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Ramaciotti Centre for Genomics

Annual Report 2015

conservation

environment

agriculture

biomedical

DIRECTOR’S REPORT

2 The Ramaciotti Centre Annual Report 2015

Ramaciotti Centre for Genomics Biological Sciences Building (D26) UNSW NSW 2052 Australia

www.ramaciotti.unsw.edu.au

Tel: +61 2 9385 1241

Email: [email protected]

Editor: Dr Helen Speirs Design: Slingshot Design

Disclaimer The information contained in this publication is correct at the time of printing but may be subject to change without notice. Please check the Centre’s website for the latest information. UNSW assumes no responsibility for the accuracy of information provided by third parties.

ACKNOWLEDGEMENTS

The Ramaciotti Centre would like to thank Bioplatforms Australia for their continued support. We would also like to thank Chris Cannon and Nic Beatson from the Science Faculty IT, Uranina Stamos and Lynette McIntyre from Science Faculty Finance and Lucy Wu and Sarah Stuhmcke Science Faculty HR for their invaluable support throughout the year.

DIRECTOR’S REPORT

The Ramaciotti Centre Annual Report 2015 1

The Ramaciotti Centre for Genomics supports research at UNSW and Australia-wide by offering genomic services to academic and industry based research groups.

MissionTo deliver internationally competitive genomic services to the Australian Research Community.

ObjectivesThe Ramaciotti Centre for Genomics aims to:• Provide our users with enabling

technology and services, to facilitate internationally competitive research

• Provide genomics and related services to the highest possible quality

• Provide support for bespoke and niche projects

• Provide services at competitive rates

• Build the genomics community in the state of NSW and beyond


Partners

The Ramaciotti Centre exists as a collaboration between major universities and research institutes in New South Wales.

Supported by

Member of


CONTENTS

Director’s Report 5

Steering Committee 6

Centre Staff 7

Centre Services 8

Operational Report 13

Customer Profile 14

Highlights from 2015 17

Promotional Activities 21

Funding 24

Financials 25


“ … the Centre continues to be a major focus for genomics in NSW and Australia.”

Professor Marc Wilkins, Director


DIRECTOR’S REPORT

The Centre has had another successful year. One highlight was the expansion our next-generation sequencing capacity, with the acquisition and installation of the PacBio RSII instrument. This platform generates extremely long reads, and so complements the suite of Illumina short-read technology in the Centre. We are the only fee-for-service Centre in Australia with this important new instrument, and we saw an extremely quick take up by the community for projects ranging from microbial to mammalian genomics. We were particularly excited to launch the Koala PacBio genome project, in association with the Australian Museum, the University of Sydney and the University of the Sunshine Coast, to be undertaken entirely in the Centre. This project will be completed in early 2016 and is likely to generate one of the highest quality marsupial genomes to date.

The Centre continues to be a major focus for genomics in NSW and Australia, serving over 500 researchers in 2015. For this community, I am delighted to report that we analysed 11,169 samples by next-generation sequencing. This is an increase from the 9,144 analysed in 2014, and – being more than 10,000 – represents an important milestone for the Centre. In part, this has been possible through examining our processes and implementing a number of measures. This included robotics, via the acquisition and commissioning of the NGS Express and Zephyr platforms. We also commenced the rollout of a laboratory information management system (LIMS). These initiatives are important in that they improve quality and reproducibility whilst assisting in throughput. They also help keep the cost per sample at an internationally competitive level. In addition to next-generation sequencing, the Centre continues to support a large user base with Sanger sequencing, microarrays, single cell genomics, genotyping and qPCR.

The financial position of the Centre is very sound. The Centre has continued to receive Federal Government NCRIS funding, along with co-funding from the NSW State Government and UNSW. This reflects the Centre’s status as national research infrastructure.

We have continued our success with ARC LIEF grants, the 2015 grant which funded the acquisition of the PacBio RSII platform. The ongoing success of the Ramaciotti Centre Consortium is spectacular, in that it has now had 15 out of 16 LIEF grants funded. However this success is only possible due to the efforts of representatives, and generous financial support, from UNSW, the University of Sydney, Macquarie University, UTS and the Newcastle University along with those from the Garvan Institute, the Kolling Institute and the Victor Chang Cardiac Research Institute.

