From xuxun genomics.cn Tue May 8 22:29:41 2012
From: =?gb2312?B?0OzRtg==?= <xuxungenomics.cn> (by way of Jill Maddox
<jillian.maddoxalumni.unimelb.edu.au>)
Subject: Re: Minutes from Sheep Genomics Consortium Call #100
To: Multiple Recipients of <sheepmodelsanimalgenome.org>
Date: Tue, 08 May 2012 22:29:41 -0500
Hi Claire,
We can start from the blood or other tissues if
high quality DNA is a problem. Sequencing give
out real sequence data instead of signal, which
helps a lot for identify the garbage. The new
advance in sequencing now able to set up in any
labs with low cost and high stability. Illumina
and Lifetech even provide one-button solution for
the whole process. Oxford Nanopore will provide
thumb-disk-size sequencer. I believe these new
advance will help a lot in molecular breeding. We
really want to help the sheep research and
breeding community as what we did before by free
donation of the sheep genome, while we are actually not do any sheep
breeding.
Best,
Xun
On 12-5-9 上午9:06, "Claire Wade" wrote:
Hi all,
while I concur with Xun that genotyping by
sequencing offers many advantages over the use of
arrays, one of the big problems with it that we
have been struggling with is the requirement for
high quality DNA. Buccal samples will be
unsuitable due to bacterial contamination, blood
samples need special care. Buccal samples are
also unsuitable for RAD due to their alteration
of DNA fragment sizes as a result of
degradation. Sequencing really is a garbage in
garbage out situation with (Illumina) arrays
being quite robust to poor DNA quality. The
ongoing availability of arrays does remain an issue of concern.
Claire
Claire Wade | Professor, Chair of Computational Biology and Animal Genomics
Veterinary Science
University of Sydney
RMC Gunn B19-504
Regimental Cres
University of Sydney NSW 2006
AUSTRALIA
<mailto:claire.wade@sydney.edu.au>claire.wadesydney.edu.au | e
+61 2 9351 8097 |v
+61 2 9351 3957 |f
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.Cc: 陈文彬; 刘心; 韩长磊; 原辉; 谢敏
.Subject: Re: Minutes from Sheep Genomics Consortium Call #100
Hi James and all,
Sorry that I did not able to attend the consortium meeting for a period.
I notice in the argument for genotyping platform.
I think the current progress of sequencing
technology is with many advantages beyond array
based genotyping. GBS and RAD will be a good
choice for molecular breeding, with much cheaper
cost and more efficiency workflow. If you still
feel that those markers are not meet your needs,
another choice will be target region capture and
sequencing, which will specifically target those
700k SNP sites. However, I still believe GBS and
RAD will be the best choice and practice for
molecular breeding. BGI would like to help on
those. How about the following collaboration:
(1) BGI will design the capture array, target 700K SNP sites.
(2) BGI sequencing 7000 samples for the
consortium for these 700k SNP sites by the price
of 300USD (the same price as illumine offered for only Chips)
(3)BGI will do BGS for all these samples by our own cost.
(4)The consortium and BGI will work together to
compare if GBS can replace those high density
genotyping in breeding and other practice.
Best,
Xun
On 12-5-8 上午10:47,
"<mailto:James.Kijas@csiro.au>James.Kijascsiro.au" wrote:
Minutes from ISGC Conference Call #100
Participants: James Kijas, Brian Dalrymple,
Gwenola Tosser, Kristen Nowak, Steven White, John
McEwan, Jiang Yu, Rudi Brauning, Hans Daetwyler,
Josh Miller, Kim Worley, Richard Hodgson, Jill
Maddox. The minutes were recorded by the
secretary (JK) from the meeting held at 8am QLD time, May 8th 2012.
1. Release of sheep genome assembly v3.0
Jiang Yu provided the group with a summary of
progress made towards the release. He has now
completed construction of the masked version of
all chromosomes, and is on schedule to release
v3.0 at the end of this week. The improvements
incorporated in v3.0 involve gap filling.
Approximately 50% of the gaps present in v2.0
have been filled, with the percentage of the
genome in gaps reduced from 7% to 2.5%. The N50
contig length has improved, and there has been a
slight increase in the amount of coding regions
represented. Checking has been performed between
v2.0 and v3.0 using the location of SNP on the
SNP50 Beadchip. Very high levels of consistency
were observed, indicating few higher order changes have been made.
The team discussed what actions are to be
included in the genome release. Brian confirmed
v3.0 will be made available via the
livestockgenomics gbrowser, and that work to
accomplish this is well underway. Kim will
provide the team with their requirements for
submission to NCBI and the files needed to remap
the raw reads. This will require FASTA formatted
sequence and AGP files describing the arrangement
of contigs into scaffolds. Kim and Jiang Yu will
work together to transfer v3.0 to Baylor. In a
past communication, Kim indicated that remapping
the reads to generate v3.0 BAM files for the 75
genomes would require between 2 and 3 weeks.
2. Whole Genome Sequencing Experiment: HD Chip
John promoted discussion about the logic of
constructing an HD chip in light of the rapidly
changing sequencing technology and genotype by
sequencing (GBS) methods. He put the view that in
light of the large effective population size for
most sheep populations, that it would difficult
to see how existing methods could effectively be
used to sequence sufficient animals (tens of
thousands). To achieve compatibility with
existing SNP50 datasets, some combination of GBS
mixed with imputation would be required, which
again may be difficult given the high Ne in
sheep. Hans noted that imputation from SNP50 up
to whole genome sequence would benefit from an
intermediate such as an HD chip, while noting
that the GBS technology is advancing very
quickly. Gwenola indicated that an HD chip would
be useful, and no one across the group voiced a
strong opinion against proceeding with an HD chip.
