New Zealand Next Generation Sequencing Conference - Innovative ...

New Zealand 

Next Generation 

Sequencing 

Conference 

Dunedin Art Gallery 

Dunedin 

New Zealand 

21-22 August 2012

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Contents 

Sponsors ................................................................................................. 3 

Page 

Exhibitors ................................................................................................ 4 

Welcome ................................................................................................. 5 

General information ................................................................................ 7 

Programme 

Tuesday 21 st August .................................................................... 9 

Wednesday 22 nd August ............................................................ 11 

Speaker Biographies and Abstracts ..................................................... 13 

Posters .................................................................................................. 28 

List of delegates .................................................................................... 29 

Page 2

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Gold Sponsor 

At Illumina, our goal is to apply innovative technologies and 

revolutionary assays to the analysis of genetic variation and function, 

making studies possible that were not even imaginable just a few 

years ago. Illumina has developed a comprehensive line of products 

that address the scale of experimentation and the breadth of functional 

analysis required to achieve the goals of molecular medicine and 

marker assisted selection in Agriculture. Our offering includes leadingedge 

solutions for: Ultra High-throughput Next Generation 

Sequencing; Personal Next Generation Sequencing; SNP genotyping; 

Copy number variation; DNA methylation studies; Gene expression 

profiling; Low-multiplex analysis of DNA, RNA, and protein. 

Our products and services are used by a broad range of academic, 

government, pharmaceutical, biotechnology, and other leading 

institutions around the globe. 

Silver Sponsor 

Life Technologies is a global biotechnology tools company providing 

premier systems, consumables, and services for scientific 

researchers around the world. Life Technologies was created by the 

combination of Invitrogen Corporation and Applied Biosystems Inc. 

in November of 2008. Our customers conduct their research across 

the biological spectrum, working to advance personalized medicine, 

regenerative science, molecular diagnostics, agricultural and 

environmental research, and 21st-century forensics. With more than 

50,000 products used by more than 75,000 customers around the 

globe, Life Technologies is advancing scientific research in areas 

like academic research, drug discovery and development, toxicology 

and forensics, disease diagnostics, clinical cell therapy and 

regenerative medicine, and biologics manufacturing.Life 

Technologies is a strong proponent of global corporate social 

responsibility. Through the Life Technologies Foundation, our 

company has donated millions of dollars to help demystify the world 

of science, empower today’s children to become tomorrow’s 

scientific leaders, and deepen society’s appreciation of science. For 

more information about Life Technologies, visit 

www.lifetechnologies.com 

Conference Satchel Sponsor 

Roche Applied Science (RAS) as part of Roche Diagnostics NZ Ltd has been 

providing quality products to researchers in New Zealand since 1984. With 

products ranging from molecular biology kits to real-time PCR instruments 

(LightCycler®) to 454 next generation sequencing; Roche is recognised in 

New Zealand for its high quality products and superior technical support. 

Some of our leading products include: 

LightCycler® - for real-time quantitative PCR, SNP analysis, gene scanning 

MagNA Pure LC - automated DNA/RNA extraction and PCR reaction set-up. 

GS FLX and GS Junior - revolutionary technology in high throughput 

sequencing. 

Website www.roche-applied-science.co.nz 

Email biochem.nz@roche.com 

Phone 0800 652 634 

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Conference Name Badge Sponsor 

NZGL is a collaborative infrastructure providing New Zealand 

scientists with access to the significant equipment and bioinformatics 

services they need for large-scale genomics projects, thereby 

underpinning research in a broad range of areas, including medicine, 

agriculture and the environment. NZGL also provides the framework 

for coordinating projects, analytical and bioinformatics support, data 

storage and sharing. NZGL's infrastructure based at Otago, 

Auckland Massey is currently providing sequencing and microarray 

services to researchers throughout New Zealand, with a distributed 

team of bioinformaticians providing experimental design and a range 

of data analysis services. The final component of providing a fully 

integrated NZGL service package will be put in place towards the 

end of the year with provision of Bio-IT and IT services. 

Exhibitors 

HRS has been supplying and supporting software for New Zealand's 

scientists for more than 20 years. Programmes useful to NGS 

delegates are CLC bio Workbenches, STATISTICA and MATLAB 

products. CLC bio creates tools for sequencing DNA data, primer 

design, molecular cloning, RNA secondary structure prediction, 

protein function prediction and protein structure prediction. 

STATISTICA is a comprehensive analysis program with excellent 

graphing and a superb user interface. The MathWorks 

Bioinformatics Toolbox provides an open and extensible environment 

in which to explore ideas, prototype new algorithms, and build 

applications in drug research, genetic engineering, and other 

genomics and proteomics projects. 

Those who analyse biochemical pathways will want to see 

SimBiology, a product that extends MATLAB with tools for modelling 

and simulating in this area. Come to our stand and see these 

products demonstrated, or use them yourselves. 

Email 2734@hrs.co.nz or call 0800 477 776. 

Pacific Laboratory Products is the exclusive distributor for Agilent 

Genomics products in New Zealand. Think Next Gen Think Agilent’s 

SureSelect Sequence Capture Platform. 

Agilent’s SureSelect Target Enrichment System significantly improves 

the cost- and process-efficiency of next-generation sequencing. Focus 

your next-gen sequencing workflow on key genomic regions of interest 

while reducing the cost per sample. 

With HaloPlex, you can revolutionise your desktop sequencing 

workflow with complete target enrichment in less than a day. 

-Library-free target capture in less than a day – all in a single 

tube 

-Capture from 1kb to 500kb – without sacrificing specificity 

-Ideal for Desktop Sequencing as well as High-Throughput 

NGS Platforms 

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Welcome to the 2012 NGS Conference 

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Welcome to the fourth annual New Zealand Next Generation Sequencing Conference. 

A review of NGS capacity nationwide indicates the impact this technology is having on New 

Zealand science. From only two centers offering data generation capability four years ago, 

NGS now operates from at least six key research institutions throughout the country. Access to 

data generation can be gained through the New Zealand Genomics Ltd or via the strong 

presence in New Zealand of the newer, smaller bench-top devices: Illumina’s MiSeq, Roche’s 

GS Junior and the Ion Torrent from LifeTech. Coupled to this, the cost of data generation has 

greatly reduced. 

The challenge of obtaining high throughput sequence data has eased but the challenge of 

analyzing this data still remains. Every bioinformatician’s time is at a premium. At this year’s 

conference we have opened the floor to software providers to discover what sequence analysis 

tools are available, what is being developed for the future and how many of these tools are 

accessible to the biologist. We hope this session will help ease any analysis bottlenecks by 

providing guidance on appropriate analysis tools for your specific research projects. 

This year’s program again demonstrates the wide variety of uses for NGS; from pathogen 

discovery to epigenetics to the development of computational pipelines for complex genetic 

analysis. We have offerings from agriculture, aquaculture, human genetics, native flora and 

fauna and beyond. This wonderful mix should provide something to inspire everyone and 

promote cross-fertilization between our various disciplines. 

As I write this, the ‘final’ number of registrations has come in and shows attendance at this 

conference continues to grow. This reinforces the place for NGS in New Zealand research and 

the value of holding an annual meeting centered round this dynamic and rapidly changing 

technology. 

We hope you all enjoy the conference and your time in Dunedin. 

Jo Stanton 

High Throughput DNA Sequencing Unit 

Department of Anatomy, University of Otago! 

Conference Organising Committee for 2102: Jo Stanton, Lesley Collins, Susan Adams 

Page 5

General Information 

The Venue 

A on the map on the next page. 

Both the 2012 Conference and the Workshops will be held in the Dunedin Art Gallery, Dunedin, 

New Zealand. 

The Dunedin Public Art Gallery’s collection includes an excellent selection of British and 

European paintings and works on paper, gifted by generous benefactors or purchased by the 

Gallery’s founding organisation, the Dunedin Public Art Gallery Society. Many of the major 

figures in Western art since the 15th century are represented, with high points including 

paintings by Machiavelli, Claude Lorraine, Rosa, Monet, Pissarro, Reynolds, Gainsborough, 

Turner and Burne-Jones. Other international aspects of the collection include Japanese prints, 

a small selection of 20th century Australian art, and much of the decorative arts collection, 

which ranges across costume, textiles, ceramics, glass and furniture. 

