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Welcome to the FourthInternational Conference of Quantitative Genetics:Understanding Variation in Complex Traits - Edinburgh International Conference Centre, 17-22 June 2012
We invite you to join us in the beautiful city of Edinburgh for the Fourth International Conference of Quantitative Genetics, being held from 17 – 22 June 2012 at the Edinburgh International Conference Centre. Variation in quantitative and other complex phenotypes underpins most important traits in human health and disease, agriculture, natural populations and evolution. The genomics revolution has provided the tools to start the dissection of such traits, enhancing both their
understanding and exploitation. This has led to an explosion of interest and new studies across all of biology.
The aim will be to present and discuss state-of-the-art results, theoretical developments, understanding and methodology across the whole range of quantitative genetics - the genetic analysis and interpretation of data on complex traits - and to provide a stimulating conference in an
attractive locale. Topics will include statistical methods for parameter estimation, including analysis of trait, genomic and functional genomic data; methods
for QTL and gene identification; genetic control of complex traits; prediction
of breeding value and individual risk, and interpretation of evolutionary change.
The meeting will pertain to and span results from, for example, humans, livestock, crops, micro-organisms
and natural and experimental populations of all species. The conference will be held at the Edinburgh International
Fourth International Conference of Quantitative Genetics will meet the highest expectations. We look forward to welcoming you to Edinburgh.
Bill Hill (Chair), On Behalf of the Local Organising Committee.
To view the photos from the conference click here
Conference Publicity
We would be extremely grateful if you could assist us in publicising the conference. Please click on these links to download a Poster, PowerPoint slide or Flyer.
If you wish, please display them in a prominent place in your work place where it can be viewed by people who would find this conference of interest. We would also like to encourage you to use the PowerPoint slide during any presentations you may be giving over the coming year. We thank you in advance for helping us to promote this important conference.
You may also be interested in the forthcoming conferences:
- Behavior Genetics Association4
thInternational Conference on
Quantitative Genetics:
Understanding Variation in Complex Traits
Edinburgh, 17 – 22 June 2012
Programme
&
Information
CONTENTS
Page
Welcome/Committees
2
Scientific Programme
5
Industry Lunchtime Symposia
13
General Information
14
Social Programme
17
Poster Information
18
Conference Partners, Supporters & Gold Sponsors
19
Exhibitors and Sponsors
22
Exhibition Floorplan
25
Edinburgh City Centre Map
26
EICC Floorplan
27
Oral Abstracts
29
Student Symposia Abstracts
60
Poster Abstracts
65
Information
WELCOME
Welcome to Edinburgh and the Fourth International Conference on Quantitative
Genetics.
This is a time of rapid developments towards understanding the genetics of complex
traits and in utilising that knowledge to improve health, food production and the
natural environment. We have continuously improving technology for the collection
and interpretation of molecular and cellular data and new ways to analyse these in
combination with phenotypic data. Yet still we have much to learn and understand
because many key traits are, indeed, very complex. We value this opportunity to
bring you together to exchange ideas, discuss the latest results and consider the new
challenges and opportunities.
We have organised a diverse programme which we hope you will find informative
and stimulating. It was designed to cover most areas from genes to phenotypes,
the molecular to the mathematical, and from the laboratory to farmed and wild
populations. We shall be in plenary session throughout with the aim of maximising
information exchange and interaction of ideas and knowledge across disciplines.
We have over 600 delegates registered from over 50 countries. In addition to the
invited and contributed lectures we have around 400 posters to view and discuss,
particularly in the early evening sessions on Monday and Tuesday. There will be
considerable opportunity in the coffee and lunch breaks for further interactions as
we shall be together the whole time in this fine facility, the Edinburgh International
Conference Centre.
We hope also that many will participate in the student symposium and subsequent
social activities on Wednesday.
Out of hours (only, of course) there is much else to occupy you in the beautiful and
compact city of Edinburgh, with restaurants for all tastes and pockets, bars, museums
and historic sights. In addition we start with the Sunday evening mixer and finish
with a banquet at Dynamic Earth.
Information
Conference Organisers
ICQG Secretariat
c/o In Conference Ltd, 4-6 Oak Lane, Edinburgh, EH12 6XH, Scotland, UK
Tel: +44 (0)131 339 9235 Fax: +44 (0)131 339 9798
Email: icqg4@in-conference.org.uk
COMMITTEES
LOCAL ORGANISING COMMITTEE
Bill Hill (Chair)
Lutz Bünger
Chris Haley
Mike Kearsey
DJ de Koning
Loeske Kruuk
Josephine Pemberton
Alan Wright
Kay Boulton (PG Symposium)
INTERNATIONAL ADVISORY COMMITTEE
David Allison, USA
David Balding, UK
Piter Bijma, Netherlands
Rachel Brem, USA
Ed Buckler, USA
Andrew Clark, USA
Mark Daly, USA
Rebecca Doerge, USA
Marie-Anne Felix, France
Jonathan Flint, UK
Greg Gibson, USA
Mike Goddard, Australia
Ary Hoffman, Australia
Fred Hospital, France
