New Zealand Next Generation Sequencing Conference Palmerston North Convention Centre Palmerston North New Zealand 18-19 August 2015
Sponsors and Exhibitors .................................................................................................... 3 Welcome ........................................................................................................................... 8 General information ........................................................................................................ 10 Programme Tuesday 18th August .............................................................................................. 14 Wednesday 19th August ........................................................................................ 19 Speaker Biographies and Abstracts ................................................................................ 25 Posters ............................................................................................................................. 54 Discussion Session .......................................................................................................... 55 List of delegates ............................................................................................................... 56
Page 2
SILVER SPONSOR
New Zealand Genomics Limited: Customised genomics solutions for New Zealand scientists NZGL provides an end-to-end genomics service for New Zealand’s genomics researchers – from experimental design and data sequencing, through to bioinformatics support and data storage. The NZGL team provides a personalised service, working alongside researchers to offer customised solutions and ongoing support as required. Specific services include: • Bioinformatics support • Data storage and software tools (including Galaxy), and scalable access of up to a 900GB RAM working environment on the cluster using your own VM workspace • Data generation on HiSeq, MiSeq, Affymetrix Array, Ion Torrent platforms, and nanoString nCounter Analysis System. NZGL is a collaboration between The University of Auckland, Massey University and the University of Otago, supported by the New Zealand Government through the Ministry of Business, Innovation and Employment.
Page 3
SILVER SPONSOR
Thermo Fisher Scientific is the world leader in serving science. Our mission is to enable our customers to make the world TM healthier, cleaner and safer. From Applied Biosystems gold standard Sanger sequencing to simple and scalable Ion Torrent™ next-generation sequencing, we have a platform to meet your needs. Achieve fast, accurate, and affordable results with optimized applications, high-quality consumables, and simplified analysis solutions.
CONFERENCE DINNER SPONSOR Bio-Strategy is a locally-owned, ISO 9001:2008 accredited distributor, supplying leading-edge technology solutions throughout Australia and New Zealand, from quality renowned suppliers. Our experienced staff are highly qualified and trained. With a culture of innovation and service, under-pinned by our core values of EXCELLENCE – INTEGRITY – TEAM, we focus on providing the best solutions for our customers, backed by technical support from our Applications Scientists and Service Engineers.
! ! Page 4
CONFERENCE BAG SPONSOR VWR is a leading, independent provider of laboratory products, services and solutions to the global life science, general research and applied markets with over 50 local associates based across New Zealand. We represent leading scientific brands and our specialists have strong networks in their field of expertise; life sciences, clinical, instrumentation, chromatography, chemicals and consumables. We are proud to represent Agilent Genomics in New Zealand. This portfolio encompasses leading technology for NGS enrichment and QC of DNA, RNA and proteins. The industry standard has been Agilent's Bioanalyzer, and is now extended by the TapeStation for faster and fully automated quality control.
CONFERENCE NAME BADGE SPONSOR Roche NimbleGen, part of Roche Sequencing, an innovator in genomics, is focused on developing target enrichment solutions for next-generation sequencing. Our technologies allow researchers to selectively target DNA sequences of interest in their genome of interest, human or non-human, either through focused exomes or custom designed gene panels, for variant discovery and validation. With our ever growing suite of tools for targeted DNA sequencing, we are enabling the life science community to achieve their research goals more efficiently in order to understand the association genomics and epigenomics have with diseases and biological processes. Page 5
DISCUSSION SESSION SPONSOR
Illumina is a leading developer, manufacturer, and marketer of life science tools and integrated systems for large-scale analysis of genetic variation and function. We have developed a comprehensive line of products that address the scale of experimentation and breadth of functional analysis to advance disease research, drug development, and the development of molecular tests. Our broad portfolio of leading-edge sequencing and array-based solutions address a range of genomic complexity and throughput, enabling researchers to select the best solution for their scientific challenge. Our customers include a broad range of academic, government, pharmaceutical, biotechnology, and other leading institutions around the globe.