Notable New Zealand artists represented in the collection include George O’Brien, Petrus van 

der Velden, C.F. Goldie, Rita Angus, Colin McCahon, Gordon Walters, Ralph Hotere as well as 

younger artists like Richard Killeen, Philip Trusttum, Jacqueline Fraser, Peter Robinson and 

Michael Parekowhai. Occupying a special place in the collection is the work of painter Frances 

Hodgkins, whose father founded the Gallery. Born and raised in Dunedin, she left early in her 

career to live and work in England where she gained a significant reputation in the context of 

Britain’s Neo-Romantic movement. 

Today the Dunedin Public Art Gallery focuses its acquisitions funds on the purchase of 

contemporary New Zealand work, although other areas of the collection continue to be 

expanded through gifts and bequests. 

Conference Dinner 

B on the map on the next page. 

The Conference Dinner will be held at “Etrusco at the Savoy”, an Italian restaurant providing 

that authentic Italian experience. 

The restaurant is an easy walk from the conference venue, and it should take around two 

minutes to walk there. Turn right as you leave the Art Gallery by the main entrance. Walk down 

towards Princes Street and turn right into Princes Street. Walk down Princes Street until you 

get the next cross-street, Moray Place. Turn right into Moray Place. Etrusco is just around the 

corner, on your right hand side, inside a building and up to the first floor. 

At the conference dinner there will be wine and orange juice on the tables. If you would like 

more to drink than will be provided then this will be for your account. 

Parking 

C on the map on the next page. 

All day parking is available in the Wilson Parking Building behind the Art Gallery, at 54 Moray 

Place. They are open everyday from 7am to 2am and charge $2 per hour Monday to Saturday, 

or $1 per hour if you are in before 10am. Parking on a Sunday is free. They accept cash and 

credit card with a 50c surcharge if you choose to pay by credit card.

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A = Dunedin Art Gallery 

B = Etrusco at the Savoy, venue for the Conference Dinner. 

C = Entrance to the Wilson carpark 

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2012 NGS Programme 

Tuesday 21 st August 

8.30am 

9.00am 

Registration and Coffee 

Welcome to the 2012 New Zealand NGS Conference 

Jo Stanton 

Session 1 

Chair: Richard Spence 

9.10am 

9.30am 

9.50am 

10.10am 

Earthquake induced stress cardiomyopathy: is it a Mendelian condition 

Martin Kennedy 

University of Otago 

HiSeq transcriptomics to discover genes associated with reproductive 

success in kiwi 

Kristina Ramstad 

Victoria University of Wellington and Illumina 

A method for designing NGS transcriptomics experiments that includes insilico 

biological replication 

Alan McCulloch 

AgResearch 

Morning Tea 

Session 2 

Chair: Mike Hendy 

10.40am 

11.00am 

11.20am 

Hybrid origin of a parthenogenetic genus: the genomic evidence 

Mary Morgan-Richards 

Massey University 

Reduced representation bisulphite sequencing indicates widespread 

epigenetic variation among normal individuals 

Aniruddah Chatterjee 


Index-free de novo assembly and deconvolution of mixed mitochondrial 

genomes 

Bennet McComish 


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11.40am 

An update on year two of the PGP Dairy Genomics Sequencing project 

Michael Keenan 

Livestock Improvement Corporation 

12:00 pm Lunch 

Session 3 

Chair: Lesley Collins 

1.00pm 

International Speaker 

A Small Genome Centre’s Adoption of New Generation DNA Sequencing 

for Research and CORE Service 

Si Lok 

The Chinese University of Hong Kong 

Session 4 

Chair: Kristina Ramstad 

2.00pm 

2.20pm 

2.40pm 

De novo sequencing of the genome of Streptococcus trichosurus, a new 

oral bacterial species isolated from the New Zealand brushtail possum 

Trichosurus vulpecula 

Nick Heng 


High-throughput Genotyping-by Sequencing (GBS) in Sheep 

Tracey van Stijn 

AgResearch 

Using Next Generation Sequencing techniques to identify Single 

Nucleotide Polymorphisms in Chinook Salmon 

Hayley Baird 

AgResearch, Invermay 

3:00 pm Afternoon Tea 

Session 5 

Posters 

Chair: Jo Stanton 

3.30pm 

4.30pm 

to 6.30pm 

7pm 

Poster Speakers – Selected from poster abstracts 

8 speakers talking for 5 mins each 

See page 27 of the programme for the names of those who will be talking 

Poster Session 

Conference Dinner 

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Wednesday 22 nd August 

8:45 am Early morning Coffee 

Session 6 


9:00 am International Speaker 

Tailoring high-throughput sequencing approaches to next-generation plant 

virology in south-west Australia 

Steve Wylie 

Murdoch University, Australia 

10:00 am Morning Tea 

Session 7 

Chair: Martin Kennedy 

10:30 am Diagnosis of Plant Pathogens using Next-Generation Sequencing 

Lia Liefting 

Ministry for Primary Industries 

10.50am 

11.10am 

11.30am 

11.50am 

12.10pm 

12.30pm 

New Zealand Ostreid herpesvirus – application of high throughput 

sequencing in a biosecurity context 

Richard Spence 


Pipelines, Pedigree & Polymorphism 

Chad Harland 


Differential Methylation Analysis using RRBS: Challenges and New Insights 

Peter Stockwell 


Development of epigenomic pipelines for use in agricultural animals 

Christine Couldrey 

AgResearch 

Calling variants in populations with pedigrees 

John Cleary 

Real Time Genomics 

Lunch 

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Session 8 

Bioinformatics Software 

Chair: Lesley Collins 

1.30pm 

1.50pm 

2.00pm 

2.10pm 

2.20pm 

2.30pm 

NGS project analysis on small-scale computing (aka You did WHAT on a 

laptop) 

Lesley Collins 


Geneious 

Shane Sturrock, Senior Scientist – Geneious Support and Professional Services 


Graham Gaylard, Founder 

LifeTech 

John Davis, Senior Field Bioinformatics Scientist 

New Zealand Genomics Limited 

Tony Lough, Chief Executive 

CLC 

Ray Hoare, Hoare Research Software 

Session 9 

Gold Sponsor Presentation 


2.40pm 

Current and imminent state of the art for Illumina’s sequencing 

technologies 

Brian Fritz 

Illumina 

2.55pm 

Afternoon Tea 

3.20pm 

Poster Prizes Awarded 

Jo Stanton 

3.45 pm Conference Close 


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Speaker Biographies and Abstracts 

Listed in the order they appear in the Programme 

Session 1 

Earthquake induced stress cardiomyopathy: is it a Mendelian condition 


Department of Pathology, University of Otago, Christchurch 

Biography 

Martin Kennedy obtained his PhD in bacterial 

genetics at the University of Auckland, and carried 

out postdoc research in leukaemia genetics at the 

Laboratory of Molecular Biology, Cambridge (UK) 

before returning to Christchurch, New Zealand in 

1991. His current research interests include the 

genetics of complex disease, gene by environment 

interactions, and pharmacogenomics. He also 

holds a Marsden grant to examine the role of G- 

quadruplex structures in DNA and their relevance 

to genomic imprinting 

Abstract 

The major earthquakes of 4th September 2010 and 

22nd February 2011 both triggered case clusters of 

a rare condition called stress cardiomyopathy (also 

known as broken heart syndrome or Takotsubo 

cardiomyopathy). Many of these patients received 

critical care in the coronary care unit of 

Christchurch Hospital, and some required intensive 

care with ventilatory support, but ultimately all 

survived. The resulting very well characterised, 

tightly homogenous cohort of 30 patients is 

unprecedented. Almost all patients presenting with 

the condition were post-menopausal females, 

consistent with other reports. This provides a 

unique opportunity to study the underlying causes 

and presentation of this perplexing disorder. The 

exact aetiology of stress cardiomyopathy remains 

unknown with catecholamine induced myocardial 

stunning a proposed pathway. Many forms of 

cardiomyopathy have genetic origins, and it is 

reasonable to propose that this syndrome arises 

from a very rare underlying genetic predisposition 

that is exposed in times of major, acute stress. We 

hypothesised that stress cardiomyopathy is a rare 

Mendelian predisposition that is exposed with 

acute major stress. The rarity of the underlying 

mutation requires that large numbers of people 

must be exposed to the stressor, which only 

happens in times of natural disaster such as major 

earthquakes. This is rather speculative, although 

two prior reports describe occurrence of the 

syndrome in relatives. Exome sequencing provides 

a method to test this hypothesis. We obtained 

exome data on 12 of the Christchurch earthquake 

stress cardiomyopathy patients using Illumina 

TruSeq exome enrichment and the Illumina HiSeq 

platform (New Zealand Genomics Ltd). The data 

have been processed through the GATK pipeline, 

and we are examining candidate variants that 

occur in patient samples with a higher than 

expected distribution based on 1000 Genomes 

Project data. This presentation will describe these 

preliminary analyses and some of the pitfalls 

encountered so far. 

