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Pig Genome Newsletter #122
From cktuggle@iastate.edu Thu Oct 1 11:45:06 2015
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmap@animalgenome.org>
Subject: US Pig Genome Newsletter #122
Date: Thu, 01 Oct 2015 11:45:06 -0500
Pig Genome Update # 122:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.122.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.122.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 122 ****************
* *
* October 1, 2015 *
*****************************************
==========================================================================
1. Summer meetings summary- ISAFG and JAM
2. Update on new functional genomics project FAANG – Washington Meeting
Oct 7-8, 2015
3. Reminder on PAG registration and abstract deadlines.
4. Upcoming additional meetings information
5. Recent conference call of Swine genome interest group initiated
6. We want to hear from you!
==========================================================================
1. Description of important summer meetings attended by Coordinators
The two Coordinators split responsibilities to cover summer meetings this
year; Dr. Tuggle attended the International Symposium on Animal Functional
Genomics (ISAFG) in Piacenza, Italy, and Dr. Ernst attended the American
Society of Animal Science/American Dairy Science Association Joint Annual
Meeting (JAM) in Orlando, Florida. Here is a brief summary of what was
discussed at these two meetings.
a. ISAFG
The 6th International Symposium on Animal Functional Genomics (ISAFG 2015)
was held in Piacenza, Italy from the 27th to the 29th of July, 2015.
The purpose of ISAFG 2015 is to bring together academic researchers, industry
representatives and policy makers to exchange knowledge on the leading-edge
developments in functional genomics and its applications in the livestock
sector. The symposium themes included important topics, ranging from
structural and comparative genomics to systems biology. (ISAFG website; see
http://www.isafg2015.it/) Although Piacenza was very hot in July, the
accommodations and science were excellent. The Conference Themes included
Comparative genomics, Epigenetics, Transcriptomics, Proteomics, Microbiome,
Systems Biology. Speakers describing porcine genomics included M. Groenen who
described his recent work on selective sweeps (Frantz nature Genetics 2015)
and the effect of such selection- associated genotypes on phenotypes. A.
Archibald discussed how animal genomics data can enable prediction, and
outlined how the new FAANG project can accelerate the development of such
data. T. Sonstegard described his new position at Acceligen, where the focus
is genome editing to improved practical phenotypes in swine as well as work
at a related company Surrogen to create swine models for biomedicine. T.
Smith described his new results using PacBio technology to generate a genome
assembly from a Duroc/Landrace/Yorkshire cross pig. The 187 Gb of data looks
very good, and he expects to be able to report in early 2016 on this project.
Beyond swine, there were excellent talk on how European groups are funding
animal genetics/genomics research from J.C. Cavitte (European Commission,
Belgium); the use of genetics and genomics data from blood to predict disease
in humans (N. Soranzo, U. Cambridge, UK); miRNA biology and function (A.
Pasquinelli, UCSD, USA); and network biology tools (D. Lynn, EMBL, Adelaide,
Australia).
b. JAM
The ASAS/ADSA JAM Conference was held in Orlando, FL, USA from the 12th to
the 16th July, 2015. The animal breeding and genetics program was very strong
with 10 oral sessions and over 100 posters. International partnerships were a
highlight of the program including a pre-meeting joint symposium with
Interbull and a symposium sponsored by the European Federation for Animal
Science (EAAP) on the topic of Breeding for Environmental Sustainability.
General sessions focused on genomic analysis methods, as well as species-
specific applications. More details on the program and abstracts can be found
at the meeting website (http://www.jtmtg.org/JAM/2015/index.asp).
Please be aware that JAM will meet in Salt Lake City UT next year (July 19-
23) in conjunction with the International Society of Animal Genetics (July
23-26). There is a joint symposium on Functional Genomics planned for the
overlap day of July 23, so don't miss it! Available deadlines for JAM: early
registration deadline is February 18, 2016 with Abstract submissions due by
March 23, 2016). ISAG deadlines will be forthcoming.
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2. Update on new functional genomics project FAANG – Washington Meeting Oct
7-8, 2015
As described in the February PG Update, a major event at PAG was the
announcement and further organization of the Functional Annotation of ANimal
Genomes (FAANG) Consortium. The following text is a summary of the activities
of FAANG since the PAG meeting; for further information please see the FAANG
website (http://www.faang.org).
a. Summary of FAANG group's and their activities
We have developed a number of committees dedicate to specific aspects of the
Consortium's goals. These committees have met approximately monthly during
2015 to organize FAANG efforts. The following summaries are provided here so
that you can decide if one or more committees would be of interest to join;
all committees welcome new members.
First, the overall objective of the Animals, Samples and Assays Committee
(ASA) is to achieve and share standardized protocols for adequate sample
collection, storage, processing, and respective assays as required for FAANG
core assays. Standardization of the different steps involved is the essential
prerequisite for integration of multiple datasets. Second, the purpose of the
Bioinformatic and Data Analysis Committee (BDA) is to agree and define
standard pipelines for the analysis of FAANG data, with the aim that data
sets are comparable because they have been analyzed using the same pipeline,
as well as work together to investigate methods to integrate the primary
analysis results to high level summaries of functional state. Third, the
objective of the Metadata and Data Sharing (MDS) committee is to recommend
standard methods to record information for all samples, experiments and
analyses carried out by FAANG consortium members; recommend best practice for
data archiving; and define data sharing methodologies that encourage sharing
within the FAANG consortium and rapid public release of raw data and analysis
results. Fourth, the Communications committee (COM) aims to provide the
community with information about FAANG activities and provide links between
the various FAANG groups; a major effort lies with developing and maintaining
http://www.faang.org. The website aims to provide the scientific community
and the public with information about the project and its working groups, and
facilitate information exchange between working groups. The Com committee
also organizes meetings to promote the goals and objectives of FAANG.
