New Zealand Next Generation Sequencing Conference - Innovative ...

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New Zealand Ostreid herpesvirus – application of high throughput sequencing in a
biosecurity context
Richard Spence
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
Livestock Improvement Corporation
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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