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HiSeq transcriptomics to discover genes associated with reproductive success in kiwi 


Victoria University of Wellington 

Biographies 

Kristina Ramstad completed a PhD in Ecological 

Genetics at the University of Montana, USA. She 

emigrated to New Zealand in 2006 to conduct 

postdoctoral research with the Allan Wilson Centre 

at Victoria University of Wellington. Kristina 

research focuses on mechanisms (genetic drift, 

selection, migration and mutation) and patterns of 

diversification within and among species. She has 

worked with a diverse array of taxa, including 

sockeye salmon, tuatara and, most recently, 

kiwi. Applied species conservation is the primary 

goal of her work. 

Abstract 

Little spotted kiwi (LSK) and rowi have the smallest 

population sizes and lowest neutral genetic 

diversity of the five currently recognized species of 

kiwi (Family Apterygidae). Both LSK and rowi 

exhibit low hatching success and high variance in 

reproductive success. The latter effect is 

particularly dramatic in rowi where a full third of 

adult birds do not breed. Poor reproductive 

performance may be due to historical bottleneck 

effects and the subsequent inbreeding effect of 

small population size. We have performed RNAsequencing 

of 16 individual kiwi across the two 

species from whole blood isolates. As there is no 

current genome, we performed transcriptome de 

novo assembly using a subset of the read 

data. The de novo assembly output identified 

13,000 unique protein coding transcripts with 

homology to human and/or chicken. More than 

3,000 of these transcripts are predicted to cover the 

full length of the ORF and a majority of the 

remainder nearly full length. Realignment of each 

species against the reference easily identified 

numerous SNPs/indels, with high confidence that 

they represent species and individual specific 

markers. These mutations are being evaluated for 

changes to known breeding genes and will act as 

markers for determining genetic variation among 

individuals with varying reproductive success. 

A method for designing NGS transcriptomics experiments that includes in-silico 

biological replication 


AgResearch 

Biography 

Abstract 

Alan McCulloch is a bioinformatics software 

engineer at AgResearch in Dunedin who has 

worked on postgres and oracle sequence and gene 

expression database design and management, 

sequence clustering and assembly pipeline and 

method design and implementation, NGS 

processing and pipelines, HPC systems 

architecture and administration, and everything in 

between. Pre human-genome he was involved in 

helping set up a clinical trials research unit at 

Auckland University, including database design, 

implementation, management and reporting, 

treatment randomisation design and 

implementation, for several large international 

clinical trials. He has a Bachelors degree in 

Mathematics and Philosophy from Canterbury 

University. 

Page 14 

An NGS transcriptomics experiment usually 

involves alignment of the sequenced transcripts to 

a reference ‘ome (genome or transcriptome), in 

order to identify and quantify the expressed loci. 

However a given reference ‘ome is but a single 

sample from a large space of potential alternative 

assembled ‘omes. Because we only take a single 

sample from this ‘ome space (either we choose an 

‘ome assembled by somebody else, or we 

assemble one on the fly ourselves), the experiment 

provides no information at all about the influence 

our sample of reference ‘ome has on NGS 

expression observations, yet there is evidence that 

reference ‘ome assemblies can vary significantly 

due to both technical factors and underlying 

genetic variation. While it is straightforward to align 

transcripts to multiple references, establishing the

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homology relationships between the references 

needed to compare the results is difficult, and this 

cannot be fully automated, so that this type of insilico 

biological replication is seldom if ever 

included in experimental designs. Here we suggest 

a method for designing NGS transcriptomics 

experiments that includes in-silico biological 

replicates, in a way that could be automated and 

included as part of a standard NGS transcriptomics 

pipeline. This design would deliver stabler NGS 

transcriptomics assay results robust against 

common variations in reference `ome, and may 

extend the applicability of NGS transcriptomics to 

more highly variable species, in which NGS 

expression observations obtained from alignment 

to a single reference `ome may be too unreliable to 

be useable. 

Session 2 

Hybrid origin of a parthenogenetic genus: the genomic evidence 



Biography 

Mary Morgan-Richards is an academic within the 

Ecology Group at Massey University, Palmerston 

North. She and her research group 

(http://evolves.massey.ac.nz) study speciation, 

evolutionary ecology and conservation genetics 

using endemic New Zealand animals (weta, stick 

insects, snails). Mary gained her PhD from Victoria 

University of Wellington, she then did postdoctoral 

fellowships at the University of St Andrews, 

Scotland, University of Otago NZ, the Natural 

History Museum London UK, and University of 

Canterbury NZ. She has experience working with 

plants, and animals, invasive species and 

endangered species and is interested in using NGS 

datasets for testing theories in evolutionary biology. 

Abstract 

Hybridization between species can combine 

divergent genomes and create new species when 

reproductive isolation from parentals accompanies 

the novel genome fusion (Bullini 1994). It has been 

estimated that approximately 70% of plants are the 

result of allopolyploidy. Hybrid species can be 

recognized by the presence of alleles distinct to 

two species co-occurring in the same genome. 

A hybrid origin for an endemic New Zealand genus 

of stick insects (Acanthoxyla) was suggested 

(Morgan-Richards & Trewick 2005) with the related 

bisexual species, Clitarchus hookeri, named as a 

putative paternal species. A maternal bisexual 

species has not been identified and is likely to be 

extinct (Trewick et al. 2008; Buckley et al. 2010). It 

is also likely that some lineages of Acanthoxyla are 

triploid, and it is possible that Clitarchus hookeri 

was not involved in the origin of all Acanthoxyla 

species (Buckley et al. 2008; Myers et al. unpub). 

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Next generation DNA sequencing provides large 

datasets for testing hybrid origin hypotheses and 

here we set out a procedure for evaluating such 

data. Using de novo assembled transcripts to 

compare ‘allelic’ diversity in putative hybrids and 

their putative parents, we have used mRNA 

sequences to examine the allelic diversity within 

one Acanthoxyla lineage and compared this to 

homologous gene sequences from Clitarchus 

hookeri. The hybrid origin hypothesis predicts that 

at each locus Acanthoxyla will contain an allele 

similar to that of Clitarchus hookeri, and one allele 

from the unidentified maternal ancestor. If

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Acanthoxyla is not of hybrid origin then the two 

alleles within Acanthoxyla will be more similar to 

each other than either is to the Clitarchus hookeri 

alleles. We also present evidence to address the 

questions: Is Acanthoxyla diploid or triploid And 

does Acanthoxyla use apomictic or automictic 

parthenogenesis to reproduce 

Reduced representation bisulphite sequencing indicates widespread epigenetic variation 

among normal individuals 

Aniruddah Chatterjee 


Biography 

Aniruddha Chatterjee obtained his BSc (triple 

major in biotechnology, biochemistry and 

chemistry) from Osmania University, Hyderabad 

and MSc in biotechnology from VIT University, 

Vellore, India. Aniruddha is member of Professor 

Ian Morison’s group and is based in the department 

of Pathology at the University of Otago. 

Aniruddha’s current research focuses on 

unraveling epigenetic signatures in humans. He is 

using the technique of reduced representation 

bisulphite sequencing (RRBS) to quantify human 

methylomes. He played a key role in establishing 

an analysis pipeline to analyze large-scale 

methylation data and further developing advanced 

(together with Dr. Peter Stockwell) tools which 

enables bench-scientists to analyze complex 

epigenomic data at greater ease. His methods has 

applicability to other species, for e.g., zebrafish and 

the findings will be a big step forward in 

understanding the role of specific epigenetic marks 

in normal individuals. DNA methylation analysis of 

human genome at this global scale is one of the 

first attempts made in New Zealand. Aniruddha 

was awarded the “AGRF Young Investigator 

Award” in 2011 (Melbourne, Australia) in 

appreciation of his work. 