Mark Lathrop, France
Trudy Mackay, USA
Albrecht Melchinger, Germany
Juha Merilä, Finland
Bill Muir, USA
Patrick Phillips, USA
Daniel Pomp, USA
Pak Sham, China
Information
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Information
09.05 Welcome from Bill Hill, Chair, Local Organising Committee
09.05 - 10.40
Session 1
The genetic architecture of quantitative traits
Chair: Bruce Walsh (University of Arizona, USA) 09.05 –
09.20
Introduction: The quantitative genetics landscape in 2012
Bruce Walsh 09.20 –
10.00 O-1From Galton to GWAS: genetics of quantitative traits in human populations Peter Visscher (University of Queensland, Australia)
10.00 - 10.40
O-2
Uniting the world’s maize diversity for dissection of complex traits and accelerated breeding
The genetic architecture of quantitative traits
Chair: Bruce Walsh (University of Arizona, USA)
O-3
An improved method for heritability estimation provides insights into the genetic architecture of epilepsy
Doug Speed (University College London, UK)
11.40 – 12.40
Genetics Society Mendel Lecture
Chair: Veronica van Heyningen (President, Genetics Society)
O-4
Secrets of the human genome
Eric Lander (Broad Institute of MIT & Harvard, USA) 12.40 –
Chair: Derek Roff ( University of California Riverside, USA) 13.40 –
14.20 O-5Evolution of genetic variance under selection Mark Blows (University of Queensland, Australia) 14.20 –
14.40 O-6Plants in heterogeneous environments: determining when phenotypic plasticity is adaptive
Information
Monday 18th June
14.40 –
15.00 O-7Discovery of cryptic genetic variation in C. elegans embryogenesis
Annalise Paaby (New York University, USA) 15.00 –
15.20
O-8
Genomic comparisons between selected and relaxed chicken lines
Mats Pettersson (Swedish University of Agricultural Sciences, Sweden) 15.20 –
15.50 Tea/Coffee
15.50 - 17.20
Evolutionary quantitative genetics
Chair: Derek Roff (University of California, USA) 15.50 –
16.30
O-9
Gene interactions underlying the evolution of complex traits Patrick Phillips (University of Oregon, USA)
16.30 –
17.00 O-10What, me natural? Patterns of selection in wild systems and their theoretical implications Jarrod Hadfield (Universities of Edinburgh and Oxford, UK)
17.00 –
17.20 O-11The deceit of monogamy: Quantitative genetic insights into the evolutionary ecology of polyandry in the wild
Chair: Alan Archibald (Roslin Institute, University of Edinburgh, UK) 09.00 –
09.40
O-12
Causes and consequences of new mutations
Matt Hurles (Sanger Institute, UK) 09.40 –
10.00 O-13The role of genetic variations on gene expression and splicing in multiple regions of control in human post-mortem brain tissue
Daniah Trabzuni (University College London, UK & King Faisal Specialist Hospital, Saudi Arabia)
10.00 –
10.20: O-14Population genetics revealed by enormous structural variations discovered by population-scale sequencing
Information
Tuesday 19th June
11.50 –
12.20 O-17The role of tandem repeats in mRNA and protein expression homeostasis
Sreenivas Chavali (MRC Lab Molecular Biology, UK) 12.20 –
12.40
O-18
Dissecting the contribution of regulatory sequence variation to quantitative haematological traits using maps of open chromatin in primary human blood cells
Cornelis Albers (University of Cambridge & Sanger Institute, UK) 12.40 –
13.40 Lunch/Exhibition/Poster viewingAffymetrix Lunchtime Symposium:
How can you accelerate your genomics program from discovery to results?
Professor David W. Burt, Chair of Comparative Genomics (The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, UK)
13.40 - 15.20
Session 4
Advances from numerical methods
Chair: David Balding (University College London, UK) 13.40 –
14.20
O-19
Statistical methods for the genetic analysis of arbitrarily structured populations
John Storey (Princeton University, USA) 14.20 –
14.40 O-20CLIP Test: a new fast and simple method to distinguish between linked or pleiotropic quantitative trait loci in linkage disequilibrium analysis
Jean-Michel Elsen (INRA, France) 14.40 –
15.00
O-21
Sparse factor models for estimating the genetic architecture of gene expression traits
Daniel Runcie (Duke University, USA) 15.00 –
15.20 O-22Big data, small cost – combining low-pass genome sequencing with long-range phasing and haplotype library imputation to create more powerful data for genomic prediction in plants and animals
John Hickey (University of New England, Australia) 15.20 –
15.50 Tea/Coffee
15.50 - 17.20
Advances from numerical methods
Chair: David Balding (University College London, UK) 15.50 –
16.30 O-23Haplotype phasing using next-generation sequencing reads
Jonathan Marchini (University of Oxford, UK) 16.30 –
17.00 O-24Whole-genome regression and prediction of human complex traits using data from related and unrelated individuals
Gustavo de los Campos (University of Alabama, USA) 17.00 –
17.20 O-25Relaxing the genetic model to identify quantitative trait loci having heterogeneous effects
Hugues Aschard (Harvard University, USA) 17.20 –
19.30
Information
Chair: Marie-Anne Felix, (École Normale Supérieure, Paris, France) 09.00 –
09.40
O-26
Rare variant patterns in 14,000 human samples and lessons for study design
Sebastian Zöllner (University of Michigan, USA) 09.40 –
10.00
O-27
Low depth, whole genome sequencing of Dai population demonstrates superiority over use of whole genome genotyping arrays in uncovering population structure, demographic history, selective pressures and phenotype associations in non-european populations
Lachlan Coin (BGI Shenzhen, China & Imperial College London, UK) 10.00 –
10.20
O-28
The relationship between binary disease status and underlying heterogeneity in susceptibility and infectivity