EXHIBITOR medi’Ray Ltd suppliers of high quality products and service for many years in the New Zealand market acquired Norrie Biotech Ltd in April 2015. We are suppliers of innovative, leading edge biotechnology products to the Diagnostic, Molecular Biology and Cell Biology market. We represent Clontech and Lucigen, both supplying a variety of Sequencing options: RNA sequencing (RNA-seq) products for expression analysis of the entire transcriptome, with high sensitivity from all types of low-input RNA, including compromised RNA, ChiP Seq Library Prep Kits and kits which offer the longest mate pair reads available for NGS libraries giving you the power to close and finish genomes. Page 6
EXHIBITOR
Ngaio Diagnostics, established in 1991, is a privately owned supply company based in Nelson, New Zealand. We represent some of the world leading developers and manufacturers of high quality analytical technologies, and specialise in the distribution of these technologies and provision of associated technical support to a variety of laboratories throughout New Zealand. Zymo Research, Intron Biotechnology and Bio Scientific are some of the many companies that we represent, which manufacture high quality molecular biology research products for nucleic acid purification, PCR, RT-PCR, qPCR, NGS, etc.
Page 7
Page 8
!!! We have a vibrant and rich program for this year’s NGS Conference. Our three, top-flight invited keynote speakers are all at the forefront of their respective research fields, using NGS technologies in innovative ways. Dr Highlander will tell us about her research on the microbiome and how she is unlocking its secrets. Dr Forshew is exploring NGS for clinical use, detecting tumour DNA in ‘liquid biopsies’. Dr O’Grady studies human pathogens and is exploring NGS for diagnostics. Once again our loyal sponsors will be joining us. They have put together a great exhibition and their technical teams can help get your next NGS project started. Particular thanks to Thermo Fisher Scientific for sponsoring Dr O’Sullivan’s presentation and to Roche for making Dr Richmond’s attendance possible. Finally I’d like to thank all of you who put forward abstracts and discussion topics for consideration in this year’s program. Without your efforts we would not have such an interesting and informative conference. I’m looking forward to catching up with you all over the next two days. th
Welcome to the 7 annual New Zealand NGS Conference. Jo Stanton High Throughput DNA Sequencing Unit Department of Anatomy, University of Otago
The Venue 'A' on the map on the next page Both the 2015 Conference and the Workshops will be held on the first floor of the Palmerston North Convention Centre, 326 Main Street, Palmerston North. The Palmerston North Convention Centre was New Zealand's first purpose built convention facility, opening in 1980. It was extensively redeveloped in 2001 and has an enviable reputation for professionalism and service excellence that sets it apart from the competition. The Convention Centre is conveniently located in the heart of the city and offers the very best proximity to a large range of superb hotels and motels and is surrounded by vibrant bars, cafes, restaurants, cultural institutions and retail shops. Conference Dinner 'B' on the map on the next page. The Conference Dinner will be held at Wabi Sabi, 74 Broadway Ave. The restaurant is an easy walk from the conference venue, and according to Google should take seven minutes to walk there. Exit the Convention Centre by the front entrance, turn right. walk through The Square. When you exit The Square turn left. The next road in your right is Broadway. Wabi Sabi is on your right, just after the Downtown Shopping Centre. The restaurant is BYO and we will be supplying wine for the meal. Orange juice will also be on the tables. If you would like any additional drinks these will be for your account.
Parking 'C' on the map on the next page. There are a limited number of free car parks associated with the Convention Centre and these are allocated on a firstcome first-served basis to registrants. These car parks are accessed from Church Street. Driving from town go past the brick church on your left hand side, past Kiwibank on your left hand side and at the roundabout in front of you (corner Main and Linton Streets) take the third turnoff off the roundabout into the car park. The front area of the car park is leased, the next portion is ‘Pay and Display’ but at the rear there is a section associated with the Convention Centre. Park in the Convention Centre allocated area. Should the free Convention Centre parking be full then please park in the 'Pay and Display' area that will cost $5 for the day. Free internet while in Palmerston North Inspire Free Wi-Fi is Inspire Net’s way of extending our award-winning home and business internet services to the general public, while you’re in town and on the go with your mobile devices. The network and this website are specially designed to work on almost all Wi-Fi-enabled tablets, laptops, and mobile phones. It allows both web browsing and access to your email. The service offers 1000 megabytes a month of traffic free for each one of your devices, with no advertising. Go to http://inspirefreewifi.co.nz/register.php to join.