The sustained growth in the Centre’s activity has only been possible because of its wonderful, skilful staff. I warmly congratulate them all for their ongoing dedication, the pride they take in their work, and their professionalism with which they serve the research community. In 2015, we welcomed Dr. Alper Yassar, Dr. Zena Kassir, and Dr. Darshi Ramesh to the next-generation sequencing team. Yet we were sad to see the departure of Dr. Bronwyn Robertson, one of the founding staff of the Centre, and of Dr. Hannah Ginn. We thank them for all of their hard work and wish them the very best in their future endeavours.

Last but by no means least, I’d like to thank Dr. Helen Speirs and the Centre’s Steering Committee. Dr. Speirs, the Centre Manager, plays a central role in all aspects of our operations. Its successes are a reflection of her ongoing enthusiasm, commercial nous and managerial talent. Institutional representation is also essential to the functioning of the Centre and its consortium and I thank the Steering Committee, and its chair Prof. Ian Dawes, for their time and support in 2015. We look forward to further supporting the genomics research community in 2016.

Professor Marc Wilkins Director


STEERING COMMITTEE

Independent Chair Professor Ian Dawes

Director Professor Marc Wilkins University of New South Wales

Deputy Director A/Professor Kevin Morris University of New South Wales

Professor Merlin Crossley University of New South Wales

A/Professor Aaron Darling University of Technology, Sydney

Professor Edward Holmes University of Sydney

Professor John Mattick Garvan Institute for Medical Research

A/Professor Debbie Marsh Kolling Institute of Medical Research

Professor Ian Paulsen Macquarie University

Professor Rodney Scott University of Newcastle

Dr Catherine Suter Victor Chang Cardiac Research Institute

Alternates

Professor Steven Djordjevic for Professor Ian Charles

Professor Nicki Packer for Professor Ian Paulsen

Professor Claire Wade for Professor Edward Holmes


CENTRE STAFFSTEERING COMMITTEE

The Ramaciotti Centre Team

Our professional team of scientists have many years of experience delivering personalised service in genomics. The team has been growing steadily and we welcomed two new staff members to the team towards the end of the year.

Back row (L-R): Jason Koval, Bronwyn Robertson, Kylie Cairns, Marc Wilkins, Carolina Correa Ospina, Erika Becker, Caitriona Murray, Helena MangsFront row (L-R): ): Helen Speirs, Tonia Russell, Kristin North

Centre Manager Dr Helen Speirs

Next Generation Sequencing Specialists Dr Helena Mangs Jason Koval Tonia Russell Dr Caitriona Murray Dr Kylie Cairns Dr Alper Yassar Dr Zena Kassir Dr Darshi Ramesh

Microarray Specialists Dr Bronwyn Robertson Dr Erika Becker

Sanger Sequencing Specialists Dr Jackie Chan Dr Carolina Correa Ospina

qPCR & Single Cell Genomics Specialist Dr Kristin North

IT Support Robin Heron


CENTRE SERVICES

The Ramaciotti Centre is committed to building world-class genomic research capability and capacity. As a National Collaborative Research Infrastructure (NCRIS) funded facility we provide access to state-of-the-art technologies and deliver data of the highest quality to the research community. Our technology suite includes next-generation sequencing, Sanger sequencing, single-cell genomic analysis, microarrays, and high-throughput qPCR. Our ongoing commitment to delivering high quality data is demonstrated in our Illumina Certified Service Provider (CSPro), PacBio Certified Service Provider and Authorised Affymetrix Service Provider status.

next generation sequencing microarray genotpying and qPCR

single cell analysis Sanger sequencingquality control service bioinformatics


Next Generation Sequencing

The Ramaciotti Centre delivers next-generation sequencing services using a range of technologies, allowing us to support a broad range of sequencing projects.

Sequencing Services • Whole genome

• Exome

• Targeted/panel sequencing

• RNA and small RNA seq

• ChIP and methyl seq

• Single cell sequencing

• Metagneomics

• Microbial profiling – amplicon

Sequencing Technology • Pacific Biosciences RSII

• Illumina HiSeq 2500

• Illumina NextSeq 500

• Illumina MiSeq

• Illumina XTMTen (Kinghorn Centre for Clinical Genomics)

Microarray

We provide a comprehensive range of services on three different microarray technology platforms. We have access to an extensive portfolio of arrays for RNA and DNA analysis for a diverse range of species.