Debby Lipschutz-Powell (Roslin Institute, University of Edinburgh, UK) 10.20 –
10.40 O-29How do hosts shape their microbial communities?
Matthew Horton (University of Chicago, USA)
Chair: Marie-Anne Felix, (École Normale Supérieure, Paris, France) 11.10 –
11.50 O-30Quantitative association genetics of high dimensional cellular traits: extending beyond expression QTLs
Richard Durbin (Sanger Institute, UK) 11.50 –
12.20 O-31Integrating gene expression into predictive health genomics
Greg Gibson (Georgia Tech, USA) 12.20 –
12.40 O-32Whole genome sequence analysis of a large Scottish family with bipolar disorder
Information
14.20 SO-1 / P-43Markers as traits in multivariate BLUP: using REML for association testing and integration with breeding value prediction
Jeremy Brawner (Commonwealth Scientific and Industrial Research Organisation, Australia)
14.20 – 14.35
SO-2 / P-46
Genetic markers as instruments for Mendelian randomization studies on vitamin D
Diane Berry (University College London, UK) 14.35 –
14.50
SO-3 / P-41
Using KEGG pathways and expression studies and stuff for genomic partitioning
Stefan M. Høj-Edwards (Aarhus University, Denmark) 14.50 –
15.05 SO-4 / P-283Genetic interactions in the human liver
Darren J. Fitzpatrick (University College Dublin, Ireland) 15.05 –
15.20
SO-5 / P-265
Evidence of shared polygenic risk among smoking behaviors and body composition
Roseann Peterson (Virginia Commonwealth University, USA) 15.20 –
15.35
SO-6 / P-214
Direct and indirect genetic effects for survival in purebred and crossbred laying hens
Katrijn Peeters (Wageningen University, The Netherlands) 15.35 –
15.50 SO- 7 / P-79Maternal genetic effects set the potential for evolution in red squirrels
S.E. McFarlane (University of Guelph, Canada)
Chair: Michel Georges (University of Liege, Belgium) 09.00 –
09.40
O-33
Charting the genotype-phenotype map: lessons from Drosophila
Trudy Mackay (North Carolina State University, USA) 09.40 –
10.00 O-34Heterosis as a systemic property emerging from the non-linearity of the genotype-phenotype relationship: evidence from metabolic models and test-tube genetics
Dominique de Vienne (University Paris XI, France) 10.00 –
10.20
O-35
Discovering early and late regulators of haematopoiesis through large-scale genomic analyses
Information
Thursday 21st June
10.20 –
10.40 O-36A sexual ornament in chickens is determined by pleiotropic alleles at HAO1 and BMP2, selected during domestication
Chair: Michel Georges (University of Liege, Belgium) 11.10 –
11.50 O-37Diamonds in the dirt: biological and translational insights into type 2 diabetes from large-scale genetic studies
Mark McCarthy (University of Oxford, UK) 11.50 –
12.20 O-38The biologic relevance of eQTLs: a genome wide confirmation of eQTLs using two types of inbred populations in C. elegans
Mark Sterken (Wageningen University, The Netherlands) 12.20 –
12.40
O-39
Quantitative genetics of Drosophila lifespan
Michael Magwire (North Carolina State University, USA) 12.40 –
13.40 Lunch/Exhibition/Poster viewing
13.40 - 15.20
Session 7
The genetic architecture of quantitative traits 2
Chair: Bruce Weir (University of Washington, USA) 13.40 –
14.20 The Genetics Society Balfour LectureO-40
Variance controlling genes and their role in the genetic architecture of complex traits
Orjan Carlborg (Swedish University of Agricultural Sciences, Sweden) 14.20 –
14.40
O-41
GWAS: 2D, or not 2D: that is the question
Gibran Hemani (Roslin Institute, University of Edinburgh, UK & University of Queensland, Australia)
14.40 – 15.00
O-42
Knowledge-driven analysis identified a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations
Alon Keinan (Cornell University, USA) 15.00 –
15.20 O-43The genetic architecture of quantitative traits: lessons from biochemical markers for disease
Information
Thursday 21st June 15.50 -
17.20
The genetic architecture of quantitative traits 2
Chair: Bruce Weir (University of Washington, USA) 15.50 –
16.30: O-44From Castle to the Collaborative Cross: evolution of the mouse in quantitative genetics research
Daniel Pomp (University of North Carolina, USA) 16.30 –
17.00 O-45Genetic architecture and evolution of quantitative traits
Mike Goddard (University of Melbourne, Australia) 17.00 –
17.20 O-46The quantitative genetics of phenotypic robustness
Hunter Fraser (Stanford University, USA)
Interactions among individuals and with the environment
Chair: Albrecht Melchinger (University of Hohenheim, Germany) 09.00 –
09.40 O-47Studying the genotype-phenotype map in Arabidopsis
Magnus Nordborg (Gregor Mendel Institute, Austria) 09.40 –
10.00
O-48
Novel methods of GWAS for mapping genes of complex traits and their applications in crop breeding
Jun Zhu (Zhejiang University, China) 10.00 –
10.20 O-49Nonlinear genotype x environment interaction
Rong-Cai Yang (University of Alberta, Canada) 10.20 –
10.40
O-50
Applying quantitative genetics to epidemics and disease resistance: implications of dynamic and noisy data
Steve Bishop (Roslin Institute and R(D)SVS, UK) 10.40 –
11.10 Tea/Coffee
11.10 - 12.40
Interactions among individuals and with the environment
Chair: Albrecht Melchinger (University of Hohenheim, Germany) 11.10 –
11.50 O-51The consequences of indirect genetic effects for heritable variation and response to selection
Piter Bijma (Wageningen University, The Netherlands) 11.50 –
12.20
O-52
The genetics of social dominance: does competition cause constraint?
Alastair Wilson (University of Edinburgh, UK) 12.20 –
12.40 O-53Simple and effective methods of addressing competitive effects in animal breeding programs
William Muir (Purdue University, USA) 12.40 –
13.40
Information
Chair: Theo Meuwissen (Norwegian University of Life Science, Norway) 13.40 –
14.20
O-54
Towards genomic prediction from genome sequence data and the 1000 bull genomes project
Ben Hayes (Victorian Department of Primary Industries, Australia) 14.20 –
14.40 O-55Using whole genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster
Ulrike Ober (Georg-August-University Göttingen, Germany) 14.40 –
15.00 O-56Next generation breeding using genotyping-by-sequencing
Jose Crossa (International Maize and Wheat Improvement Center, Mexico) 15.00 –
15.20 O-57Genomic-BLUP decoded: a look into the black box
David Habier (Iowa State University, USA)
Chair: Theo Meuwissen (Norwegian University of Life Science, Norway) 15.50 –
16.30
O-58
Predicting disease risk from marker genotypes under a polygenic model Pak Sham (The University of Hong Kong, Hong Kong)
16.30 – 17.00
O-59
Genome-based prediction in highly structured plant populations
Chris-Carolin Schoen (Technical University Munich, Germany) 17.00 –
17.20 O-60Genomic prediction of colorectal cancer risk using GBLUP
Information
INDUSTRY LUNCHTIME SYMPOSIUM
Affymetrix Lunchtime Symposium
Tuesday 19
thJune
12.55 – 12.25
Lomond Suite, located on the ground floor level of the Conference Centre
Bagged lunches will be available for collection to be taken into the Lomond Suite for
the lunchtime symposium.
How can you accelerate your genomics program from discovery to results?
Abstract:
With so many genomics technologies available, knowing how to integrate them
for maximum efficiency can be challenging. This is true whether the objective is to
dissect complex traits, identify disease genes or improve breeding. The prevailing
strategy is to integrate NGS and other technologies to quickly progress genomic
markers from discovery into downstream studies and applications. For mid to high
density marker sets, microarrays are widely preferred due to the high data quality,
throughput, analytical efficiency and cost effectiveness they offer. Taking genomics
in the chicken as an example, this scientific seminar will discuss best practice that is
equally relevant across diverse species and applications.
