From James.Kijas csiro.au Mon May 7 22:55:54 2012
From: <James.Kijascsiro.au>
To: Multiple Recipients of <sheepmodelsanimalgenome.org>
Subject: Minutes from Sheep Genomics Consortium Call #100
Date: Mon, 07 May 2012 22:55:54 -0500
Hello everyone,
With apologies for cross-posting, please see below the minutes from the most
recent meeting of the International Sheep Genomics Consortium.
Best Regards
James
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
.To: Kijas, James (LI, St. Lucia); Alan Archibald; ancartatiscali.it;
arsenosgvet.auth.gr; atcgnmbiyahoo.com.cn; banosvet.auth.gr; Barendse, Bill
(LI, St. Lucia); beatriz.gutierrezunileon.es; Ben Hayes;
Bertrand.Servintoulouse.inra.fr; Brian Sayre; c.wadeusyd.edu.au; Carole
Moreno; cbottemawaite.adelaide.edu.au; cemal_iyahoo.com;
chanda.nimbkargmail.com; choijungwooneo.tamu.edu;
chris.warkupgenesis-faraday.org; clare-gilltamu.edu;
cord.droegemuelleritz.unibe.ch; curtvtanri.barc.usda.gov;
cyril.robertscavehill.uwi.edu; Dalrymple, Brian (LI, St. Lucia);
dave.burtroslin.ed.ac.uk; david.machughucd.ie; David.Mageeucd.ie;
dcoltmanualberta.ca; del2aber.ac.uk; despoina.miltiadoucut.ac.cy;
elenacianibiologia.uniba.it; fanoellecc.usu.edu; faruque_mdomaryahoo.com;
fdrivermla.com.au; franknvetsci.usyd.edu.au; fyubcm.tmc.edu;
gcamillumina.com; Georg.Erhardtagrar.uni-giessen.de; Gibbs, Richard (TMC) -
Contact; gootwinevolcani.agri.gov.il; h.blairmassey.ac.nz;
h.jianlincgiar.org; hans.daetwylerdpi.vic.gov.au; hsimiangwdg.de;
Hutton.Oddyune.edu.au; Huw Jones; huw.jonesgenesis-faraday.org; iabnsg.no;
j.a.lenstrairas.uu.nl; j.bennewitzuni-hohenheim.de; j.pembertoned.ac.uk;
j.slatesheffield.ac.uk; JGreeffagric.wa.gov.au; jhcalvoaragon.es; Jiang, Yu
(LI, St. Lucia); jillm (UNIMELB) - Contact; jjarrsunileon.es;
jmm1ualberta.ca; John.Daniasdownstate.edu; john.mcewanagresearch.co.nz;
juha.kantanenmtt.fi; julius.vanderwerfune.edu.au; K.Marshallcgiar.org;
Keith.Ballingallmoredun.ac.uk; kgietzenillumina.com;
lherrmanvetmed.wsu.edu; Li, Yutao (LI, St. Lucia); Lutz.Bungersac.ac.uk;
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martykardosgmail.com; massoud.malekiaea.org; matthew.peter.kentumb.no;
McWilliam, Sean (LI, St. Lucia); mike heaton; mohammadvetsci.usyd.edu.au;
msalyayahoo.com; msanderyillumina.com; neelamgnbagrgmail.com;
neil.gemmellotago.ac.nz; ocobanoglunku.edu.tr;
Ottmar.Distltiho-hannover.de; paolo.ajmoneunicatt.it;
PAScheetmdanderson.org; Paul.Boettcherfao.org; Paul.Goodingagrf.org.au;
pillaunimol.it; pradeepaspdn.ac.lk; Raadsma (AR - SGP HRSP) - Contact;
rgodfreuvi.edu; riccardo.negriniunicatt.it; richard.talbotroslin.ed.ac.uk;
Rudiger.Brauningagresearch.co.nz; samuelcenargen.embrapa.br;
Shannon.Clarkeagresearch.co.nz; simon.boitardtoulouse.inra.fr;
sqanbargwdg.de; stefan.hiendlederadelaide.edu.au;
stephen.bishopbbsrc.ac.uk; Steve Moore; swhitevetmed.wsu.edu; Tellam, Ross
(LI, St. Lucia); Thomas.Farauttoulouse.inra.fr; tizianasechigmail.com;
tlonghurstmla.com.au; vs.guptancl.res.in; wangjgenomics.org.cn; Worley, Kim
(BCM) - Contact; wwangmail.kiz.ac.cn; xuxungenomics.org.cn; zhuiastate.edu;
'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
James Kijas
Principal Research Scientist
Stream Leader: Genetics and Genomics Products and Services
CSIRO Livestock Industries
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