Abstract 

Detailed understanding of inter-individual variation 

in epigenetic signatures will help establish their role 

in altering gene expression, disease susceptibility 

and phenotype. We are quantifying the methylation 

status of almost 24,633 CpG islands (87% of all 

CpG islands in the genome, 18,500 of which are 

promoter associated) across a normal human 

population, by using reduced representation 

bisulfite sequencing (RRBS) (1) . Good sequencing 

results have been obtained for seven individuals 

(Illumina) and more libraries are being sequenced. 

We establised an effective bioinformatics pipeline 

for analysing genome-scale DNA methylation data 

(2). Further, new command line tool (DMAT) is 

being developed to detect differential methylation 

patterns and identify genes involved. Then by 

focussing on genes that show inter-individual 

variation, we will explore specific cohorts to 

document epigenetic influences on human 

phenotypes and disease. 

Index-free de novo assembly and deconvolution of mixed mitochondrial genomes 



Biography 

Bennet McComish obtained his BSc and MPhil 

from Massey University in the 1990s. He is 

currently completing his PhD in computational 

biology under the supervision of David Penny, also 

at Massey University. Bennet's PhD research 

covers several areas of sequence analysis, 

including assembly of next-generation sequence 

Abstract 

In order to make use of the high throughput 

available with next-generation sequencing 

technology, we developed a pipeline for 

sequencing and de novo assembly of multiple 

mitochondrial genomes without the costs of 

indexing. We first used simulations to explore the 

ability of existing sequence assembly algorithms to 

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data, estimation of mutation rates, and 

phylogenetics. 

separate and assemble sequences from different 

sources. Once optimised, the same methods were 

successfully applied to reads from a single lane of 

an Illumina Genome Analyzer flow cell containing a 

mixture of PCR products from six different 

mitochondrial genomes. More recently, we applied 

a modified version of the same pipeline to four 

more mixtures, this time using total genomic DNA, 

and successfully assembled 17 mitochondrial 

genomes. 

An update on year two of the PGP Dairy Genomics Sequencing project 

Michael Keenan 


Biography 

Mike Keehan is a Senior Bioinformaticist at LIC. 

He is currently involved in the LIC genomic 

selection project and the Primary Growth 

Partnership Dairy Genomics project. With a career 

background in applied mathematics, software 

development and systems administration he has 

undertaken a variety of bioinformatics tasks for LIC. 

Mike has a masters degree in Operations 

Research and a post graduate diploma in Science 

from Massey University. He is interested in 

obtaining genotype phase from sequence read 

information and in the application of population 

deNovo assemblers. 

Abstract 

The second year of the Dairy PGP project will have 

seen LIC and Vialactia receive an additional 11 

TBase of whole genome sequence data. 

Preliminary results from applying this tranche of 

data to phase and impute whole genome sequence 

from 50K SNP chips will be presented. Practical 

experiences from year one and two will be 

summarised. The state of the bovine genome 

assembly will be discussed. The project offers an 

opportunity for biologists who would like to examine 

a large whole genome population dataset. 

Session 3 

A Small Genome Centre’s Adoption of New Generation DNA Sequencing for Research 

and CORE Service 

Si Lok 


Biography 

Professor Si Lok has 20 years experience in the bioindustrial 

sector and academia. At ZymoGenetics (Novo 

Nordisk) he helped develop technologies establishing 

the company as a world leader in therapeutic protein 

discovery. His team discovered the long sought and 

contested megakaryocytic-lineage growth factor, 

Thrombopoietin (TPO). As principal scientist, he 

instigated massive scale sequencing of cDNA libraries 

driving the company’s pioneering use of EST mining to 

discover new biologic entities that contributed to the 

company’s successful IPO in 2002. Since 2007, he was 

the Chair Professor of Genomic Medicine and the 

Scientific Director of the Genome Research Centre of 

Hong Kong University and most recently as Professor of 

Practice in Applied Genomics at the Chinese University 

of Hong Kong where his small group continues to 

Abstract 

New generation DNA sequencing offers 

unique opportunities and challenges to a small 

genome centre. At our centre, we focus the 

use of the technologies and expertise for 

difficult collaborative projects not generally 

suited for the routine commercial service 

providers. The present talk highlights the 

latest technologies, methodologies and 

applications in the field as well as some of our 

centre’s efforts. We compare solution-based 

hybridization enrichment and high throughput 

Amplicon-based targeted resequencing of 

exomes or candidate genes. The newly 

established RainDance platform for massively 

parallel amplicon generation combined with 

454-pyrosequencing is particularly powerful for 

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develop genomics technology and translate their use in 

research and discovery. His group assumes a lead role 

in nano-scale and strand-specific cDNA library 

construction to dissect regulatory pathways, and the use 

of targeted sequencing to identify mutations contributing 

to diseases. Professor Lok has also developed methods 

for pair-end read sequencing of up to 50-kb separation 

to identify genomic rearrangements that are otherwise 

not readily detectable. Under his leadership, the centre 

has begun to apply genomics in the non-medical 

disciplines. 

small targeting studies. Other research efforts 

are in the areas methylomics, transcriptomics, 

and pathogenic genomics where the power of 

DNA sequencing is used to identify emerging 

pathogens and to study host and pathogen 

interactions. 

Session 4 

De novo sequencing of the genome of Streptococcus trichosurus, a new oral bacterial 

species isolated from the New Zealand brushtail possum Trichosurus vulpecula 

Nick Heng 


Biography 

Nick Heng is currently a senior lecturer in the 

Department of Oral Sciences (Faculty of Dentistry), 

University of Otago. Over the past decade or so, he 

has been “moving up” in the microbiological world, 

starting with gastrointestinal bacteria (PhD 

research), rumen microbiology (postdoctoral 

studies) and now oral bacterial species. His 

primary research expertise is in prokaryotic 

(bacterial) genetics and his current research 

projects that involve the use of next-generation 

DNA sequencing platforms are: (i) whole-genome 

sequencing of oral bacteria (from any source), and 

(ii) surveying the oral microbiota in health and 

disease. Nick’s other research interests include 

oral immunology and oral pathology but he does 

not claim, in any way, to be proficient in either. 

Abstract 

Members of the bacterial genus Streptococcus 

inhabit a multitude of sites in humans and many 

animals. Whilst some species are pathogenic, most 

are commensals. During a recent survey of oral 

streptococci from New Zealand brushtail possums 

(Trichosurus vulpecula), a new species 

(provisionally called Streptococcus trichosurus) 

was identified. The genome of S. trichosurus was 

sequenced using the new Ion 318 sequencing 

chip in combination with the Life Technologies Ion 

Torrent-based Personal Genome Machine, yielding 

~485 Mbp (~210-fold coverage) of sequence data. 

Here, the draft S. trichosurus genome sequence is 

presented and the bioinformatic procedures 

associated with its assembly are discussed. 

High-throughput Genotyping-by Sequencing (GBS) in Sheep 


AgResearch 

Biography 

Tracey van Stijn is a research associate working 

for AgResearch Animal Genomics at Invermay. 

Her main focus previously was on identifying 

genes and polymorphisms that affect meat traits 

in the New Zealand Sheep industry. She assisted 

in sequencing for the Sheep HapMap project, 

which led to the currently used 50K SNP Chip. 

Her current project is to optimise Genotyping by 

Sequencing methods in agricultural species. 

Abstract 

Recent advances in next generation sequencing 

technology have increased the output/cost to a level 

that now allows for the potential of GBS in 

livestock. We have explored GBS in sheep with the 

aim of developing a cost effective, reproducible and 

high-throughput SNP genotyping method that can be 

manipulated to return varying genome 

coverage. Restriction enzymes have been employed 

together with adapter based multiplexing for next 

generation sequencing, a technique that has been 

well established for high-density SNP discovery and 

genotyping in numerous species. We utilised the 

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GBS method described by Elshire et al., 2011 (PLoS 

ONE 6:e19379), however, through the addition of 

specific nucleotides within and following the 

restriction enzyme cut site to the PCR primer we are 

able to reduce the complexity of the genome in a 

controlled manner. Varying the number of samples 

and the ‘size’ of the reduced genome per lane on an 

Illumina HiSeq2000 allows for differing magnitudes 

of SNPs to be genotyped and interrogated. The 

method for reducing the complexity of the genome, 

sequencing and bioinformatics pipeline for GBS in 

sheep will be presented. 