Invited presentation:
Development and characterization of a high-density SNP genotyping assay for the
chicken
Professor David W. Burt, Chair of Comparative Genomics,
Information
GENERAL INFORMATION
Registration/Information Desks
All delegates will receive their name badge, meeting documents, ordered tickets and
all relevant conference information upon arrival at the Conference Centre.
The Registration and Information Desks will be open at the following times:
Sunday 17
thJune
14.00 – 19.30
Monday 18
thJune
08.00 – 19.30
Tuesday 19
thJune
08.00 – 19.30
Wednesday 20
thJune
08.00 – 16.00
Thursday 21
stJune
08.00 – 17.30
Friday 22
ndJune
08.00 – 17.30
Exhibition Opening Hours
Sunday 17
thJune
18.00 – 19.30
Monday 18
thJune
08.00 – 19.30
Tuesday 19
thJune
08.00 – 19.30
Wednesday 20
thJune
08.00 – 16.00
Thursday 21
stJune
08.00 – 17.30
Friday 22
ndJune
08.00 – 15.50
Tea/Coffee Breaks and Lunch Arrangements
Catering points will be located with the exhibition in the Cromdale Hall which is
located on the lower level of the Conference Centre.
On Tuesday lunchtime there will also be secondary catering points on the ground
level of the Strathblane Hall for those attending the lunchtime symposium. Please
follow the directions of the staff at the Conference Centre.
Information
Congress Etiquette
Delegates are advised that they are not allowed to take photographs of any posters or
presentations without the author’s/presenter’s consent. Delegates should also obtain
consent from an author before citing any of their work that was presented at the
conference.
If you intend to ‘blog’ or ‘twitter’ results from this conference you must inform the
conference organisers in advance and get the permission of the author or presenter.
Mobile phones should be switched off or placed on ‘silent’ during sessions. Thank
you for your co-operation.
WiFi Access
The conference is providing WiFi access free to delegates who have their own
laptops. Please see the registration notice board for password and log in details.
Please note that there are printing facilities in the Business Centre although this will
be chargeable to delegates.
Thank you to Genetics Society of America Journals (GENETICS and G3) who have
sponsored the WiFi.
Certificate of Attendance
A certificate of attendance will be emailed to all participants following the
conference.
Speaker Preview Room
This is located in Harris Room 1, on the first floor. All presenters are required to
check in their presentation a minimum of 4 hours prior to their talk.
The Speaker Preview Room will be open at the following times:
Sunday 17
thJune
14.00 – 19.30
Monday 18
thJune
08.00 – 17.30
Tuesday 19
thJune
08.00 – 17.30
Wednesday 20
thJune
08.00 – 16.00
Thursday 21
stJune
08.00 – 17.30
Information
Insurance
The Conference Organisers cannot accept any liability for personal injuries or for
loss or damage to property belonging to delegates, either during, or as a result of the
conference. Please check the validity of your own personal insurance before travelling.
Security
Your name badge must be worn at all times otherwise you will not be allowed entry
to the conference centre. Exhibitor staff
do not
have access to the scientific sessions.
Please leave any luggage or poster tubes with the staff at the cloakroom. This will
be manned during the normal opening hours of the conference.
Social Programme
Welcome Reception
Sunday 17
thJune 18.00 – 19.30
Cromdale Hall, Edinburgh International Conference Centre
The Welcome Reception will take place at the Edinburgh International Conference
Centre. The cost for this event is included in the registration fee.
Genetics Society Postgraduate Symposium Ceilidh
Wednesday 20th June 20.00 – Midnight
Edinburgh International Conference Centre
A Ceilidh will take place at the Edinburgh International Conference Centre following
the Genetics Society Postgraduate Symposium. The cost for this event is £5 and
tickets can be purchased at the registration desk. All delegates are welcome to
attend.
Information
Conference Dinner
Friday 22
ndJune 19.30 – Midnight
Dynamic Earth, 112-116 Holyrood Road, Edinburgh, EH8 8AS
The conference dinner will be held at Dynamic Earth on Friday evening.
The evening will start with a pre-dinner drinks reception, followed by dinner and
dancing.
Offering stunning 360 degree views across Edinburgh’s picturesque cityscape and
Royal Park, the five star Our Dynamic Earth is a perfectly situated venue with a
unique heritage twist. Located at the bottom of Holyrood Road, neighbouring the
Scottish Parliament and the Palace of Holyrood House, getting to Our Dynamic Earth
is easy and is approximately a 5 minute taxi ride from the EICC.
Tickets cost £50.00 and must have been pre-booked at the time of registration.
Should you wish to attend and have not purchased a ticket please speak to the staff
at the registration desk.
Limited shuttle buses will be available from 10.30pm – Midnight
stopping at North Bridge, mid George Street, West End and the EICC.
EICC
DYNAMIC
EARTH
Drop point
•
Drop point
•
Drop point
Information
Poster Information
Posters
All posters will be on display for the duration of the conference, however, there are
two designated poster sessions to enable delegates to discuss the author’s work in more
detail. We ask that you stand by your board during your allocated poster sessions so
that delegates can ask you questions about your work.
Poster Session 1
Monday 18
thJune
17.30 – 19.30
Sponsored by
Poster Session 2
Tuesday 19
thJune
17.20 – 19.30
•
Posters ending in an Odd-number:
Stand by your board from 17.30 to
19.30
•
Posters ending in an Even-number:
Stand by board from 17.20 – 19.30
Information
Conference Supporters
The Genetics Society
Contact: Linda Allardyce or Ivvah Chung
The Genetics Society, c/o Portland Customer Services,
Commerce Way, Colchester CO2 8HP
Tel: +44 (0)1206 796 351 / Fax: +44 (0)1206 799 331
Email: theteam@genetics.org.uk
Website:www.genetics.org.uk
The Genetics Society was founded by William Bateson in 1919 and is one of the
oldest “learned societies” devoted to genetics in the world. Its membership of over
1700 comprises the UK’s active geneticists, including academics, researchers and
students.
The Genetics Society organises meetings to promulgate genetics, supports students
to attend meetings, sponsors research through fieldwork grants and student bursaries,
and promotes the Public Understanding of Genetics.
It co-owns two leading journals in the field:
Heredity
and
Genes and Development
.