Services • Gene expression

• Transcriptome

• miRNA analysis

• SNP, CGH and CNV

• FFPE copy number

• Custom arrays

Microarray Technology • Affymetrix

• Agilent

• Illumina


CENTRE SERVICES

SNP Genotpying and qPCR Services

The Ramaciotti Centre is equipped with a Fluidigm BioMark HD system for high-throughput real time PCR. The system utilises multiple chemistries and offers unparalleled throughput for real-time PCR and SNP genotyping.

Services• Gene expression

• SNP genotyping

• Sample identity tracking (SNPTrace™)

Single Cell Services

Using the Fluidigm C1TM Single Cell Auto Prep System the Centre can provide a range of single cell services.

Services • Gene expression profiling (qPCR)

• mRNA sequencing

• Whole genome sequencing

• Exonic sequencing

• Targeted sequencing

Sanger Sequencing

We provide Sanger sequencing and genotyping services using an Applied Biosystems 3730 DNA Analyzer.

Services • DNA sequencing

• Genotyping


Quality Control Services

The Centre offers a nucleic quality control (QC) service using the Agilent 2100 Bioanalyzer and Agilent TapeStation.

Services • RNA integrity analysis (RIN)

• DNA integrity analysis (DIN)

Bioinformatics

The Centre has continued its longstanding collaboration with the NSW Systems Biology Initiative (the SBI) for the analysis of data. The SBI has expertise in:

• genome assembly and annotation

• comparative genomics

• de novo transcriptomics and differential expression analysis by RNA-seq

• pathway, network and systems-level analysis of transcriptomic data

• data analysis from microarray platforms

• network visualization

• integrative analysis of transcriptomic and proteomic data.

The SBI works with users of the Ramaciotti Centre collaboratively and also welcomes researchers to work inside the SBI on a ‘research hotel’ basis.

DIRECTOR’S REPORT


30,618 samples sequenced analysed by Sanger sequencing

11,169 samples sequenced by next generation sequencing

1,666 microarray analyses

1,242 samples analysed using Fluidigm technology

467samples analysed on the Bioanlayzer

The Centre has an excellent track record in service provision, routinely delivering high quality services in both genomics and transcriptomics.

Summary of services provided to the research community in 2015:


The Centre delivers high quality, state-of-the-art genomic and transcriptomic services to the research community. During 2015 the Centre:

• Became the only Australian genomics service provider to offer both long and short read sequencing services.

• Increased the number of analyses performed by next-generation sequencing by 22% on the previous year.

• Implemented automation platforms to streamline sample processing.

• Introduced a Laboratory Information Management System to manage workflows and reagents.

New Long Read Sequencing Service

In April the Centre launched a new long read sequencing service using the PacBio RSII single molecule real time (SMRT) sequencer. The PacBio RSII sequencer is capable of sequencing single molecules of DNA and RNA with very long reads of up to 70,000 bases. The service has already had excellent uptake within the microbial community as long reads and ability to read through repetitive regions makes the assembly of genomes more straightforward as compared to using only short read data. The service has also been used for the sequencing of small and large eukaryotic genomes. The range of services offered on the platform will be expanded to include; amplicon sequencing that will further develop our microbiome and metagenomic services and Iso-Seq

transcriptome sequencing, which can provide new insights into mRNA splice variants.

Illumina Next Generation Sequencing Service

The next generation sequencing service continues to grow and diversify into new areas. The number of samples sequenced using this technology continues to increase year on year, refer to the graph below/opposite particularly in the area of microbial diversity profiling, which is a focus of many investigators within our host institution UNSW. The ability to increase our output and maintain a fast turnaround time is the result of improvements that have implemented across all areas of the Centre, such as automation for samples processing and a laboratory information management system (LIMS).

Implementation of a Laboratory Management System

In an ongoing effort to streamline processes and increase efficiency the Centre has implemented a LIMS across the majority of our services. The system that we selected to implement, Clarity LIMS, is built specifically for genomics laboratories and provides end-to-end workflow tracking, collects data for quality control and accreditation purposes and provides a high level view for reporting and strategic planning. Clarity LIMS also provides an online portal for customers to submit their

samples providing them with a unique LIMS identity number for each sample and a unique project identifier.

Automation to Support Sequencing

In January 2015 the Centre acquired two robotic platforms from Perkin Elmer, the NGS Express and the Zephyr. These platforms are complementary, supporting different parts of the sequencing workflow. Implementation of automation has ensured that we continue to met demand and keep turnaround times to a minimum.

