From James.Kijas csiro.au Thu Jul 12 19:09:44 2012
From: James.Kijascsiro.au (by way of Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>)
To: Multiple Recipients of <sheepmodelsanimalgenome.org>
Subject: Minutes from Sheep Consortium Call #101
Date: Thu, 12 Jul 2012 19:09:44 -0500
Minutes from ISGC Conference Call #101
Participants: Daniel Pomp, James Kijas, Gwenola
Tosser, Kristen Nowak, John McEwan, Rudi
Brauning, Shannon Clarke, Hans Daetwyler, Kim
Worley, Cindy Lawley, Jill Maddox. The minutes
were recorded by the secretary (JK) from the
meeting held at 8am QLD time, July 12th 2012.
1. Whole Genome Sequencing Experiment: Remapping to v3.0 and SNP calling
The call commenced with a summary of progress in
the project. James indicated that weekly calls
have been held involving teams from Baylor (Kim
et al), DPI Victoria (Hans), AgResearch (Rudi et
al) and CSIRO (James et al). Kim provided a
summary of the work completed on 75 genome
sequences. Raw reads (> 2800 Gb) were initially
mapped to the ovine reference assembly version
2.0, but have now all been remapped to the
upgraded v3.0 assembly. In a parallel process
that has not yet been completed, v3.0 is being
submitted to NCBI. Kim described how the mapped
reads were processed through their variant
detection pipeline, and the results (.bam and
.vcf files) distributed. The status of the work
is summarised in the attached poster which has
been prepared for presentation at ISAG next week.
2. Whole Genome Sequencing Experiment: HD Chip Design and Manufacture
James indicated the objective of the call was to
gather opinion from across the group on the
choice of technology provider for an HD chip, and
he made the point this was the last opportunity
before the decision is taken. As John has been
running the process, James asked that he give a
summary of the situation until now. John
described consideration of three options for
collecting high density (> 500,000 loci) genotypes:
1) an Illumina HD SNP chip
2) an Affymetrix HD SNP chip
3) Genome by Sequencing (GBS)
John noted that by their calculation, GBS is
currently likely to cost between 2 and 5 times
more per animal than an HD chip, and was
therefore eliminated as a plausible option for
making progress in the coming few years. The
focus was therefore restricted to the first two
options, and he listed the parameters the group
is likely to use during the design phase of chip construction. This
included:
- special interest SNP, most of which will be known functional mutations
- SNP on the existing 50K and 5K platforms. This
seeks to build in reverse compatibility to all our existing datasets
- evenly spaced SNP across the genome.
- loss of function SNP
- exonic and UTR (transcribed) SNP (up to 100K)
- SNP with a range of MAF
- SNP in regions accessed by popular GBS methods.
This seeks to build in forward compatibility with GBS approaches
He has requested quotes from the two providers
which had the following specifications:
- a technical validation step is required using
192 samples. We would use the same animals
sequenced in the WGS experiment to QC the SNP calls, plus IMF
- assumes SNP lists are made available by the
consortium for preliminary assay design during August
- assumes the design (SNP list) will be finalised in Sept / Oct
- assumes the validation step can be completed,
and the first batch of chips distributed for use in mid Jan 2013
- asked for pricing at volumes points of 10K, 15K
and 20K samples across the community
John noted that the quoted prices were very
similar when compared between providers. The
indicative range in reagent cost per sample (in
USD) was $130 - $200 from both providers, for
volumes that we anticipate can be achieved by the
community. In the absence of a compelling price
differential, the group discussed considerations
around the technology and access to genotyping
hardware. Opinions from around the group:
Daniel: suggested there was no clearly better
route. He provided a perspective across the last
few years, where he noted that Affymetrix have
devoted time and expertise to get to the point
the decision was now difficult. He indicated that
sample throughput for a very high volume project
(where 10s K of samples need to be genotyped in a
short time) was more difficult with the Gene
Titan (Affy), however the group felt this was
unlikely to be a problem for a sheep HD chip.
Daniel indicated the costs associated with
providing a genotyping service (ie the cost in
addition to the reagent cost) would be about the
same for the two alternatives, and had no strong
advice towards either Illumina or Affymetrix. The
group thanked Daniel for participating in the
call as an important provider of genotyping to the community.
Gwenola: noted that they have an Illumina machine
which would make it more convenient if Illumina was selected
James: noted CSIRO has an Illumina machine, and
an interest in performing non-standard analysis off the raw intensity reads.
Hans: VicDPI has an Illumina machine, but voiced no strong perference
John: was pressed to give his view, reiterated
that he was primarily interested in hearing the
view of the group. He noted that they have an
Illumina machine, but would seek to obtain a Gene
Titan if the chip was an Affy product.
The decision will be made in a call attended by
the team that has done the development work and
those likely to be major purchasers of the tool.