The Genetics Society is proud to be the major sponsor of the 4
thInternational
Conference on Quantitative Genetics.
UNIVERSITY OF EDINBURGH
The University of Edinburgh, Old College, South Bridge,
Edinburgh EH8 9YL
www.ed.ac.uk
Information
SCOTTISH AGRICULTURAL COLLEGE
www.sac.ac.uk
Communications Unit
SAC, King’s Buildings, West Mains Road, Edinburgh, EH9 3JG
Tel: 0131 535 4000
Over the past decade we have seen agriculture move from being regarded as a
‘sunset ‘industry to one that is now core to contemporary political and societal
thinking. Our food supplies, our environment, our water quality, and our renewable
energy capability, all depend on the effective and efficient management of our land
resources. SAC’s portfolio of expertise in research, in teaching and in consultancy, is
being increasingly recognised as a core national and international resource that is
competent to tackle many of these issues.
Gold Sponsor
The EW Group: Aqua Gen AS, Aviagen, Hy-Line and Lohmann Tierzucht.
Aqua Gen AS
Aqua Gen AS, PO Box 1240, Sluppen,
N-7462 Trondheim
Phone: +47 72 45 05 00
Fax: +47 73 54 62 91
E-mail: firmapost@aquagen.no
Web: www.aquagen.no
Aqua Gen manages and further develops the world’s first family-based breeding
programs of Atlantic salmon and rainbow trout. Today’s eggs from the Aqua Gen
strain are selected for excellent performances on growth, disease resistance,
Information
Aviagen
Newbridge, Midlothian, EH28 8SZ, Scotland, UK
Tel: +44 131 333 1056
Fax: +44 131 333 3296
Email: infoworldwide@aviagen.com
www.aviagen.com
Aviagen is the world’s leading poultry breeding company, developing pedigree
lines for the production of broiler chickens and turkeys under the Ross, Arbor
Acres, Indian River, B.U.T. and Nicholas brand names. Aviagen has wholly-owned
operations on five continents, employs almost 3,000 people and a distribution
network that serves customers in 120 countries.
Hy-Line
Contact: Jerry Dreyer
Hy-Line International, PO Box 310,
Dallas Center IA 50063 USA
Tel: +1-515-992-3736
Email: jdreyer@hyline.com
www.hyline.com
Hy-Line International is the world’s oldest egg layer genetics company since being
founded by the Wallace family as part of Pioneer Seed Corn in 1936. Hy-Line layers
have become the largest selling layers across the globe and are known for their
superior livability, feed conversion and egg quality.
LOHMANN TIERZUCHT GmbH
Am Seedeich 9 – 11, 27472 Cuxhaven
Phone: +49 4721 505 0
Fax: +49 4721 505 222
E-Mail: info@ltz.de
LOHMANN TIERZUCHT – Breeding for success … together!
Information
Exhibitors
AFFYMETRIX
Mercury Park, Wycombe Lane,
Wooburn Green, HP10 0HH,
United Kingdom
Tel:
+44 (0)1628 552500
Email:
Sales_Europe@affymetrix.com
Website:
www.affymetrix.com
Affymetrix
®, part of The Genome Generation, provides genomic solutions for
agrigenomics and human health research. Our technologies for whole-genome
analysis to single-gene validation enable sequencing discoveries to be confirmed
and applied. Our solutions for expression, genotyping and cytogenetics enable your
translational and applied research… we are all The Genome Generation.
BIOCOMPUTING PLATFORMS LTD
Elina Lamponen
BC Platforms Ltd., Innopoli 2, Tekniikantie 14,
Espoo, FI-02150, Finland
Tel:
+358 9 2517 7340
Fax:
+358 10 296 1288
Email:
elina.lamponen@bcplatforms.com
Information
CAMBRIDGE UNIVERSITY PRESS
Shaftesbury Road, Cambridge, CB2 8RU, UK
Tel:
+44 (0)1223 358331
Email:
information@cambridge.org
Website:
http://www.cambridge.org
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O-1
FROM GALTON TO GWAS: GENETICS OF QUANTITATIVE TRAITS IN HUMAN POPULATIONS
Peter Visscher
University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland, Australia
Variation in quantitative traits such as human height is caused by a combination of multiple genes and environmental effects. Traditionally, since Galton in the late 1800s, the genetics of such traits has been studied using concepts that refer to the combined effect of all genes (e.g., heritability), using the resemblance between relatives. For example, estimates of heritability for adult height and schizophrenia are ~0.8, so that 80% of differences between people in the trait is due to genetic factors. Genome-wide association studies (GWAS) facilitate the dissection of heritability into individual locus effect. They have been successful in finding many SNPs associated and have greatly increased the number of genes involved in complex trait variation. To date, for many complex traits, tens to hundreds of loci have been identified that explain in total up to 20% of narrow sense heritability. The proportion of additive genetic variation explained by all common SNPs together (not just the significant ones) is one-third to one-half for a range of quantitative traits and diseases. The variation is spread over all chromosomes in proportion to their length, implying that there are many more variants with effects sizes too small to be detected with sample sizes employed to date. The identification of tens to hundreds of associated variants facilitates the study of biology and function, in particular when genetic data is combined with data on gene expression. Empirical observations from the resemblance between relatives, from within-family segregation variance captured by markers and from population based studies are all converging to a highly polygenic model of complex traits, with a surprisingly large proportion of additive genetic variation due to variants that are in linkage disequilibrium with common SNPs. We will show results from empirical data on quantitative traits and disease in human populations to quantify and partition genetic variation.