James provided feedback about the communities
likely uptake of an HD chip. Illumina set up a
web based collection point for registrations of
interest to purchase an HD chip at three price
points. The result were that at $120 USD /
sample, interest was received to genotype 27,700
samples. Assuming $200 USD / samples, this
decreased to 13,800 samples and at $300 USD /
sample it went down to 6,800 samples. He then
characterised the strengths of the two providers
of HD genotyping. No decision was taken regarding
the choice of provider. John indicated that price
is his primary driver, above technical
perfection. The group will work towards a
deadline of December 2012 to have chips manufactured and distributed.
The team discussed design criteria for a chip
housing 700K SNP. John suggested as a starting
point inclusion of four sets of SNP:
1. SNP on the existing SNP50 Beadchip
2. Special interest SNP. This might include
GDF8/myostatin, monogenic disease SNP, PRNP SNP,
markers across the MHC etc. Jill is working to compile a likely list.
3. Minimum MAF SNP across breeds. These to be
identified primarily from the diversity panel of 75 re-sequenced genomes.
4. Exonic and Loss of Function (LOS) SNP.
Following SNP annotation against the available
gene models, SNP to be include that are predicted to ablate protein function.
The group decided that a 1 page design document
needs to be distributed, debated and finalised by
consensus. This seeks to ensure that everyone has
input and we construct a chip that serves the
communities best interests. John will write a draft and distribute.
3. ISGC Workshop at ISAG
James has approached Cindy about arranging a
meeting time and room during ISAG for the group
to meet in person. Cindy indicated this should be
possible, and a tentative time was given for
Thursday lunch. James will distribute the details when finalised.
4. Other Business
Brian noted the meeting with the 100th in the
series, and thanked James for organising the calls.
James briefed the group on progress with
development of a SNP panel for parentage in
Australia, and renewed the intension to take the
89 core ISGC SNP to ISAG for accreditation. James
will work with Gwenola and other members of the
ISAG committee to identify exactly what materials
are required to receive accreditation.
This closed the meeting. Please write to the
secretary to correct any serious errors or omissions
Best Regards
James
.From: Kijas, James (LI, St. Lucia)
.Sent: Monday, 30 April 2012 10:59 AM
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<mailto:simon.boitard@toulouse.inra.fr>simon.boitardtoulouse.inra.fr;
<mailto:sqanbar@gwdg.de>sqanbargwdg.de;
<mailto:stefan.hiendleder@adelaide.edu.au>stefan.hiendlederadelaide.edu.au;
<mailto:stephen.bishop@bbsrc.ac.uk>stephen.bishopbbsrc.ac.uk;
Steve Moore;
<mailto:swhite@vetmed.wsu.edu>swhitevetmed.wsu.edu;
Tellam, Ross (LI, St. Lucia);
<mailto:Thomas.Faraut@toulouse.inra.fr>Thomas.Farauttoulouse.inra.fr;
<mailto:tizianasechi@gmail.com>tizianasechigmail.com;
<mailto:tlonghurst@mla.com.au>tlonghurstmla.com.au;
<mailto:vs.gupta@ncl.res.in>vs.guptancl.res.in;
<mailto:wangj@genomics.org.cn>wangjgenomics.org.cn;
Worley, Kim (BCM) - Contact;
<mailto:wwang@mail.kiz.ac.cn>wwangmail.kiz.ac.cn;
<mailto:xuxun@genomics.org.cn>xuxungenomics.org.cn;
<mailto:zhu@iastate.edu>zhuiastate.edu;
<mailto:'hans.daetwyler@dpi.vic.gov.au>'hans.daetwylerdpi.vic.gov.au';
'Matukumalli, Lakshmi'; Brew, Fiona; 'Hodgson, Richard'
.Subject: Agenda for Sheep Genomics Consortium Call #100
Hi everyone,
I have scheduled a sheep consortium call for next
week. There is a lot going on, even if our
conference calls are only intermittent. Hope you
can join the call for what will be the 100th time
Cheers, James
Time:
Location Local time Time zone UTC offset
Brisbane (Australia - Queensland) Tuesday,8 May
2012 at 8:00:00 AM EST UTC+10 hours
Melbourne (Australia - Victoria) Tuesday, 8 May
2012 at 8:00:00 AM EST UTC+10 hours
Wellington (New Zealand) Tuesday, 8 May 2012 at 10:00:00 AM NZST UTC+12 hours
Edmonton (Canada - Alberta) Monday, 7 May 2012 at 4:00:00 PM MDT UTC-6 hours
Houston (U.S.A. - Texas) Monday, 7 May 2012 at 5:00:00 PM CDT UTC-5 hours
San Diego (U.S.A. - California) Monday, 7 May
2012 at 3:00:00 PM PDT UTC-7 hours
Lincoln (U.S.A. - Nebraska) Monday, 7 May 2012 at 5:00:00 PM CDT UTC-5 hours
London (United Kingdom - England) Monday, 7 May
2012 at 11:00:00 PM BST UTC+1 hour
Agenda
1. Release of sheep genome assembly v3.0
Brian and Yu to present v3.0. Group to be updated
on the activities that have been performed, and
any QC that is still left to do. Major topic for the call.
2. Whole Genome Sequencing Experiment: SNP
calling and variant annotation: HD chip
Groups have been waiting on v3.0 before
re-mapping the reads from the 75 genomes, meaning
there may not be much progress to report. John
and James can provide a summary of discussions
across the community relating to construction of
the HD chip. Based on the status of item 2, team
to discuss a timeline for creation of the HD
product. Jill to report on feedback concerning
inclusion of known causal mutations.
3. ISGC workshop at ISAG Conference
James to report on details for an ISGC face to face at ISAG.
4. Other Business
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://conferencin
g.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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