Using Next Generation Sequencing techniques to identify Single Nucleotide 

Polymorphisms in Chinook Salmon 

Hayley Baird 

AgResearch, Invermay 

Biography 

Hayley Baird graduated from Otago University with 

a BSc(Hons) in microbiology. She is now a 

research associate for AgResearch Animal 

Genomics at Invermay. The majority of her time 

over the last few years has involved working with 

the Illumina iSCAN in particular the sheep 50 and 

5k chips, however the area of her research 

thatsheI’ll be talking about is the Aquaculture 

industry and the process of creating a SNP chip for 

Chinook salmon. 

Abstract 

Understanding and improving feed conversion 

efficiency (FCE) in farmed New Zealand Chinook 

salmon is a high priority for the industry. A 

research programme has been established with 

two main goals: 1) tank-based performance and 

genetic evaluation of 160 families focussing on 

growth, feed intake, body fat and FCE and 2) the 

development of a new panel of single nucleotide 

polymorphism (SNP) markers that will be used to 

search for markers linked to QTL. Since there is no 

salmon genome assembly available we had to 

come up with a strategy that did not require a 

reference genome. We utilised three different nextgeneration 

sequencing platforms (454, SOLiD and 

Illumina HiSeq) to take us straight to SNPs. After 

stringent filtering we arrived at 95,000 SNPs. 

Comparative genomics indicated that these SNPs 

were evenly distributed across the salmon genome. 

An Illumina 6K SNP chip has been developed and 

4 large families genotyped for mapping and 

eventual QTL analysis. 

Session 6 

Tailoring high-throughput sequencing approaches to next-generation plant virology in 

south-west Australia 

Steve Wylie 

Murdoch University, Australia 

Biography 

Steve Wylie attended Otago University in the 

1980s and completed an honours degree in the 

botany department before moving to Western 

Australia to study plant viruses of pasture legumes 

for his PhD. The chance discovery of viruses in 

Abstract 

Given the great age of the Australian continent, 

high endemism amongst its plant flora, and the 

varied ecosystems present, we hypothesised that 

its indigenous viral flora would be much richer than 

that currently described. Many exotic plants and 

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wild plants there sparked an ongoing interest in the 

roles of viruses of the indigenous flora. Currently 

his focus is on the threatened terrestrial orchid flora 

of the southwestern corner of Australia. 

virus vectors have become established in Australia 

over the past two centuries, and we also predicted 

that the indigenous flora would be suffering 

invasion by aggressive exotic viruses inadvertently 

imported in these new species. We are testing 

these hypotheses on a range of indigenous and 

exotic plant groups, with a focus on terrestrial 

orchids, a group of conservation 

concern. Approaches used to identify RNA viruses 

include sequencing RNA from single plants; 

sequencing RNA pooled from multiple plants 

coupled with subsequent matching of plants and 

viruses found; sequencing small RNA species 

generated by plants in defense of viruses; labeling 

RNA from individual plants before pooling and 

sequencing; and developing methods to enrich 

plant RNA for viral transcripts before 

sequencing. The pros and cons of the various 

approaches tested will be discussed, as will 

implications of this work on conservation 

management and biosecurity policy. 

Session 7 

Diagnosis of Plant Pathogens using Next-Generation Sequencing 

Lia Liefting 

Plant Health and Environment Laboratory, Ministry for Primary Industries 

Biography 

Lia Liefting has many years experience in working 

with plant pathogens, especially bacteria-like 

organisms (phytoplasmas and liberibacters). After 

completing her PhD at the University of Auckland, 

Lia spent 5 years as a postdoctoral scholar at the 

University of California, Davis. During this time she 

sequenced the complete genome of a 

phytoplasma, before the era of NGS 

technology. On return to New Zealand, Lia worked 

on a Marsden grant to sequence the genome of the 

phytoplasma that is killing our cabbage trees. Lia 

currently works at the Plant Health and 

Environment Laboratory, Ministry for Primary 

Industries performing plant disease diagnostics. 

Abstract 

MPI’s Plant Health and Environment Laboratory is 

responsible for the identification of new pests and 

diseases affecting plants, plant products and the 

environment. In some cases identification can take 

an extended period, especially for new pathogens 

and emerging diseases. Metagenomic analysis 

using next-generation sequencing (NGS) has the 

potential to detect the full spectrum of pathogenic 

organisms in a single test. Therefore this 

technology is being implemented in our laboratory 

for plant pathogen diagnosis. Our strategy is to 

use total RNA in order to detect all pathogen 

types. The processes involved in the preparation 

of the RNA for NGS will be described as well as 

validation of the method on at least one 

representative from each of the major groups of 

plant pathogens and genome types. 

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New Zealand Ostreid herpesvirus – application of high throughput sequencing in a 

biosecurity context 


Bacteriology and Aquatic Animal Diseases Team, Investigation and Diagnostic Centre, 

Compliance and Response, Ministry for Primary industries 

Biography 

Richard Spence has worked for the last three 

and a half years as a Senior Scientist at the 

Investigation and Diagnostic Centre, Ministry for 

Primary Industries. Prior to working in New 

Zealand Richard worked as a Clinical Scientist in 

the NHS running a molecular diagnostics 

laboratory within a clinical microbiology 

department. He has a PhD in molecular 

diagnostics from the University of Nottingham. 

Richard's main area of interest is the application 

of molecular tools for identification and 

characterisation of new and/or emerging 

pathogens. 

Abstract 

In November 2010 the Ministry for Primary Industries 

(formerly MAF) was notified of high mortality levels in 

juvenile Pacific oysters in the North Island of New 

Zealand. Ostreid herpesvirus was identified in 

association with the mortalities. Ostreid herpesvirus 

has plagued the European Pacific Oyster industry for 

over a decade resulting in significant economic 

losses. Although it appears the virus has been 

present in New Zealand for several years this was 

the first significant mortality event associated with 

the virus in New Zealand. A metagenomic analysis 

of highly infected oyster larvae was undertaken using 

the Roche GS Junior sequencer to try and facilitate a 

better understanding of factors contributing to the 

mortality event. Primary analysis of the data resulted 

in assembly of an Ostreid herpesvirus genome 

against a reference genome. More detailed analysis 

revealed that the New Zealand Ostreid herpesvirus 

harboured several significant deletions in 

comparison to the reference genome. In addition, de 

novo assemblies performed on the data identified the 

presence of a number of Vibrio species that may 

also have contributed to the observed 

mortalities. Further analysis of this data set is 

focused on the observed differences between the 

New Zealand Ostreid herpesvirus and the reference 

genome and what impact this may have on the 

pathogenicity of the strain. 

Pipelines, Pedigree & Polymorphism 

Chad Harland 


Biography 

Chad Harland graduated from University of 

Canterbury with an MSc in Biochemistry. As a 

member of the LIC Bioinformatics team he has 

been heavily involved in analysis of the first 

phase of the Dairy PGP sequencing project. 

During which he focusing on the testing and 

developing the Bioinformatics pipelines that can 

scale from tens of sequenced individuals to 

hundreds of sequenced individuals while 

making maximal use of existing genotype and 

pedigree data. 

Abstract 

A variety of different bioinformatics pipelines exist for 

NGS datasets, each with slightly different trade offs. 

Having tested a number of these pipelines for the 

DairyPGP project we have settled on a mixed solution 

that offers high performance, high sensitivity and 

specificity for SNP and Indel detection. Secondly due 

to the population structure of the NZ Dairy Herd we 

have a significant amount of Pedigree information that 

can be used to improve Variant calling. As such we 

have looked at the use of trios, pedigree and 

Mendelian inheritance of variants in Variant calling 

and filtering and will discuss the tools used and the 

advantage this additional information provides. 