O-2
UNITING THE WORLD’S MAIZE DIVERSITY FOR DISSECTION OF COMPLEX TRAITS AND ACCELERATING BREEDING
Edward Buckler
Or
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O-3
AN IMPROVED METHOD FOR HERITABILITY ESTIMATION PROVIDES INSIGHTS INTO THE GENETIC ARCHITECTURE OF EPILEPSY
Doug Speed, David Balding UCL Genetics Institute, London, UK
The 2010 Nature Genetics paper of Yang, Visscher et. al. first promoted the idea of performing heritability analysis using SNP data for unrelated individuals. Their key insight was that by using unrelated
individuals, the heritability estimates no longer correspond to the trait’s overall heritability, but rather the proportion of variance which can be attributed to the causal variants among (or tagged by) the genotyped SNPs. Their work has provided strong evidence that the apparent missing heritability of many complex traits might be due to many causal variants of low influence; this would explain the failure of GWASs as most of the causal variants effect sizes would be too small to detect with standard sample sizes. For all the method’s strengths, we discover that its results are highly sensitive to LD. Depending on the location of causal variants, the method’s estimates can be out by up to a factor of two. This finding is pertinent for rare variant traits, as the method performs particularly poorly when the frequency of the causal alleles is low. In response, we propose a solution which corrects for the impact of LD, allowing unbiased heritability estimation regardless of the distribution of causal variants. We have applied our revised method to Susceptibility to Epilepsy, yet another trait known to be highly heritable, but for which GWASs have failed to explain much variation. We deduce that almost all the heritability can be explained by considering the contribution of all SNPs simultaneously. We show how this leads us to a prediction model with practical applications in determining personalised treatment, and by partitioning the genome provides insights into the areas most likely to harbour causal variants.
O-4
SECRETS OF THE HUMAN GENOME
Eric Lander
Broad Institute, MIT & Harvard, USA
No Abstract.
O-5
EVOLUTION OF GENETIC VARIANCE UNDER SELECTION
Mark Blows
University of Queensland, Brisbane, Australia
Or
al
However, it is the pleiotropic associations between the sexually-selected traits and other (unmeasured) traits under natural selection that have been revealed to play the key role in limiting the response to sexual selection, and the maintenance of multivariate genetic variance in traits under sexual selection.
O-6
PLANTS IN HETEROGENEOUS ENVIRONMENTS: DETERMINING WHEN PHENOTYPIC PLASTICITY IS ADAPTIVE
Diane L. Byers1, Rebecca R. Miller1,2
1Illinois State University, Normal, IL, USA, 2Missouri Dept of Conservation, Blue Springs, MO, USA
The quality of natural environments is highly heterogeneous, imposing selection on the local populations. As plants are sessile for much of their life history, it has been proposed that phenotypic plasticity is a critical mechanism that allows plants to adapt to environmental heterogeneity. However, increased phenotypic plasticity does not necessarily lead to increased fitness. Furthermore, the evolution of increased phenotypic plasticity may be limited by strong cross-environment genetic correlations. We have been studying the response of wild Arabidopsis thaliana populations to the natural variation in soil nutrients. Using inbred lines from 18 populations located in USA, we tested and found extensive phenotypic plasticity in many fitness-related traits in response to different soil phosphorous treatments. We used a typical approach (modified phenotypic selection analysis, van Kleunen and Fischer 2001) for determining if the expressed phenotypic plasticity is adaptive. Using this approach we found very limited evidence for increasing phenotypic plasticity associated with greater seed production. We have done a simple mathematical alteration on this approach that uses a more realistic simulation of the environmental variation. Results from this analysis give different conclusions and insights for determining if and when phenotypic plasticity is adaptive. Even though phenotypic plasticity is adaptive under some environmental conditions, strong genetic correlations across the phosphorus treatments indicate that some of the traits will be constrained, as they will not evolve independently in the soil environments. Other traits, including root biomass (a trait likely critical for tolerance of lower nutrient soils), are not constrained. Our populations of A. thaliana show significant phenotypic plasticity in response to differences in availability of phosphorous, some of this plasticity is adaptive, while the evolution of plasticity will be constrained due to the cross-environment genetic correlations.
O-7
DISCOVERY OF CRYPTIC GENETIC VARIATION IN C. ELEGANS EMBRYOGENESIS
Annalise Paaby, Amelia White, Kris Gunsalus, Fabio Piano, Matthew Rockman New York University, New York, NY, USA
In the evolution of complex traits, natural genetic variation may accumulate in pathways that determine robust phenotypes. Such variation is “cryptic” if it has no effect on phenotype under normal conditions, but an effect when the organism is perturbed, either environmentally or genetically. Thus cryptic genetic variation demonstrates conditional dynamics in the relationship between genotype and phenotype. Conditional effects are probably common in biological systems, but they pose barriers to the identification of causal alleles that underlie complex traits. Accumulation of cryptic genetic variation in developmental pathways may lead to evolution by developmental system drift, a phenomenon with consequences for speciation.
Or
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including the identification of a novel candidate locus for germline RNAi sensitivity.
The cryptic genetic variation we observed is pervasive. Of the 41 germline genes we silenced, about half exhibited phenotypes that correlate significantly with one or more SNPs across the strains, indicating candidate loci for cryptic variants. However, of the significant SNPs we observed, few are shared across silenced genes. These results describe a genetic architecture of many variants of moderate effect, with low pleiotropy. Silenced genes that revealed particularly strong cryptic variation include par family members, perhaps a surprising result given their fundamental role in polarizing the early embryo. We are currently evaluating candidate loci for functional cryptic variants that may act in the polarity pathway.
O-8
GENOMIC COMPARISONS BETWEEN SELECTED AND RELAXED CHICKEN LINES
Mats Pettersson1, Anna Johansson1, Paul Siegel2, Örjan Carlborg1
1Swedish University of Agricultural Sciences, Uppsala, Sweden, 2Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
In an earlier study, we genotyped individuals from generations 40 and 50 in a bi-directional selection experiment for body-weight in chickens, using a 60k SNP-chip to examine the genome wide effects of selection. The results showed that although selection had acted on many (likely hundreds) of genes, any one point in time selection was focused on a smaller set of genes.
Here, we describe results from a new analysis based on individuals from the selected lines at generation 53, as well as individuals from generation 9 of two relaxed selection lines spliced from the high- and low-selected lines at generation 45. We study genomic patterns on several spatial scales and compare over time, within the populations, as well as across the four different populations. Effects on e.g. expected heterozygosity, haplotype block size and allele frequencies were examined, to unravel the effects of applying, and subsequently relaxing, single trait directional selection over more than 50 generations. Initially we identified small stretches of markers with a consistent trend of allele frequency change over time that likely represent regions under current selection. Sliding windows covering a few hundred markers detected extended regions of near complete fixation, which were used to reconstruct a timeline of fixation based on the shared history of the studied lines. A particularly interesting example is a region on chromosome 1, which displays a drastic drop in diversity in late generations – likely due to a novel mutation that appeared in the high-weight selected line during the selection experiment. Finally, genome wide divergence was found to be higher between the low-weight selected and relaxed lines than in the high-weight selected pair. This is interesting, given that the low-weight selected line has reached a selection plateau, and suggests purging of deleterious alleles from the low-weight relaxed line.