OPERATIONAL REPORT

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Number of samples dequenced per year using Next Generation Sequencing Technology

Number of Next Generation Sequencing runs performed per year

July 2015 - the Centre sequenced a record 2,663 samples in a single month.


CUSTOMER PROFILE

The Centre has a customer base of over 500 researchers from academia and industry. We serve all the leading universities and research institutes in Australia and support a wide range of research covering many disciplines.

Customers by State or Country

NSW

QLD

VIC

TAS

Overseas

ACT

SA

NZ

WA

Customers by Type

University

Medical Research Institutes

Government

Publically Funded Research Organisations

Industry/Corporate

Other

Customers by Discipline

Biomedical

Environmental/ Conservation

Agriculture and Food

Basic Biology

Biotechnology and Biogengineering

Diagnostics

other


A Academia Sinica – Taiwan Australian Biologics Testing Services Australian Institute of Marine Sciences Australian Maritime College Australian Museum Australian National University Australian Wine Research Institute ANZAC Research Institute

B Baiaida Poultry Biosceptre Australia BMR Genomics – Italy

C Centenary Institute Children’s Cancer Institute Australia Children’s Hospital at Westmead Cincinnati Children’s Hospital CSIRO Agriculture Flagship CSIRO Animal, Food and Health Sciences CSIRO Biosecurity CSIRO Black Mountain CSIRO Energy CSIRO Food & Nutrition Flagship CSIRO Health & Nutrition CSIRO Land & Water CSIRO Material Science & Engineering CSIRO National Research Collections of Australia CSIRO Oceans & Atmosphere Flagship CSIRO Plant Industry Curtin University Cytox – United Kingdom

D DairyNZ Deakin University Department of Economic Development, Jobs, Transport and Resources

G Garvan Institute of Medical Research Genea Griffith University

I Institute of Dental Research

J James Cook University

H Hunter New England Health

K Kirby Institute Kolling Research Institute

L Langebio - Mexico La Trobe University Lincoln University – New Zealand

M Macquarie University Melanoma Institute Australia Microbiogen Monash University Murdoch Children’s Research Institute

N Nanosonics National Centre for Genetic Engineering and Biotechnology – Thailand National Measurement Institute Neuroscience Research Australia

O Olivia Newton John Cancer Centre

P Peter MacCallum Cancer Centre Plant and Food Research – New Zealand Prince of Wales Hospital

Q Queensland Berghofer Institute of Medical Research

R Royal Botanic Gardens Royal North Shore Hospital Royal Prince Alfred Hospital

S Save Sight Institute Singapore Centre for Environmental Life Sciences Engineering Stephen Sanig Research Institute Southern Cross University Strain Biotech - Mexico St George Clinical School St George Hospital St Vincent’s Centre for Applied Medical Research St Vincent’s Institute Swinburn University Sydney Children’s Hospital Sylvan Pharmaceuticals

T Tasmanian Institute of Agriculture Technical University of Denmark Telethon Kids Institute

U University of Adelaide University of Auckland – New Zealand University of Canberra University of Newcastle University of New South Wales University of Queensland University of Melbourne University of the Sunshine Coast University of Sydney University of Tasmania University of Technology, Sydney University of Western Sydney University of Western Australia University of Wollongong

V Victor Chang Cardiac Research Institute

W Westmead Millennium Institute


HIGHLIGHTS FROM 2015

ARC LIEF Grant Success

The Ramaciotti Centre Consortium successfully applied to the ARC Linkage Infrastructure, Equipment and Facilities (LIEF) scheme for a complete systems biology capability. This is the consortia’s sixteenth successful LIEF grant. The grant was lead by the University of Sydney and intends to provide a complete systems biology workflow, including improved data analysis for next-generation sequencing, tissue preparation and imaging, and mass spectrometry for proteomics and metabolomics. This will enable a systems approach to biological problems and support researchers and projects that focus on microbial and mammalian metabolism, carbohydrate chemistry and synthetic biology.

New Building

In August, the UNSW Council provided final project approval for a new biosciences building that will provide the Centre with a new home. The Centre will be afforded custom-built laboratories and a much needed increase in floor space. We will be co-located proteomics, live cell analysis and bioinformatics, providing researchers with easy access to mulit-omic expertise. Construction commenced in September with completion expected in mid-2017.