Page 12
A = Palmerston North Convention Centre, 326 Main Street B = Wabi Sabi venue for the Conference Dinner, 74 Broadway Ave C = Entrance to the Convention Centre car park, cnr Linton and Church Streets. Page 13
Tuesday18th August 9.00am
Registration and Coffee
10.00am
Welcome to the 2015 New Zealand NGS Conference Jo Stanton
SESSION 1 CHAIR:
JO STANTON
10.05am
KEYNOTE SPEAKER Sequencing and dPCR analysis of circulating tumour DNA. The challenges and potential applications of liquid biopsy analysis Tim Forshew University College London, UK
11.05am
Morning Tea
SESSION 2 MINION CHAIR:
JENNY DRAPER
11.25am
Nanopore Sequencing - A Rhapsody of Errors David Eccles Gringene Bioinformatics and Malaghan Institute of Medical Research, Wellington, New Zealand
11.45am
Long-read nanopore sequencing for the detection of genetic polymorphisms in the CYP2D6 gene Simone Cree University of Otago, Christchurch
SESSION 3 CHAIR:
JO STANTON
12.05pm
Speaker sponsored by Thermo Fisher Scientific Connecting the microbiome and phenotypes in children born very preterm Justin O'Sullivan Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland
12.25pm
Lunch Page 16
SESSION 4 CHAIR:
DAVID HAYMAN
1.15pm
KEYNOTE SPEAKER Nanopore sequencing for Microbial diagnostics - the perfect fit? Justin O'Grady University of East Anglia, Norwick, UK
SESSION 5 ALL THINGS GENOME CHAIR:
JAN SCHMID
2.15pm
Update: Dairy Genomics PGP Project Mike Keehan Livestock Improvement Company
2.35pm
Roles of protein-coding DNA repeats in Saccharomyces cerevisiae Asad Razzaq Massey University, Palmerston North
Page 17
2.55pm
Developing a pipeline for Genotyping-by-sequencing (GBS) of the New Zealand TM Greenshell Mussel Rachael Ashby AgResearch
3.15pm
Genotyping-by-Sequencing: Opportunities for NZ Research Rob Elshire The Elshire Group Ltd
3:35 pm
Afternoon Tea
4.00pm
Identification of copy number variations in New Zealand dairy cattle Christine Couldrey Livestock Improvement Company
4.20pm
Developing genomic selection tools for radiata pine Natalie Graham Scion, Rotorua
Page 18
4.40pm
Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata Lukas Hunziker 1st year PhD student, Massey University Winner of an NGS Conference Student Scholarship
5.00 pm to 6.15pm
Discussion Session Sponsored by Illumina Enjoy a glass of wine with colleagues and participate in one of the discussion forums See the programme pg 55 for the titles of the forums and those chairing sessions
6.30pm
Conference Dinner Sponsored by Bio-strategy Wabi Sabi (a Japanese restaurant), 74 Broadway Avenue See map on pg 12 for directions
Page 19
W ednesday 19th August 8:45 am
Early morning Coffee
SESSION 6 CHAIR:
LIA LIEFTING
9:00 am
KEYNOTE SPEAKER NextGen Sequencing of Metagenomes: Exploring the Dark Matter Sarah Highlander J. Craig Venter Institute, La Jolla, CA, USA
10:00 am
Morning Tea
Page 20
SESSION 7 METAGENOMICS AND PATHOGEN DETECTION CHAIR:
NICK HENG
10.15am
Application of next generation sequencing technology to characterise the normal microbial gut flora of New Zealand farmed salmon Milica Ciric, presented by Jenny Draper New Zealand Ministry for Primary Industries, Wallaceville
10.35am
A pipeline to integrate fungal and bacterial microbiome data from rizospheres Ruy Jauregui AgResearch, Ruakura
10.55am
The surprising virus discovery in one of world's weirdest plants Shu Hui Koh 3rd year PhD student, Murdoch University, Australia Winner of an NGS Conference Student Scholarship
11.15pm
Detection of Dengue Virus, Leptospira and Rickettsia using Next-Generation Sequencing Tri Susilawati College of Medicine and Dentistry, James Cook University, Cairns, Australia Page 21
11.35pm
Whole-genome characterisation of the first neuropathogenic strain of equine herpesvirus type 1 (EHV1) isolated in New Zealand Edna Gias Ministry for Primary Industries, Wallaceville