O-9
GENE INTERACTIONS UNDERLYING THE EVOLUTION OF COMPLEX TRAITS
Patrick Phillips
Or
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O-10
WHAT, ME NATURAL? PATTERNS OF SELECTION IN WILD SYSTEMS AND THEIR THEORETICAL IMPLICATIONS
Jarrod Hadfield1,2
1University of Oxford, Oxford, UK, 2University of Edinburgh, Edinburgh, UK
Most biologists believe that natural selection is stabilising and that trait means are close to their optimum. Contrary to this, evidence from wild populations suggests that selection is often directional. It has therefore been suggested that our estimates of natural selection are unrepresentative because incomplete fitness measures have been used or that short-term studies of selection fail to observe the temporal reversals in sign that would lead to no overall selection (i.e. fluctuating selection). However, studies that use complete fitness measures generally show stronger directional selection and reversals in the sign of selection are uncommon and largely due to measurement error. Given that abundant genetic variance segregates for most traits evolutionary change is expected and indeed has been documented using BLUP methodology. However, the observed response to selection usually falls far short of the expected cumulative response, and in many cases the evidence for a response to selection is not supported by more rigorous hypothesis tests. Measuring selection on the genetic component has been advocated in order to equate expectation with observation. However, because estimates of evolutionary change and estimates of `genetic selection’ use the same information in the data they will always be concordant even when the true values are not. Moreover, `genetic selection’ conflates selection and inheritance and therefore provides little insight into the two main remaining hypotheses regarding the lack of evolutionary change in natural populations: selection on unmeasured ‘traits’ resulting in the overestimation of i) the strength of selection on the focal trait or ii) the amount of useful genetic variance (through antagonistic genetic correlations). It is suggested that selection and inheritance should be kept distinct in empirical work and that both observational and experimental approaches need to be brought to bear on identifying the causal agents of fitness variation.
O-11
THE DECEIT OF MONOGAMY: QUANTITATIVE GENETIC INSIGHTS INTO THE EVOLUTIONARY ECOLOGY OF POLYANDRY IN THE WILD
Jane Reid
University of Aberdeen, Aberdeen, UK
Or
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selection on polyandry in the wild and predicted evolutionary responses, and demonstrate the potential for modern quantitative genetic approaches to provide major new insights into long-standing questions in evolutionary and behavioural ecology.
O-12
CAUSES AND CONSEQUENCES OF NEW MUTATIONS
Matt Hurles
Sanger Institute, Cambridge, UK
No Abstract
O-13
THE ROLE OF GENETIC VARIATIONS ON GENE EXPRESSION AND SPLICING IN MULTIPLE REGIONS OF CONTROL IN HUMAN POST-MORTEM BRAIN TISSUE
Daniah Trabzuni1,2, Adaikalavan Ramasamy4, Mina Ryten1, Colin Smith3, Robert Walker3, Michael Weale4, John Hardy1
1Institute of Neurology, University College London, London, UK, 2Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia, 3Department of Neuropathology, University of Edinburgh, Edinburgh, UK, 4Department of Medical & Molecular Genetics, King’s College, London, UK
Introduction:Over the past few years there has been a realization of the importance of understanding the underlying molecular mechanism of complex neurodegenerative diseases. GWAS studies confirmed a significant association between SNPs with common complex neurodegenerative diseases. This highlights the importance of the genetic variations in individuals and how they contribute to increase susceptibility to neurodegenerative diseases by modulating the gene expression and splicing pattern in the relevant tissue. In this project we are assessing the correlation between genetic SNPs variations with gene expression and alternative splicing regulation in control post-mortem human brain tissues from 10 different regions, which support different functional roles. The regions presented here are frontal cortex, temporal cortex, occipital cortex, white matter, hippocampus, thalamus, putamen, substantia nigra, medulla and cerebellum.
Material and Methods:A total of 1231 RNA samples from 134 control human post-mortem brains were extracted. The QC assessed RNA samples were run on Affymetrix GeneChip® human Exon 1.0 ST Arrays. In parallel, DNAs from brains were run and analysed using the Illumina Omni 1M Beadchips. A regression correlation analysis was performed to identify gene expression and alternative exon splicing in different brain regions.
Results: We report highly significant region-specific exon and gene quantitative trait loci (xQTL and wQTLs respectively) with p-values <10-35. Cerebellum and white matter show more unique QTLs in comparison with other brain regions. Furthermore, some QTLs have stronger effect on specific group of regions together than others such as cortical regions.
Or
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O-14
POPULATION GENETICS REVEALED BY ENORMOUS STRUCTURAL VARIATIONS DISCOVERED BY POPULATION-SCALE SEQUENCING
Quan Long1, Dazhe Meng1,2, Fernando Rabanal1, Christian Huber4, Bjarni Vilhjalmsson1, Qingrun Zhang1, Alexander Platzer1, Viktoria Nizhynska1, Ashley Farlow1, Petar Forai1, Kai Ye4, Ines Hellmann3, Magnus Nordborg1,2
1Gregor Mendel Institute, Vienna, Austria, 2University of Southern California, Los Angeles, USA, 3University of Vienna, Vienna, Austria, 4Leiden University Medical Center, Leiden, The Netherlands
Objectives: To understand the population genetics of Arabidopsis thaliana when structural variations are considered.
Methods: We sequenced ~180 Arabidopsis thaliana inbred lines with Illumina at deep coverage (ranging from 20 to 60). By combining eight different methodologies based on read-pair, read-depth, split-reads, as well as de novo assembling, we discovered enormous number of indels and structural variants. We used Sanger sequencing and chip based genotyping data to validate the indels. Flow Cytometry data that measures the genome sizes is also generated.
Results: (1) Totally 38% of the variance of genome size can be explained by the structural variations. Ribsome repeats and centromere explains most of them, whereas insertions called from de novo assembly explains little variance. This indicates that the genome size variation is largely due to the repetitive region, instead of unique region. (2) We observed a large number of genes that have compensating frame-shift indels. Those pairs of indels are in LD and some of the genes shows footprint of selective sweep. (3) We find that most of the SNPs in long range LD are caused by structural variations, population structure, as well as TEs. In the retained ones after above filtering, we observed enrichment of regions under selection. (4) The recombination hotspots estimated from LD pattern (LDHat) are biased at the region of structural viable region, indicating the necessity of new methodology.
