From James.Kijas csiro.au Mon Feb 8 20:36:04 2010
From: "James Kijas" <James.Kijascsiro.au>
Postmaster: submitted from web posting form
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: International Sheep Genomics Consortium Newsletter#1
Date: Mon, 08 Feb 2010 20:36:04 -0600
This is the first newsletter from the ISGC. Our aim for these short
information sheets is to provide a summary of our activities and to
encourage participation from researchers who have a common interest in
the genomics of sheep. We will be distributing a newsletter every 4
months
Best Regards, James Kijas
ISGC Secretary (James.Kijascsiro,au)
SNP50 BeadChip Starts to Leave its Mark
Release of the ovine SNP50 BeadChip in January 2009 represented a
landmark for the consortium. The chip, developed by researchers from
AgResearch, Baylor UCSC, CSIRO, and USDA in partnership with Illumina
Inc, contains approximately 50,000 SNPs that are evenly spaced across
the sheep genome. Research groups across the community started using
the tool as soon as it became available, and the Plant and Animal
Genome conference in January was the first time many of the results
were presented. High call rates across populations and good quality
data was reported by each of the groups. The chip has been used to
successfully map a number of single gene traits including
chondrodysplasia in Texels, yellow fat in Perendales (picture provided
by John McEwan) and microphthalmia in Texels. Other data presented
included GWAS for infectious disease (White et al), detailed analysis
of genetic diversity and the impact of selection across breeds (Kijas
et al) as well as a first look at genome wide levels of linkage
disequilibrium (Raadsma, Khatkar, Hayes et al). Copies of the abstracts
are available (http://www.intl-pag.org/) and the presentations have
been uploaded at (http://www.sheephapmap.org/pag.php). Looking forward,
the first half of 2010 is likely to see many more results emerge,
particularly from researchers within the ISGC HapMap project which will
be the focus of the next newsletter.
Background on the Design of the SNP50 BeadChip
We are regularly asked what strategy was used to design the 50k chip
and whether any known functional mutations were included on it.
Illumina required that the SNP selection process exclude any DNA
variants with known intellectual property claims. As a result the
consortium was unable to include any SNP, which at the time, were known
to directly underpin disease or production phenotypes. The consortium
developed an algorithm which used genomic position, predicted MAF, SNP
type and assay suitability to select 49,545 SNP. Some were also chosen
based on how well they performed in the pilot 1.5k SNP project (Kijas
et al., 2009). In addition a SNP on chromosome Y was included, along
with several mitochondrial SNPs and some SNPs representing unpositioned
sequences (ChrUn). We also endeavoured to include as many SNPs as
possible from the parentage SNP set that is being developed by Mike
Heaton (http://cgemm.louisville.edu/...sheep/isgc_snps.html). The
algorithm used for SNP selection was developed by Wes Barris and Brian
Dalrymple (CSIRO) and further details will be published during 2010.
Ongoing Access of the SNP50 Chip and a New Low Density Array
Interest is growing for the consortium to again coordinate placement of
a large order (> 10,000 samples) for SNP50 genotyping later in 2010.
Feedback gathered at PAG indicates likely demand from Utah State,
USDA/ARS, EU 3SR, U Wyoming, AgResearch, U Sydney and Virginia Tech is
projected to exceed 8,000 samples and representatives from additional
groups (eg sheepCRC and INRA) were not present. The team from Illumina
reaffirmed their ongoing willingness to work with the consortium on
pricing. The consortium encourages anyone intending to purchase chips
to register their interest with John McEwan
(john.mcewanagresearch.co.nz), James Kijas (james.kijascsiro.au) and
Diane Lince (dlinceillumina.com). Looking beyond the existing product,
a group led by John McEwan is working on design of a 3 – 5K Golden Gate
chip. The opportunity exists to manage the content and associated cost
through coordination across the community, contact John for details.
Work Underway on the Reference Genome
The consortium’s major planned activity for 2010 is construction of the
sheep reference genome. The work is being coordinated by Alan Archibald
and Richard Talbot (Roslin Institute), Donna Muzny and Richard Gibbs
(Baylor College of Medicine), John McEwan and Rudi Brauning
(AgResearch), Brian Dalrymple and James Kijas (CSIRO Livestock
Industries), Hutton Oddy (University of New England) and Noelle Cockett
(Utah State University). The operational approach consists of two
stages. In the first phase, a mix of Next Gen sequence will be
generated at the Roslin Institute (Illumina GAII) and Baylor College
(454) using the single inbred Texel ram used previously for
construction of a CHORI BAC library and the virtual sheep genome. The
resulting sequence will be assembled and evaluated before a second
phase of sequencing is undertaken to fill gaps and improve the interim
de novo assembly.
The first phase commenced in December 2009 at the Roslin Institute and
preliminary evaluation of the first 40 Gb of sequence returned
promising results. The team at the Roslin is working to generate a 30 x
genome coverage using 100 bp paired end reads from libraries
constructed across a range of insert sizes (220 bp up to 5 kB). To
assist in the assembly process, researchers at Baylor College will
focus on 454 sequencing of larger insert libraries (8 – 20 kB). All of
the data will be deposited in the public domain and the assembly made
available for the benefit of the research community.
Additional information on the activities of the ISGC can be found at
http://www.sheephapmap.org
The ISGC represents a community of those interested in sheep genomics.
It is free to join and the only requirement is that you have an
interest in sheep genomics. The ISGC has regular phone meetings,
generally each fortnight, on Tuesdays at 9:00 a.m. Australian Eastern
Standard time and minutes of the meetings are placed on the ISGC web
site (http://www.sheephapmap.org/).
ISGC funding comes from participants pooling their resources to drive
projects that are of interest to the genomics community. Where
researchers recognise potential value in leveraging their funding
applications with other researchers in the field, they are encouraged
to interact within the consortium. Our aim is to achieve maximal
benefit for the sheep genomics community from the sometimes limited
funding for available ovine genomics.
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