New Zealand Next Generation Sequencing Conference - Innovative ...

!
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
Livestock Improvement Corporation
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
The Chinese University of Hong Kong
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
Page 17