National Framework Dataset Programs

The Centre continues to work on a number of Bioplatforms Australia-funded framework dataset projects. These projects seek to build biomolecular datasets that have impact on problems of importance to Australia. They include:

• Biome of Australian Soil Environments – metagenomic and amplicon sequencing to map soil biodiversity

• DNA barcoding – sequencing genetic markers to enable rapid species identification and aid conservation

• Great Barrier Reef – sequencing coral and symbionts to protect and preserve the coral reef

• Wine – sequencing chardonnay varieties and yeast to enhance wine characteristics

Refining the Art of Wild-ferment Winemaking

Dr Anthony Borneman, a principal research scientist at the Australian Wine Institute in Adelaide is using whole and targeted genomic techniques to study the yeasts and bacteria involved in winemaking. The Centre has a collaborative sequencing project with Dr Borneman that aims to use metagenomics to identify every microbe present in the early stages of the wild ferment and identify whether different winemaking areas have their own unique strain of yeast or bacteria producing different metabolites that in turn affect the flavour, bouquet and alcohol content of the wine. Gaining an understanding of how wild fermentations work is hoped to provide winemakers with information that will make wild ferments more manageable and customisable.

Artists impression of the new building, due for completion in mid-2017.


Installation of Pacific Biosciences RSII Long Read Sequencer

In 2014 the Ramaciotti Centre Consortium was successful in its bid to the ARC Linkage Infrastructure, Equipment and Facilities (LIEF) scheme for a PacBio RSII single molecule sequencer. The PacBio RSII sequencer was delivered via crane and installed in April 2015. The first DNA samples to be sequenced were from the short hairy nosed wombat and a strain of E. coli from collaborators at the University of Sydney and the University of Technology Sydney, respectively. This acquisition ensures that the Ramaciotti Centre remains at the forefront of genomic research in Australia. The service was formally launched on the 10th of June with a presentation from Professor Vanessa Hayes from the Kinghorn Centre for Clinical Genomics.

Farewell to Dr Brownyn Robertson and Dr Hannah Ginn

This year we said farewell to two long serving Centre staff, Dr Bronwyn Robertson (15 years) and Dr Hannah Ginn (7 years). We would like to thank them both for their tremendous contribution the Centre. The Centre has been a success, thanks mainly to the staff who have made it a vibrant and effective operation. Bronwyn, in particular, played a significant role in the establishment of the Centre and was instrumental in setting up and providing a microarray service to the research community. Brownyn leaves us to take on the position as manager of the Sydney-West Translational Cancer Research Centre, and Hannah to pursue her career as a very busy mum of three with a successful online business. We wish them both every success in the future.

Professional Women in Leadership

Congratulations go to Dr Helena Mangs was accepted into the UNSW Professional Women in Leadership (PWIL) Program. The program aims to identify, grow and retain a pool of high-potential, talented women to take up leadership roles within UNSW. Helena was one of only 20 professional staff selected from over 300 eligible candidates. Helena follows on from the Centre manager, Dr Helen Speirs, who graduated from the inaugural PWIL program in 2014.

HIGHLIGHTS FROM 2015

Top and centre:Delivery and installation of the PacBio RSII Sequencer

DIRECTOR’S REPORT


workshops

seminars

special interest groups

centre tours

trade displays

As part of our commitment to the Australian genomics community we organise educational workshops, special interest group meetings, seminars, and support scientific meetings and conferences. Activities in 2015 included:

Activities in 2015 included:


PROMOTIONAL ACTIVITIES

Workshops

Partek Data Analysis Workshop – 26th March The Centre hosted a one-day data analysis workshop delivered by Partek. This free workshop provided instruction on analysing transcriptome data from microarrays and NGS sequencing. The workshop was held in a computing laboratory at UNSW and provided 24 researchers with hands on training in analysing transcriptomic data. The Ramaciotti Centre has a Partek license, allowing workshop attendees to subsequently analyse their experimental results independently.

qPCR Workshop – 30th JuneThe Centre organised a free one-day qPCR workshop covering sample quality control, experimental design, primer design and data analysis. The workshop was well attended, by 67 researchers from academia and industry. The workshop was sponsored by BioRad, Fluidigm, Life Technologies and Qiagen..