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Differential Methylation Analysis using RRBS: Challenges and New Insights 



Biography 

Peter Stockwell started a PhD in protein chemistry 

at Otago University but was diverted on to 

numerical projects, including population genetics 

and early DNA sequence data 

handling. Postdoctoral work at ICRF, London, 

established the importance of computational 

methods and homology comparisons as tools in the 

developing field of biological sequence 

analysis. Subsequent work has included the 

development of SW tools for sequence analysis 

and assembly and data mining of sequence data 

repositories. The size and complexity of sequence 

data has evolved rapidly alongside computational 

resources and Peter has used a variety of 

computer languages in order to handle data in 

practical time frames. Most recently, Peter has 

been working on the processing of data from NGS 

Reduced Representation Bisulphite Sequence work 

in association with Aniruddha Chatterjee and 

Professor Ian Morison and has an involvement with 

N.Z. Genomics Limited. 

Abstract 

Reduced Representation Bisulphite Sequencing 

(RRBS) resolves DNA methylation status at basepair 

resolution and enriches for promoter 

associated CpG islands (CGI) in the 

genome. Since CGI methylation plays a key role in 

the epigenetic regulation of gene expression, there 

is interest in elucidating differential methylation 

patterns of CGIs and neighbouring genes in normal 

individuals and in disease conditions. We describe 

the unique challenges associated with DNA 

methylation data analysis and our efforts in 

quantifying differentially methylated regions in 

RRBS contexts and in relating them to known 

genomic elements. The challenges relate to the 

nature and volume of data, the sizes of genomes 

and the complexity of scanning for differential 

methylation of RRBS fragments which are 

discontinuously distributed along the genome.. 

Development of epigenomic pipelines for use in agricultural animals 

Christine Couldrey 

AgResearch 

Biography 

Christine Couldrey's career has been dominated 

by molecular biology, although her fields of study 

have varied considerably. She completed a PhD 

reproductive biology at Cambridge University in the 

Laboratory of Nobel Laureate Sir Martin 

Evans. From there she completed a postdoctoral 

position at the National Institutes of Health 

investigating the role of epithelial stem cells in 

breast cancer. This stem cell work led to a second 

postdoctoral position with the American Red Cross 

identifying genes involved in hematopoietic stem 

cell signalling. A short stint curating DNA 

sequences for GenBank provided her with a 

greater understanding of the intricacies of DNA, 

after which she headed back to New Zealand to 

work at AgResearch, where she has been 

investigating epigenetic nuclear reprogramming (in 

particular DNA methylation) in large animal cloning. 

More recentlyshe has been adapting protocols for 

genome wide DNA methylation analysis (reduced 

representation bisulfite sequencing) used in 

humans and mice to agricultural animals with the 

ultimate goal in using epigenetics to improve 

production efficiency and performance. 

Abstract 

The creation of single nucleotide polymorphism 

chips and the development of genome wide 

selection will allow the animal breeding industry to 

take a quantum leap in the rate of genetic 

progress. However, soon all sequence variations in 

each individual in closed breeding schemes will be 

known. What is not currently known is how to rank 

these variations, especially those that involve 

changes in gene expression rather than amino acid 

sequence. One of the key determinants in the 

control of gene expression in mammals is DNA 

methylation – a mechanism known to play a central 

role in regulating many aspects of growth and 

development. High-throughput sequencing has 

recently become a vital tool in the analysis of DNA 

methylation and reduced representation bisulfite 

sequencing (RRBS) has proven to be effective in 

understanding DNA methylation landscapes. 

However, to date, mammalian genome wide 

epigenetic studies have focused on humans and 

mice. Here we describe development of RRBS in 

sheep. The Carwell phenotype, used as a proof of 

principle, is a desirable inherited muscular 

hypertrophy for which, in spite of considerable 

resequencing efforts, the causative mutation has 

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not been identified. Muscle DNA was used for 

RRBS and epigenomic pipeline development to 

generate single nucleotide resolution analysis of 

DNA methylation in sheep. Sequence read quality 

was assessed and displayed the expected 

nucleotide composition. Analysis of 1% of the 

genome resulted in analysis of >20% of all CpG 

sites. DNA methylation analysis was precise with 

biological replicates showing high repeatability 

(r>0.9). Methylation measurement was accurate as 

illustrated by the comparison of RRBS methylation 

data and the gold standard Sequenom analysis 

within the Carwell region where proportion 

methylation measured matched at 132/134 CpG. 

Sheep were different from other species; as silico 

analysis of the sheep genome highlighted greater 

CpG island enrichment by RRBS than expected. 

We have generated the first sheep methylome and 

optimised RRBS for use in agricultural 

animals. This protocol and bioinformatic pipeline 

will have widespread use in the future – by 

facilitating the identification of superior individuals 

to enhance productivity through further selective 

breeding. 

Calling variants in populations with pedigrees 

John Cleary 


Biography 

Professor John Cleary has 40 years experience 

in commercial software engineering and computer 

science. Originally a pure mathematician he gained 

a PhD in electrical engineering from Canterbury 

University. He spent 12 years in Calgary Canada 

where he did research on distributed computing 

systems and data compression and was cofounder 

of a software company that simulated 

systems on high performance distributed 

computers. For the last 10 years he has been 

developing new algorithms and software for high 

performance computing for NGS data. This has 

included both read mapping to genomes and 

variant calling. Currently he is Chief Scientist at 

Real Time Genomics and an Adjunct Professor of 

Computer Science at Waikato University. 

Abstract 

The data tsunami coming out of sequencing 

machines now enables us to compare NGS data 

from thousands of individuals. These populations 

can be from species that are important 

commercially and medically as well as humans 

(that are presumably both). These populations are 

often of related individuals. A number of techniques 

are available for leveraging this population and 

pedigree information to obtain either high quality 

variants or good quality ones using very low 

coverage NGS data. Of particular note here is the 

need to provide good statistical confidence when 

attempting to extract differential calls such as de 

novo mutations. Bayesian algorithms for such 

applications will be described along with results on 

humans and other species. These 

include: improvements in the quality of variant calls 

given population pedigrees and how this varies with 

the coverage; detection of de novo 

mutations; detection of potentially causative alleles 

for traits; and detection of mutation in tumors when 

compared with normal cells. In the most extreme 

cases I will show it is possible to get a good set of 

variant calls for an individual where no sequencing 

has been done at all. 

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Session 8 

Bioinformatics Software 

NGS project analysis on small-scale computing (aka You did WHAT on a laptop) 



Biography 

Lesley Collins has extensive experience in 

working with NGS data and was instrumental in 

getting the Illumina Genome Analyser at Massey 

University up and running. Her hands-on approach 

has seen her tackle many NGS-focused 

bioinformatics demands and she will share her 

experience and knowledge with you in the postconference 

workshop. Lesley has been coursecontroller 

for highly successful Workshops on NGS 

and Bioinformatic workshops run over the last few 

years as well as researching and teaching in RNA 

evolution. Recently, Lesley edited the book "RNA 

Infrastructure and Networks". 

Abstract 

Benchtop NGS sequencing is now offering 

researchers a chance to answer genome-wide 

questions on smaller projects (and smaller 

budgets). However, these projects often do not 

have access to large computer servers or expert 

bioinformaticians without spending large parts of 

their research budget, so researchers try to do it 

themselves. The most common question that 

these DIYers ask is: How big does my computer 

have to be to get things done To address this 

question some publically available data was 

downloaded and run through two typical analysis 

pipelines on available desktop and laptop 

computers. This talk will present results to show 

what is at present possible for small-scale NGS 

analysis and where common problems lie. Of 

course with all bioinformatics, if symptoms persist, 

please seek professional advice. 

Geneious 

Shane Sturrock, Senior Scientist – Geneious Support and Professional Services 

Geneious Pro is a bioinformatics workbench developed by Biomatters Ltd. It is widely used for traditional 

alignment, phylogenetics and cloning work as well as more recently with NGS analysis. The software is 

extended by Geneious Server which provides seamless access to NGS tools on a 64 bit Linux server or 

cluster without requiring the user to run Linux themselves. This talk will provide an overview of the 

Geneious Pro application and server platform. 

Contact information: Biomatters Ltd, 76 Anzac Ave, Auckland. Tel: +64 9 379 5064. 