Finally, the purpose of the Steering Committee (SC) is to develop and
implement policy to advance the FAANG project. The SC gathers information
from FAANG committees and members, as well as directing Committees to
evaluate proposals for new directions and project structures.
b. Update on GO-FAANG, a Washington DC Meeting Oct 7-8, 2015
A major effort of the COM has been to develop a Workshop named Gathering On -
FAANG, or GO-FAANG, to be held October 7-8, 2015. The main objective of the
GO-FAANG Workshop is to advance the goals of the FAANG initiative. This will
be accomplished through discussions and decision-making in three areas; 1)
establishing priorities for functional genomics research efforts within and
across species; 2) planning the management structures required for efficient
use and sharing of samples, data and computational tools; and 3) identifying
resources needed to accomplish these goals.
Until the meeting starts, you can sign up to participate via a web simulcast.
Details can be found here: http://www.faang.org/bbs?s=go-faang.zoom.txt. Both
Dr. Tuggle and Dr. Ernst will attend, as well as many other members of the
NRSP-8 community. GO-FAANG has been supported by funding from National
Science Foundation USDA-NIFA-AFRI Animal Genomes Program, USDA NRSP-8
Bioinformatics, Poultry, Sheep, and Swine National Genome Coordinators, and
Illumina as well as Iowa State University. The Program is listed here:
http://www.animalgenome.org/community/FAANG/bbs?s=go-faang.txt and includes
welcomes by Dr. Catherine Woteki (USDA Deputy Undersecretary, October 7) and
Dr. Sonny Ramaswamy (USDA-NIFA Director, October 8), as well as three plenary
lectures and presentations by five funding agencies and FAANG
representatives. A substantial portion of the Workshop is devoted to small
group and unstructured discussions on the main goals of GO-FAANG.
A recording (audio/video) will be made of this two-day Workshop and is
planned to be available on the FAANG website. If you are not able to attend
or participate in the web simulcast, you can view the main sessions of the
meeting there.
Please join our initiative by signing up at the website!
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3. Reminder on PAG registration and poster abstract deadlines.
A big reminder that PAG registration has opened! See
https://pag.confex.com/pag/xxiv/registration/call.cgi). Also, a call for
abstracts came out September 29! To submit a poster abstract, remember you
must first be registered. Please see https://pag.confex.com/pag/xxiv/cfp.cgi.
Poster abstracts must be submitted by October 30, 2015. Early registration
rates through October 30, 2015 are as follows: Student: $390; Non-profit
($590; weekend only rate is $460). There are also rates that apply to for-
profit ($900/$600 weekend).
Nominations are encouraged for the Neal A. Jorgenson Graduate Student Travel
Award. The award is for up to $1000 for travel expenses and registration for
a graduate student in the USA to travel to and attend PAG XXIV, and the Swine
Genome Coordinators will select a recipient from applicants in the pig
category. To be eligible, an applicant must be a current graduate student
residing in the USA. Applications are due by October 30, and application
information is available at
http://www.intlpag.org/2016/images/pdf/PAGXXIV-grants-jorgenson.pdf.
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4. Upcoming additional meetings information Besides the GO-FAANG, PAG
meetings including the NRSP-8 Swine Subcommittee and Animal Genome meetings
as well as JAM and ISAG meetings discussed above, there are many other
meetings coming up. For meetings of relevance to the genomics community over
the next 6-12 months, see: http://www.animalgenome.org/pig/community/meetings.
o o o o o o o o o o o
5. Recent conference call of Swine genome interest group initiated
Prompted by a suggestion from Dr. Lakshmi Matukumalli, C. Ernst organized a
conference call with many members of the NRSP-8 Swine Subcommittee, as well
as other interested swine researchers. On September 29, 2015, C. Ernst, C.
Tuggle, L Matukumalli, A. Archibald, D. Ciobanu, Z. Jiang, G. Rohrer, D.
Nonneman, T. Smith, R. Prather, K. Lee, J. Lunney, C. Anthon participated in
the call. The PAG Swine workshop was discussed and a request for speakers for
both the overall NRSP-8 meeting (Jan 10) and the Swine Subcommittee Workshop
(Jan 9) was made (D. Ciobanu and C. Ernst). The GO-FAANG Workshop was
summarized (C. Tuggle), and an update of NIFA events was made (L.
Matukumalli). A request was again made for research project applications for
Coordinator fund support.
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6. We want to hear from you! The swine genome coordinators are always glad to
hear from NRSP-8 members and other readers about ways that the coordination
effort can be improved or provide resources that are needed. If you have
items of general interest to the swine genetics and genomics communities that
can be included in this newsletter please share. Our issues are now planned
for February 1 and October 1 each year. Any contribution should be sent to
the Coordinators one week prior to these dates.
===========================================================
Joint Coordinators:
Christopher Tuggle Catherine Ernst
2255 Kildee Hall Anthony Hall, 474 S. Shaw Lane, Room 1205
Department of Animal Science Department of Animal Science
Iowa State University Michigan State University
Ames, IA 50011 East Lansing, MI 48824
Phone: 515-294-4252 Phone: 517-432-1941
Fax: 515-294-2401 Fax: 517-353-1699