Next Generation Sequencing Targeted Sequencing Workshop – 21st MayThe Centre hosted and presented at a half-day targeted next generation sequencing workshop. The workshop, which was sponsored by Agilent showcased capture sequencing methods and their utility in the clinic.

Transcriptome Analysis Console Workshop – 23rd SeptemberThe Centre hosted a half-day data analysis workshop provided by

Millennium Science. This free, hands on workshop trained 22 researchers in the analysis of microarray data using the Affymetrix software package Transcriptome Analysis Console.

Next-Generation Sequencing Special Interest Group Meetings

The Ramaciotti Centre, in association with the Australian Genome Research Facility, organises the ‘NSW Next-Generation Sequencing Special Interest Group meeting’. This special interest group was established to encourage discussion and interactions around next generation sequencing. Seminars are held at different locations across Sydney.

29th April | University of SydneySpeakers: Dr Emily Remnant (USyd) “Viral prevalence and diversity in worldwide populations of honey bees.” Professor Claire Wade (USyd) “Mutation detection for low frequency canine disorder phenotypes using Next Generation Sequencing.”

25th June | UNSW: Speakers: Belinda Wright (USyd) “Whole genome sequencing of the Tasmanian devil - using genomics in conservation” Dr Marlien van der Merwe (National Herbarium of NSW) - “Using next generation sequencing for plant ecological studies: from single species to rainforest assemblages”

22nd October | UTS, Sydney:Speakers: A/Prof Shauna Murray (UTS) “Using transcriptomics to investigate gene function and evolution in marine microbial eukaryotes.” Dr Richard Edwards (UNSW) “The SMRT way to sequence a genome: adventures in PacBio sequencing.”

16th December | Garvan Institute for Medical Research:Speakers: A/Prof Kevin Morris (UNSW) “Long non-coding RNA BGAS regulates the cystic fibrosis transmembrane conductance regulator” Dr Daniel Thomson (Garvan Institute for Medical Research) “Pseudogenes are dynamically expressed in human brain providing a template for both plasticity and genomic instability.”

Technology Seminars

The Ramaciotti Centre regularly hosts technology seminars by vendors that showcase the latest developments in the field of genomics:

16th April New from the Front – Update on PacBio technology Dr Stephen Turner (Co-Founder & Chief Technology Officer, Pacific Biosciences)

18th August Generating the Most Comprehensive View of Genomic Complexity in CancerDr Meredith Ashby (Senior Scientist, Pacific Biosciences)


PROMOTIONAL ACTIVITIES

25th August: Uncovering Biomarkers Deep within the Complex TranscriptomeDr Anthony Schweitzer (Principal Scientist and Head of Bioinformatics, Affymetrix)

15th October: Preparing Clinical Research Samples for Future Use: Innovative Methods for Working with Limiting and Compromised Samples and Bio-banking Best Practices. A/Prof Andrew Brooks (Chief Operating Officer, Rutgers University Cell and DNA Repository)

30th October: Ingenuity Pathway Analysis and Variant Analysis Dr Rupert Yip (Director – Variant Analysis Pipeline, Qiagen Ingenuity)

Education and Training

Microarray and sequencing data generated by the Centre features in the work of many Honours and PhD students. Students from UNSW and other educational organisations benefit from its resources. In a typical year over 100 PhD/Honours/Diploma/MPhil students will benefit from the Centre’s resources and expertise.

The Ramaciotti Centre provides tours of the facility to groups of university and school students. This year we provided tours of the Centre to over 200 second and third year students studying cell biology, pathology, biotechnology and genomics, providing students with an overview of high throughput genomics and its application in their area of study.

The PacBio single molecule sequencer was a great focal point for discussion on the future of genomics.

As part of our commitment to educating the broader community on the applications of genomics we provided tours of the facility to 10 pre-school students from a local childcare Centre, 25 work experience students from high schools in the Sydney area and 20 students attending the UNSW Gifted Education Research and Resource Centre (GERRIC).