Graham Gaylard, Founder 

RTG Investigator bioinformatics application software applies the highest sensitivity in sequence alignment 

to deliver the most accurate results in downstream variant and metagenomic analysis. The product's 

plug-and-play bioinformatics tools enable researchers to deploy efficient and effective analysis pipelines 

in just days. Fast, comprehensive pipelines allow quick comparison of data from multiple sources, 

reducing false positives and increasing confidence in your results. http://www.clcbio.com 

Contact information: NZ: Real Time Genomics, 2nd Floor, 18 London Street, Hamilton 3493 USA: Real 

Time Genomics Inc., 576 Folsom Street, 2nd Floor, San Francisco, CA 94105. 

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LifeTech 

John Davis, Senior Field Bioinformatics Scientist 

As the volume of data produced via Ion Torrent semi conductor sequencing continues to increase, 

Torrent Suite software provides scientists with a powerful yet intuitive solution for data analysis. This talk 

will present the features of the Torrent Suite package, describing the workflows for basic analysis 

(reference alignment, variant calling, de novo assembly etc) and explaining how it’s functionality can be 

built upon via the Ion Torrent Plugin store. It will also illustrate how the community-driven open source 

nature of the software is driving continual improvement, meeting the needs of a wide variety of researcher. 

http://www.iontorrent.com/ 

Contact information: Jacqui Kent Tel: 09 578 3141, 021 775 995 


Tony Lough, Chief Executive 

New Zealand Genomics Limited – NZGL – is now providing New Zealand scientists with access to a 

genomic infrastructure to promote research throughout the country. Access to equipment and 

bioinformatic expertise for both small and large-scale genomics projects is provided via its collaborating 

partners at Massey, Otago and Auckland universities. 

Sequencing services on a HiSeq2000 have been operating since September 2011 at the Otago 

Sequencing Facility, MiSeq sequencing at Massey became operational in March 2012, and NZGL’s 

alliance with Auckland’s Centre for Genomics and Proteomics Sequencing now includes provision of 

further MiSeq capability, Ion Torrent and 454 GS Junior sequencing and a Microarray service. 

NZGL now has a distributed team of Bioinformaticians operating at each of the collaborators and 

providing services to clients. The final component of providing a fully integrated service package involves 

our delivery of Bio-IT and IT services, anticipated to be available in the last quarter of 2012. 

NZGL’s role is to provide genomics technology and bioinformatics services to New Zealand scientists – 

thereby underpinning research in a broad range of areas, including medicine, agriculture and the 

environment. NZGL’s Chief Executive will describe NZGL’s provision in its first year of service delivery, 

with examples of projects delivered to clients in New Zealand; and outline the future scope and 

possibilities for what the NZGL infrastructure can achieve. 

Contact information: Suite 6a, Centre for Innovation, 87 St David Street, Dunedin 9016 : PO Box 56, 

New Zealand. Phone +64 3 470 3543 

CLC 

Ray Hoare, Hoare Research Software 

Why you should use the CLC Bio Genomics Workbench Data analysis represents a serious bottleneck 

in NGS pipelines of most R&D departments, which in turn dramatically reduces the Return on Investment 

of current NGS assets. CLC Bio Genomics Workbench solves this problem by enabling researchers 

themselves to rapidly analyse and visualise genomic, transcriptomic, and epigenomic data from all major 

sequencing platforms. The user-friendly and intuitive interface essentially takes High Throughput Analysis 

away from hardcore bioinformatics programmers doing command-line scripts, and hands it to scientists 

searching for biological results. Furthermore, the versatile nature of CLC Genomics Workbench allows it 

to blend seamlessly into existing sequencing analysis workflows, easing implementation and maximising 

return on investment. CLC bio is the major player in this field - more than 100,000 users, more than 4,000 

licenses sold, to more than 500 organisations – the talk will show you why it has been so successful. 

http://www.clcbio.com 

Contact information: Hoare Research Software, 10 Grey St, Hamilton East, New Zealand. Phone +64 7 

839 9102 

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Session 9 

Gold Sponsor Presentation 

Current and imminent state of the art for Illumina’s sequencing technologies 

Brian Fritz 

Illumina 

Biography 

Brian Fritz is a Senior Field Applications Scientist 

with Illumina. Brian supports experimental design 

consulting, training, troubleshooting and a variety 

of other customer-support activities relating to 

Illumina’s genotyping and sequencing technologies 

and applications. His customer support portfolio 

runs from single researchers up to Genome 

Centers and encompasses diverse applications 

across agricultural, plant, wildlife, infectious 

disease and model organisms as well as researchuse 

only and translational human studies. Brian’s 

training and research background is in genetics, 

cell, molecular and developmental biology applied 

to model organisms and human research models of 

development, molecular evolution and disease. He 

holds a PhD from the University of Wisconsin- 

Madison and undertook Postdoctoral Research 

studies at the Fred Hutchinson Cancer Research 

Center in Seattle, WA (USA) before moving to 

Illumina in early 2008. 

Abstract 

Illumina develops, markets and supports innovative 

and integrated sequencing technologies, 

applications and data analysis solutions for genetic 

and genomic analysis. Our tools and services 

accelerate genetic analysis research and fuel 

advances in consumer genomics, diagnostics, 

plant and animal genetics and many additional 

applied genetics markets. In this presentation we 

will outline the current and imminent state of the art 

for Illumina’s sequencing technologies including the 

current output specifications for Illumina’s 

sequencing instruments. We will then detail 

Illumina’s current end-to-end workflows, from 

sample preparation through sequencing to 

analysis, for diverse DNA, RNA and epigenetic 

research applications. 

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Posters 

Posters are listed in alphabetical order by the surname of the presenter. 

Posters will be on display in the area to the rear of the conference room between 10am Tuesday 21 st 

August and 1pm Wednesday 22 nd August. An author associated with posters marked with an asterisk 

will present their research in a five minute presentation during the 3.30pm session on Tuesday 21st 

August. Directly after this session, at around 4.30pm finishing 6.30pm, there will be an opportunity to 

meet with the authors of all posters to ask them questions about their research. 

All posters marked with an asterisk have been entered into the poster competition with the posters being 

judged by the Conference Programme Committee and our two invited speakers. Cash prizes will be 

awarded to the posters judged the best. Prizes will be handed out during Session 9 at 3.20pm on 22 nd 

August. 

Poster 

Number 

Poster author/s 

Poster Title 

1 Christopher Brown Assembly and annotation of RNA-Seq data 

2 Gareth Gillard De novo transcriptome assembly of the New Zealand sea urchin Kina, 

to discover transcripts of proteins relating to undesirable colour 

change in the kina's roe. 

3* Hannah Henry A high-throughput DNA extraction method for sheep ear tissue. 

4* Maina Kokila Children with Birth Defects and Disability...An analysis of ethical and 

legal issues 

5* Thomas Lopdell Investigation of the UMD3 Bovine reference Genome 

6* Lucy MacDonald SNP discovery in Pinus radiata 

7* Xavier Pochon 

& S Wood 

Evaluating Detection Limits of Next Generation Sequencing for the 

Surveillance and Monitoring of International Marine Pests 

8 Jessie Prebble Populations genetics of the smallest forget-me-nots 

9* Ingrid Richter Protective biochemical response to biotoxins from sea squirts 

10 Kim Rutherford PomBase: a comprehensive database for Schizosaccharomyces 

pombe 

11* Miriam Sharpe Transcriptome of the New Zealand Glowworm, Arachnocampa 

luminosa 

12* Monika Zavodna Parallel tagged next-generation sequencing for population genetics 

and phylogeography: a case study using the New Zealand frog 

Leiopelma hochstetteri 

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List of Delegates 

Kelly Atkinson 

Operations & Business Development Manager 

The University of Auckland 

k.atkinson@auckland.ac.nz 


Senior Research Fellow 


lesleycollins.nz@gmail.com 

Hayley Baird 

Research Associate 

AgResearch 

hayley.baird@agresearch.co.nz 

Chris Couldrey 

Senior Scientist 

AgResearch 

christine.couldrey@agresearch.co.nz 

Zsuzanna Barad 

Assistant Research Fellow 


zsuzsanna.barad@otago.ac.nz 

John Davis 

Senior Field Bioinformatics Scientist 

Life Technologies 

john.davis2@lifetech.com 

Mik Black 

Senior Lecturer 


mik.black@otago.ac.nz 

Robert Day 

Post Doc 


robert.day@otago.ac.nz 

Rudi Brauning 

Computational Biologist 

AgResearch Limited 

rudiger.brauning@agresearch.co.nz 

Alicia Deng 

Account Manager/Applications Specialist 

Roche Diagnostics NZ Ltd. 