11.55pm
An abundance of viruses co-inhabit Australian indigenous terrestrial orchids and their fungal partners Jamie Ong 4th year PhD student, Murdoch University, Australia Winner of an NGS Conference Student Scholarship
12.15pm
One Genome to Rule Them All: sequencing a partially clonal population of Helicobacter pylori SS1 Jenny Draper Ministry for Primary Industries, Wallaceville
12.35pm
Lunch
Page 22
12.40pm
Lunchtime Workshop Sponsored by Roche Maximizing Genomics Research using Targeted Enrichment Todd Richmond Roche NimbleGen
SESSION 8 NEW APPROACHES AND TOOLS CHAIR:
DAVID ECCLES
1.15pm
Interplay of Epichloë festucae var. lolii and its host Lolium perenne as assessed by tissue-specific transcriptome analysis Jan Schmid Massey University, Palmerston North
1.35pm
Dual species transcriptomics: Host and endosymbiont association Paul Maclean AgResearch
1.55pm
Analysis of Rumen Methanogens CRISPR-Cas systems Bradley Croft Masters student, University of Otago Winner of an NGS Conference Student Scholarship Page 23
2.15pm
Next Generation Sequencing Panel for Pharmacogenetic Screening Kim Ton 2nd year PhD student, University of Otago Winner of an NGS Conference Student Scholarship
2.35pm
Detection of Grapevine Pathogens using NanoString nCounter and Illumina MiSeq Lia Liefting Ministry for Primary Industries, Auckland
2.55pm
Afternoon Tea
SESSION 9 TRANSCRIPTOMES AND BIOMARKERS CHAIR:
RICHARD HALL
3.15pm
Prolactin influence on the mouse choroid plexus transcriptome Holly Phillipps University of Otago, Dunedin
3.35pm
Novel and unconventional RNA sequencing enabling the latest advances for forensic analysis Meng-Han Lin Institute of Environmental Science and Research Limited, Auckland Page 24
3.55pm
Application of Next Generation Sequencing in Determining Trans- generational Effects of Gestational Under-nutrition Peter Smith PhD student, University of Otago Winner of an NGS Conference Student Scholarship
4.15 pm
Conference Close Jo Stanton
Page 25
Session One Sequencing and dPCR analysis of circulating tumour DNA. The challenges and potential applications of liquid biopsy analysis Tim Forshew University College London, UK Biography Tim is a group leader at University College London (UCL), UK, and a co-founder of a new circulating tumour DNA sequencing company (Inivata). His academic research is based on detecting cancer DNA released by solid tumours into bodily fluids such as blood and urine and exploring how this can be used to improve cancer patient care. Major clinical areas of focus within his UCL group are sarcoma and childhood brain tumours. Within the company he leads the development of cutting edge technologies for low frequency cancer DNA detection. During his time at Cambridge University Tim was part of the team that first demonstrated detecting solid tumour mutations through next generation sequencing of blood plasma. As a postdoctoral Researcher at QMUL he won the 2009 Jeremy Jass Prize for his role in identifying fusion genes in Pilocytic astrocytoma.
Abstract There is growing evidence that many different cancer types release their DNA into a patient’s blood stream. This circulating and cell free tumour DNA (ctDNA) has a broad range of potential applications including non-invasive cancer detection, molecular stratification and disease monitoring. The main challenges with the analysis of ctDNA are its dilute and fragmented nature and the often low tumour DNA fractions. Advances in digital PCR and next generation sequencing have recently made the detailed analysis of this DNA possible. I will outline recent results for a range of cancers and highlight strengths and weaknesses of different analysis methods.
