awareness among NZ health system stakeholders and decision makers of the potential for translational genomics programs similar to the Genome England program. During his visit Dr Ahn gave seminars and held informal workshops in Auckland (see above), Wellington, Christchurch and Dunedin, and participated in meetings with Ministry of Health and MBIE representatives.
November 13th 2018 – GIM supported seminar in conjunction with the Auckland Cancer Society Research Centre
Comprehensive Genomic Profiling and Precision Medicine for Cancer.
Professor Jeffrey S. Ross
Founding Scientific Advisor and Medical Director, Foundation Medicine, Cambridge MA, and Jones-Rohner Professor of Pathology, Oncology & Urology, Upstate Medical University, Syracuse NY.
Hybrid capture-based comprehensive genomic profiling has been widely applied to novel anti-cancer drug development and has the potential to maximize patient options for both targeted and immunotherapies. Professor Ross discussed how the ability of the hybrid capture system to determine both microsatellite instability status and tumour mutational burden could be combined with PD-L1 immunostaining to personalise the use of immune checkpoint inhibitor therapies. He also discussed the utility of hybrid capture to identify individual genomic alterations associated with both immunotherapy drug efficacy and resistance. A Radio New Zealand interview with Professor Ross about advances in cancer treatment can be listened to here (LINK).
October 24th 2018 – GIM supported seminar in conjunction with the NETwork! neuroendocrine programme
Pancreatic Cancer: from Genome Discovery to Precision Oncology.
Professor Sean Grimmond
Director of the University of Melbourne Centre for Cancer Research.
Pancreatic cancer is currently the third leading cause of cancer mortality in the US and is projected to be the second-most frequent cause of cancer related death within a decade, with median survival of post-diagnosis remaining at <12 months. Professor Grimmond has led Australia’s International Cancer Genome Consortium (ICGC) efforts to redefine the root causes and major drivers of this recalcitrant disease. He provided an up-to-date summary of the mutational landscape of pancreatic cancer and the pioneering of a new Precision Oncology platform to tackle the disease using whole-genome analysis and patient-matched drug screening using organoids. Information about the research of Professor Grimmond and colleagues at the University of Melbourne Centre for Cancer Research can be found here (LINK).
8th & 16th October, 2018 – GIM held two workshops/hands-on discussions targeted specifically to genomic analysis by clinical laboratory scientists at Canterbury Health Laboratories in Christchurch and LabPLUS in Auckland, respectively.
9th September 2018 – Stephen Robertson and Cris Print appeared in a TV3 news item and mini-documentary about the diagnosis of a whānau with the rare Carey-Fineman- Ziter syndrome, some of which can be viewed here.
29th August 2018 – Cris Print hosted a ‘Future Health’ event at Auckland Museum, in which Auckland clinicians spoke about the future of medicine in Auckland.
7th June & 17th August 2018 – GIM members contributed to a plenary session and a genomics workshop in each of the general practice continuing medical education (GPCME) events held in Rotorua and Christchurch, respectively.
15th June 2018: GIM and Genomics Aotearoa (GA) held a workshop on cancer genomics. Seventy-eight clinicians, scientists, geneticists and industry reps attended. Experts in the field from Australia (Stephen Fox, Peter MacCallum Cancer Centre, Melbourne) and New Zealand (Cris Print, UoA) discussed aspects of variant analysis and participants were led through exercises in somatic mutation analysis. Panel discussions included the Director of GA, Peter Dearden (University of Otago) and oncologists and pathologists, Ben Lawrence & Andy Wood (UoA/ADHB) and Gavin Harris (CDHB), who surveyed the landscape of cancer genomics in NZ, with Stephen Fox providing a perspective on developments across the Tasman. For more details see the GIM Cancer Genomics page.
May 3rd 2018 – GIM supported seminar in conjunction with the Department of Molecular Medicine and Pathology
From History to Health: Transitioning Genome-Scale Research in the Pacific.
Professor Murray Cox
Professor in Computational Biology, Institute of Fundamental Sciences, Massey University.
The history of the Pacific – the extraordinary process of settling an island world – has long caught the attention of genetic researchers. Yet the fields of molecular anthropology and biomedical science were firmly separated – islands unto themselves. Professor Cox’s talk surveyed how genome-scale research is now both confirming and rewriting our understanding of the past. He explored how – far from being disparate subjects – history and health are deeply interrelated. He also touched on the disparity of whose genomes are being studied, including what that may mean for underrepresented communities including Māori and Pasifika. More on Professor Cox’s work, at the interface of biology, statistics and computer science, can be found here (LINK).
5th April 2018: Many Science, Technology, Engineering and Math (STEM) education efforts are underway in schools in the Auckland region. To identify how the Genomics Into Medicine program could most productively partner with primary and secondary schools, and with the Auckland Museum, the GIM held a STEM education symposium at the UoA Medical School. Over 60 participants interested in promoting science engagement and literacy in schools and the public at large attended. Presentations at the symposium and subsequent discussions with teachers and members of the museum have guided the direction of GIMs science education partnership activities. Further information about the symposium and Genomics Into Medicine’s plans for developing genomics education and hands-on next-generation DNA sequencing by school students can be found on the GIM Education page.
19th March 2018: To raise public awareness of genomics, the GIM program is partnering with Auckland schools and the Auckland Museum, as well as conducting outreach efforts with other interested groups. In March, members of the Auckland Museum Institute / Royal Society of New Zealand (Auckland) toured the research lab of Prof. Cris Print to hear about next-generation sequencing and cancer biology. They also had the opportunity to visit the thought-provoking Auckland Medical Research Foundation (AMRF) Medical Sciences Learning Centre.
19th – 23rd February 2018: William Schierding (Liggins Institute/UoA) and Peter Tsai (UoA) ran an intensive week-long course on RNAseq bioinformatics. The principal motivation behind this workshop, involving a select group of participants, was to sufficiently develop their expertise to a level where they would feel equipped to provide guidance and help train other researchers in the Faculty of Medical and Health Sciences.
14th December 2017: The GIM initiative held an introductory workshop on bioinformatic analysis of RNAseq data. Elizabeth Permina (University of Otago) and Aleksandra Pawlik (NESI) ran the course with Cris Print and University of Auckland bioinformaticians Nooriyah Poonawala, Peter Tsai and William Schierding. Participants gained experience of Genomics Virtual lab and command line automation of data file handling. Liam Williams and Phillip Shepherd (UoA) discussed technical requirements for RNAseq experiments and the genomics platforms available in Auckland.
27th & 28th July 2017: As part of a University of Auckland Strategic Research Infrastructure program designed to boost research, education and clinical use of genomics, Faculty of Medical and Health Sciences ‘Genomics Into Medicine’ program – Cris Print, Cherie Blenkiron and Patrick Yap –hosted a workshop on clinical interpretation of gene sequencing. The workshop involved significant contributions from Melbourne Genomics and included planning for the next steps in NZ-wide clinical genomic programs. Over 50 clinicians and scientists attended, including all but three of NZ’s clinical geneticists and genetic counsellors.