Marketing

The Centre continues to promote its services in various ways. Tonia Russell presented to the Kinghorn Cancer Centre and the Garvan Institute for Medical Research on the applications of PacBio long read sequencing (19th June) and Helen Speirs presented on the advances in genomic technology at the Genomics in NSW symposia hosted by the NSW Government Office for Health and Medical Research (24th August). In addition to its website, the Centre increased its online presence by joining Twitter and Facebook. Follow us on Twitter @RAMACgenomics

Conferences

The Ramaciotti Centre exhibited at key conferences over the last 12 months:

• Lorne Cancer, Lorne (12–14th February 2015)

• Lorne Genome, Lorne (15–17th February 2015)

• ASMR – NSW meeting, Sydney (1st June 2015)

• Australian Genomics Technologies Association Hunter Valley (11–14th October 2015)

• ASMR – National meeting, Adelaide (15–8th November 2015)

Publications

The Ramaciotti Centre does not conduct its own research; nonetheless, in 2015 the Centre was acknowledged as the service provider in 85 peer reviewed publications, some examples are listed below. These publications demonstrate the diversity of projects supported by the Ramaciotti Centre.

Selected Publications by ServiceSequencing ServiceMethylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Stirzaker C, Zotenko E, Song JZ, Qu W, Nair SS, Locke WJ, Stone A, Armstong NJ, Robinson MD, Dobrovic A., Avery-Kiejda KA, Peter KM, French JD, Stein S, Korbie DJ, Trau M, Forbes JF, Scott RJ, Brown MA, Francis GD, Clark SJ. Nature Communications (2015)

Chemotaxis by natural populations of coral reef bacteria. Tout J, Jeffries TC, Petrou K, Tyson GW, Webster NS, Garren M, Stocker R, Ralph PJ, Seymour JR. The ISME Journal (2015)

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics. Ruvindy R, White RA, Neilan BA, Burns BP. The ISME Journal (2015)


Genomic analysis of HPV-positive versus HPV-negative oesophageal adenocarcinoma identifies a differential mutational landscape. Rajendra S, Wang B, Merrett N, Sharma P. Journal of Medical Genetics (2015)

Genomic evidence for role of inversion 3RP of Drosophila melanogaster in facilitating climate change adaptation. Rane RV, Rako L, Kapun M, Lee SF, Hoffmann AA. Molecular Ecology (2015)

Fluidigm qPCR ServiceEditing the genome to introduce a beneficial naturally occurring mutation associated with increased fetal globin. Wienert B, Funnell A, Norton LJ, Pearson RCM, Wilkinson-White LE, Lester K, Vadolas J, Porteus MH, Matthews JM, Quinlan KGR, Crossley M. Nature Communications (2015)

Microarray ServiceMicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene. Phua YW, Nguyen A, Roden DL, Elsworth B, Deng N, Nikolic I, Yang Y, Mcfarland A, Russell R, Kaplan W, Cowley MJ, Nair R, Zotenko E, O’Toole S, Tan S, James D, Clark SJ, Kouros-Mehr H, Swarbrick A. Breast Cancer Research (2015)

Sanger Sequencing ServiceHuman organic anion transporting polypeptide 1A2 (OATP1A2) mediates cellular uptake of all-trans-retinol in human retinal pigmented epithelial cells. Chan T, Zhu L, Madigan MC, Wang K, Shen W, Gillies MC, Zhou F. British Journal of Pharmacology (2015)


FUNDING

The Australian Commonwealth Government supports the Centre’s operations through National Infrastructure Scheme (NCRIS) funding. The Ramaciotti Centre gratefully acknowledges the support it receives from this funding body and the co-contributions made by the University of New South Wales.

Funding Awarded in 2015

Australian Research Council Linkage Infrastructure, Equipment and Facilities LIEF grant LE160100204 A systems biology capability for the Ramaciotti Centre for Genomics – $550,000 S Cordwell, D James, S Simpson, R Payne, M Wilkins, R Cavicchioli, N Packer, G Guillemin;,A Goodchild, R Scott, R Thorne, H Hondermarck, S Djordjevic, D McDougald, G Myers.

Co-funding from host institutions is gratefully acknowledged: $823,500 The University of Sydney

$100,000 University of Technology, Sydney

$72,000 The University of Newcastle

$50,000 Macquarie University

$45,337 The University of New South Wales

UNSW UNSW Major Research Equipment and Infrastructure Initiative Scheme (MREII)

Expanding Next Generation Sequencing Capacity – $131,415. M Wilkins, R Cavicchioli, BA Neilan, R Lan, V Murray, H Mitchell, B Ferrari, T Thomas, K Morris, SE Egan, M Manefield, P Waters, R Edwards, J Tree, B Burns.

Continuing in 2015

Bioplatforms Australia National Collaborative Research Infrastructure Scheme II 2013–2015: $813,000

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