Page 26
Session Two Nanopore Sequencing - A Rhapsody of Errors 1,2
2
2
David Eccles , Mike Berridge , James Baty 1 Gringene Bioinformatics, Wellington, New Zealand; 2 Malaghan Institute of Medical Research, Wellington, New Zealand Abstract
Biography David Eccles is a freelance bioinformatician based at the Malaghan Institute of Medical Research in Wellington, New Zealand. He is working there with researchers looking at the differential expression of activated dendritic cells under different environmental conditions. David is also currently helping ESR with viral and bacterial metagenomic analysis, and carrying out genetic research relating to the population of Norfolk Island for QUT, Australia. David enjoys tinkering with new technology, and spends a bit of his time finding ways to use the MinION sequencer to supplement cancer and immunotherapy research carried out at the Malaghan Insititute.
The Malaghan Institute sequenced different mouse mitochondrial DNA samples with the MinION, and have investigated how the long-read sequence output could be applied to genotyping. Despite a high error rate of up to 15% for early sequencing runs, most sequencing error is random in nature and can be filtered out when multiple reads are aggregated for genotyping. The majority of the sequencing error lies at the software side of the device, after signal capture. This presents a very encouraging view of the future of MinION sequencing, allowing improved sequencing accuracy by re-calling captured events with newer base calling models.
Page 27
Long-read nanopore sequencing for the detection of genetic polymorphisms in the CYP2D6 gene Cree, S.L., Miller, A.L., Chua, E.W., Maggo, S., Kennedy, M.A. Department of Pathology, University of Otago, Christchurch, New Zealand. Biography
Abstract
Simone was awarded a PhD in biochemistry from the University of Oklahoma in 2009. She is currently a Postdoctoral Fellow at the Gene Structure and Function Laboratory, University of Otago, Christchurch where she is investigating the role of G-quadruplexes. She is also involved in identifying genetic polymorphisms that lead to adverse drug reactions and is currently exploring the use of the nanopore based MinION Sequencer (Oxford Nanopore Technology) for sequencing pharmacogenes.
The liver enzyme cytochrome P450 2D6 metabolises many important drugs, and displays considerable genetic variability. We are investigating the ability of the MinION nanopore sequencer to detect sequence variation in a 6.6kb PCR amplicon which encompasses the full CYP2D6 gene. Sequence reads are extracted and aligned using LAST and LASTZ. As kit chemistry has improved we have seen corresponding increases in mean length of aligned segments (792bp – 6431bp). Our most recent runs have successfully used oligonucleotide indexing to carry out multiplexing of samples. Our goal is to use the MinION for rapid and accurate analysis of CYP2D6 in multiple clinical samples.
Page 28
Session Three Connecting the microbiome and phenotypes in children born very preterm (speaker sponsored by BioStrategy) 1*
1,2*
1
1
1,2
Thilini N. Jayasinghe , Valentina Chiavaroli , Cameron Ekblad , José Derraik , Paul Hoffman , Wayne Cutfield 1,2ǂ Justin O'Sullivan 1 Liggins Institute, University of Auckland, New Zealand; 2 Gravida: National Centre for Growth and Development, New Zealand
1,2ǂ
,
Abstract
Biography Justin O'Sullivan and his research group use a holistic approach to understand DNA and cell structure formation, function, and inheritance. Their goal is to incorporate the spatial organization of a genome into our understanding of the relationships between what a cell's DNA codes for (the genotype) and what we actually see (the phenotype). To do this they use cutting edge methods and technologies from molecular biology, bioinformatics, and computational biology to integrate the spatial organization of genomes with measures of their function. They currently use these approaches to understand development, diseases and the human.
Our aim was to correlate the composition and functional capacity of the gut microbiome in children born very preterm with metabolic outcomes. Participants were healthy prepubertal children (5 to 10 years old) born very preterm (