alicia.deng@roche.com 

Chris Brown 



chris.brown@otago.ac.nz 

Mark Fiers 

Bioinformatician 

Plant & Food Research 

mark.fiers@plantandfood.co.nz 

Sophia Cameron-Christie 

PhD Student 


sophia.cameron-christie@otago.ac.nz 

Angela Fleming 

Technical Officer 

Victoria University of Wellington 

angela.fleming@vuw.ac.nz 

Aniruddha Chatterjee 

PhD student 


chaan980@student.otago.ac.nz 

Michelle French 


AgResearch 

michelle.french@agresearch.co.nz 

Eng-Wee Chua 

PhD student 


engwee.chua@otago.ac.nz 

Anja Friedrich 

PhD Student 


a.friedrich@massey.ac.nz 

Shannon Clarke 


AgResearch 

shannon.clarke@agresearch.co.nz 

Brian Fritz 

Snr Field Applications Scientist 

Illumina 

bfritz@illumina.com 

John Cleary 

Chief Scientist 


john@realtimegenomics.com 

Graham Gaylard 

Business Development 


graham@realtimegenomics.com 

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Gareth Gillard 

MSc Student 


gilga472@student.otago.ac.nz 

Pam Keir 

Account Manager 

Roche Diagnostics 

pam.keir@roche.com 

Travis Glare 

Professor 

Bio-Protection Research Centre 

travis.glare@lincoln.ac.nz 


Research Professor 

University of Otago, Christchurch 

martin.kennedy@otago.ac.nz 

Wray Grimaldi 

PhD candidate 


griwr403@student.otago.ac.nz 

Hannah Kennedy 

MLT 

Canterbury District Health Board 

lloffhagen@orbit.co.nz 

Jo Hamilton 

Virology Technician 


Joanna.Hamilton@mpi.govt.nz 

Jacqui Kent 

Sales Specialist - Systems, New Zealand 

Life Technologies 

Jacqui.Kent@lifetech.com 

Chad Harland 

Sequence Analyst 


charland@lic.co.nz 

Anar Khan 

Science Team Leader 


linda.murray@agresearch.co.nz 

Michael Hendy 

Professor 

Otago University 

mhendy@maths.otago.ac.nz 

Gabe Kolle 

Technical Applications Scientist 

Illumina 

gkolle@illumina.com 

Nick Heng 



nicholas.heng@otago.ac.nz 

Rebecca Laurie 

Sequencing Manager 

Otago University 

becky.laurie@otago.ac.nz 

Hannah Henry 



hannah.henry@agresearch.co.nz 

Wellcome Ho 

Mycologist, Plant Pathologist 


wellcomeho@mpi.govt.nz 

Ray Hoare 

Managing Director 

HRS Ltd 

ray@hrs.co.nz 

Olga Kardailsky 

Research Technician 


olga.kardailsky@otago.anatomy.ac.nz 

Michael Keehan 

Senior Bioinformatician 

Livestock Improvement 

mkeehan@lic.co.nz 

Lia Liefting 

Principal Adviser 

Ministry of Agriculture and Forestry 

lia.liefting@maf.govt.nz 

Vincent Lui 

Database Manager 

Scion 

vincent.liu@scionresearch.com 

Si Lok 

Professor of Practice in Applied Genomics 


loks@cuhk.edu.hk 

Thomas Lopdell 

Research Statistician 

LIC 

tlopdell@lic.co.nz 

Tony Lough 

Chief Executive 


tony.lough@nzgenomics.co.nz 

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Ashley Lu 



ashley.lu@plantandfood.co.nz 

Barry Palmer 


Massey University, Wellington 

b.palmer@massey.ac.nz 

Lucy Macdonald 


Scion 

lucy.macdonald@scionresearch.com 

Duckchul Park 

Senior Technician 

Landcare Research 

parkd@landcareresearch.co.nz 

Simoene Macmil 

Postdoc Fellow 

University of Otago, Christchurch 

smacmil@gmail.com 

Sin Phua 

Scientist 


sin.phua@agresearch.co.nz 

Nauman Maqbool 

Science Team Leader 


nauman.maqbool@agresearch.co.nz 

Xavier Pochon 


The Cawthron Institute 

xavier.pochon@cawthron.org.nz 

Chris Mason 

Programmer 


chris.mason@anatomy.otago.ac.nz 

Jessie Prebble 

PhD student 

Massey University, Palmerston North 

jessie.prebble@gmail.com 


Doctoral candidate 


b.mccomish@massey.ac.nz 

Marian Price-Carter 

Scientist 

AgResearch 

Marian.Price-Carter@agresearch.co.nz 


Bioinformatics Software Engineer 

AgResearch 

alan.mcculloch@agresearch.co.nz 

David Pulford 

Virology Senior Scientist 


David.Pulford@mpi.govt.nz 

Les McNoe 

Research Fellow 


robyn.thomson@otago.ac.nz 

Josh Ramsay 

Postdoc 


joshramsay@gmail.com 


Academic 


m.morgan-richards@massey.ac.nz 


Postdoctoral Fellow 

Victoria University 

kristina.ramstad@vuw.ac.nz 

Eilidh Mowat 

Senior Technologist Plant Pathology 

Hill Laboratories 

rachelle.allan@hill-labs.co.nz 

Christy Rand 

Research Technician 


christy.rand@anatomy.otago.ac.nz 

Grant Munro 

Virology Manager 


grant.munro@mpi.govt.nz 

Ingrid Richter 

PhD student 

Cawthron Institute 

Ingrid.Richter@cawthron.org.nz 

Losia Nakagawa-Lagisz 

Research Assistant 


losialagisz@yahoo.com 

Euan Rodger 

Post-doctoral fellow 


Euan.rodger@otago.ac.nz 

Page 30

! 

Kim Rutherford 

Computer Programmer 

University of Cambridge 

kmr44@cam.ac.uk 

Paul Sutherland 

Agriculture Division Manager 

Hill Laboratories 

rachelle.allan@hill-labs.co.nz 

Andrew Scott 

Project Manager 

LIC 

andrew.scott@lic.co.nz 

Yoo Techataweewan 

PhD Student 


nawaporn.techataweewan@anatomy.otago.ac.nz 

Jenny Shackelford 

Business Manager 


jenny.shackelford@nzgenomics.co.nz 



AgResearch 

tracey.vanstijn@agresearch.co.nz 

Miriam Sharpe 

Postdoctoral Research Fellow 


miriam.sharpe@otago.ac.nz 

Kylie Warner 

Product Manager - Agilent Genomics 

Pacific Laboratory Products 

kyliew@pacificlab.com.au 

Karl Sluis 

Territory Account Manager, New Zealand 

Illumina 

ksluis@illumina.com 

Liam Williams 

Genomics Facility Manager 

The University of Auckland 

lc.williams@auckland.ac.nz 




richard.spence@mpi.govt.nz 

David Wharton 

Associate Professor 


david.wharton@otago.ac.nz 

Jo Stanton 

Senior Research Fellow 


jo.stanton@anatomy.otago.ac.nz 

Daniel White 


Landcare Research 

whited@landcareresearch.co.nz 




peter.stockwell@otago.ac.nz 

Susie Wood 


The Cawthron Institute 

susie.wood@cawthron.org.nz 

Roy Storey 



roy.storey@plantandfood.co.nz 

Steve Wylie 

Senior Research Associate 

Murdoch University 

s.wylie@murdoch.edu.au 

Shane Sturrock 


Biomatters Ltd 

shane@biomatters.com 

Monika Zavodna 

Post-doctoral fellow 


monika.zavodna@otago.ac.nz 

Thank you for joining us for the 2012 New Zealand Next Generation Sequencing Conference. 

We will contact you by email when details of the 2013 New Zealand Next Generation Sequencing 

Conference are available. 

We look forward to hosting you again next year. 

Page 31

New Zealand Next Generation Sequencing Conference - Innovative ...

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