3. “Next Steps” workshop at ISAG Conference
The opportunity exists to hold a face to face
meeting next week at the International Society of
Animal Genetics meeting in Cairns, Queensland,
Australia. James asked what higher level
considerations the group should debate, so he can
develop an agenda. Suggestions included:
- coordinated collection of publically available
RNAseq datasets, and use in the development of accurate gene models
- coordination of the USDA genome grant /
project. James noted that calibration to how the
grant is deployed may be required in light of the
rate of progress in the genome and re-sequencing project.
- genome annotation. Explore how groups
interested in contributing manual annotation can fit into the plans at EBI
Following the meeting, James finalised the time
and draft agenda with Cindy Bottema (ISAG organiser) as follows:
Thursday 19 July - Meeting Room 4
12:45 pm – 2:00 pm
International Sheep Genomics Consortium Meeting
Co-Chairs: Noelle Cockett and James Kijas
The format for the meeting will be ‘open discussion’ to consider:
Progress with reference genome assembly v3.0
Progress with the whole genome re-sequencing project
Future plans: genome annotation, genome browser etc
Future plans: Coordination and use of RNAseq data
Other business raised by participants
That concluded the meeting. If there are serious
errors or omissions contained within these
minutes, please contact the secretary
Cheers
James
On Behalf of the ISGC
.From: Kijas, James (CAFHS, St. Lucia)
.Sent: Monday, 9 July 2012 4:21 PM
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.Subject: Time and Agenda for Sheep Consortium Call #101
Hi everyone,
I have scheduled a sheep consortium call for
later this week in the run up to the
International Society of Animal Genetics (ISAG)
conference. The focus will be on updating the
wider group about the activities within the whole
genome sequencing project, and a key debate
relating to the choice of platforms for building
the sheep HD SNP chip. Agenda, time and dial in details are below
Cheers, James
Agenda
1. Whole Genome Sequencing Experiment: Remapping to v3.0 and SNP calling
A subgroup has been meeting weekly to drive the
project forwards. The status will be reported,
including progress with remapping all of the raw
reads to v3.0 of the reference genome, analysis
of the resulting .bam and .vcf files for the 75
genomes and the workflow for SNP calling.
2. Whole Genome Sequencing Experiment: HD Chip Design and Manufacture
Group to debate the alternatives for manufacture
of the HD chip. This is the last opportunity to
voice an opinion as the decision needs to be
finalised prior to the ISAG conference.
3. “Next Steps” workshop at ISAG Conference
James has arranged a room and time for an ISGC
meeting at ISAG. This is an opportunity to
discuss top level / strategic directions for the
consortium. Group to develop draft agenda for the meeting.
4. Other Business
Time:
Location Local time Time zone UTC offset
Brisbane (Australia - Queensland) Thursday, 12
July 2012 at 8:00:00 AM EST UTC+10 hours
Melbourne (Australia - Victoria) Thursday, 12
July 2012 at 8:00:00 AM EST UTC+10 hours
Wellington (New Zealand) Thursday, 12 July 2012
at 10:00:00 AM NZST UTC+12 hours
Beijing (China) Thursday, 12 July 2012 at 6:00:00 AM CST UTC+8 hours
Paris (France) Midnight between Wednesday, 11
July 2012 and Thursday, 12 July 2012 CEST UTC+2 hours
Cardiff (United Kingdom - Wales) Wednesday, 11
July 2012 at 11:00:00 PM BST UTC+1 hour
Salt Lake City (U.S.A. - Utah) Wednesday, 11 July
2012 at 4:00:00 PM MDT UTC-6 hours
Lincoln (U.S.A. - Nebraska) Wednesday, 11 July
2012 at 5:00:00 PM CDT UTC-5 hours
Houston (U.S.A. - Texas) Wednesday, 11 July 2012 at 5:00:00 PM CDT UTC-5
hours
Corresponding UTC (GMT) Wednesday, 11 July 2012 at 22:00:00
Dialling Information
To join, you will need to:
1. Dial the TollFree number which corresponds to your location
Tollfree AUSTRALIA:
1800 681583
Tollfree NORTHERN CHINA:
1080 06100311
Tollfree SOUTHERN CHINA:
1080 02610311
Tollfree FRANCE:
0800 907046
Tollfree HONG KONG:
800 900194
Tollfree NZ:
0800 443188
Tollfree UK:
0800 0281738
Tollfree USA:
1877 4974432
2. When prompted by the recorded voice, enter the
ACCOUNT NUMBER and PIN followed by the HASH (#) KEY.
The Account Number is: 76309443
The Pin is: 0863
That should link you into the conference call.
For additional information on the process you can visit:
<http://conferencing.telstra.com/solutions/SHphone_Kit.pdf>http://conferenci
ng.telstra.com/solutions/SHphone_Kit.pdf
James Kijas
Principal Research Scientist
Stream Leader: Genetics and Genomics Products and Services
CSIRO Livestock Industries
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