Conclusions: Sequence based whole genome analysis reveals important insight into population genetics that are not accessible by chip based genotyping platforms.
O-15
VARIATION IN TRANSCRIPTION FACTOR BINDING AMONG HUMANS
Maya Kasowski1, Fabian Grubert1, Chris Heffelfinger2, Manoj Hariharan1, Akwasi Asabere2, Sebastian Waszak3, Lukas Habegger2, Joel Rozowsky2, Minyi Shi1, Alexander Urban1, Mi-Young Hong2, Konrad Karczewski1, Wolfgang Huber3, Sherman Weissman2, Mark Gerstein2, Jan Korbel3, Mike Snyder1 1Stanford University, Stanford, CA, USA, 2Yale University, New Haven, CT, USA, 3EMBL, Heidelberg, Germany
Differences in gene expression may play a major role in speciation and phenotypic diversity. Although variations in gene expression among individuals have been documented, the origins of these differences are not clear, and studies that directly measure differences in transcription factor binding sites among humans have not been performed. We have examined genome-wide variation in transcription factor binding in different individuals and a chimpanzee using chromatin immunoprecipitation followed by massively-parallel sequencing (ChIP-Seq). The binding sites of RNA Polymerase II (Pol II) as well as a key regulator of immune responses, NFKB, have been mapped in ten lymphoblastoid cell lines derived
from individuals of African, European, and Asian ancestry, including a parent-offspring trio. Using a stringent threshold, approximately 7.5% and 25% of the respective NFKB and Pol II binding regions
Or
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binding sites identified in the chimpanzee suggests a high level of divergence in binding relative to our closest evolutionary neighbor. Our results indicate that many differences in individuals occur at the level of TF binding and provide insight into the genetic events responsible for these differences.
O-16
MAPPING THE EPIGENETIC BASIS OF COMPLEX TRAITS IN ARABIDOPSIS
Frank Johannes
University of Groningen, Groningen, The Netherlands
Inter-individual differences in DNA methylation states can provide a source of heritable phenotypic variation independent of DNA sequence changes. Accumulating evidence suggests that this mode of epigenetic inheritance is more widespread in plant populations than previously appreciated.
Here I highlight our ongoing attempts to characterize the epigenetic basis of complex trait inheritance in an experimental system of so-called Epigenetic Recombinant Inbred Lines (EpiRILs) of the plant Arabidopsis. This population was derived from two parents with nearly identical DNA sequences but drastically divergent DNA methylation profiles. Employing a combination of population genetic approaches and genome-wide epigenomic profiling techniques, we are now obtaining first glimpses of the heritable epigenetic architecture underlying a spectrum of phenotypes in this system.
Our work has relevance for understanding mechanisms of adaptation in this species.
O-17
THE ROLE OF TANDEM REPEATS IN MRNA AND PROTEIN EXPRESSION HOMEOSTASIS
Sreenivas Chavali, Madan Babu M.
MRC Laboratory of Molecular Biology, Cambridge, UK
The information encoded in the DNA not only influences its own replication but also determines the abundance and function of mRNA, the encoded proteins, their interactions and ultimately the phenotype of a cell. Repeating sequences in the genome are an important source of genetic variation and are prevalent in all eukaryotes. For instance, ~10-20% of the eukaryotic genes contain continuous repeating sequences (e.g., CAG trinucleotide repeats in Huntingtin), referred as Tandem Repeats (TRs). Previous studies have linked variation in repeat length with phenotypes such as human diseases, canine skeletal morphology and have demonstrated few functional roles. However, an integrated understanding (i.e., systems view) of how TRs influence the flow of genetic information at the molecular level, determining phenotypes, under normal physiological conditions, has remained elusive.
Or
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O-18
DISSECTING THE CONTRIBUTION OF REGULATORY SEQUENCE VARIATION TO QUANTITATIVE HAEMATOLOGICAL TRAITS USING MAPS OF OPEN CHROMATIN IN PRIMARY HUMAN BLOOD CELLS
Cornelis Albers1,2, Dirk Paul2, Augusto Rendon1, Katrin Voss1, Jonathan Stephens1, HaemGen Consortium1,2, Nicole Soranzo2, Panos Deloukas2, Willem H Ouwehand1
1University of Cambridge & NHS Blood and Transplant, Cambridge, UK, 2Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
A major challenge in genome-wide association studies (GWASs) is to translate the associated sequence variants into biological mechanisms and pathways, to identify relevant cell types and to characterize small polygenic effects. We explored these issues using data from two meta-analyses of GWASs in over 60,000 individuals of two quantitative platelet traits (platelet count and volume) and six quantitative red blood cell traits (including count, volume and haemoglobin). We generated genome-wide maps of open chromatin using the FAIRE-Seq technique in three primary blood cell types of the myeloid lineage: megakaryocytes, erythroblasts, and monocytes. Regions of open chromatin, i.e. nucleosome-depleted regions (NDRs), may represent active gene regulatory elements harboring functional variants. We used bootstrapped p-value distributions of sequence variants imputed from the 1000 Genomes project to investigate enrichment of platelet and RBC associations in open chromatin in each cell type.
Considering only the subset of high-confidence NDRs, we found that red blood cell trait associations were most enriched in NDRs from erythroblasts, the precursor cells for red blood cells, but weakly enriched in megakaryocytes, the precursor cells of platelets, and monocytes. Platelet trait associations were enriched in high-confidence megakaryocyte NDRs, and interestingly monocyte NDRs showed a similarly strong enrichment. Considering the subset of NDRs present in two biological replicates of the same cell type, which includes weak NDRs supported by relatively few sequencing reads, the strongest enrichment for platelet traits was found in megakaryocyte NDRs, and for RBC traits in erythroblast NDRs. The strength and relative orderings of enrichments in NDRs reveal interesting patterns across cell types indicating distinct biological mechanisms underlying the traits. The enrichments are particularly clear for associations not reaching genome-wide significance, suggesting that NDRs reveal polygenic effects.
We will report on ongoing eQTL analyses, and the application of variance-partitioning and genotype-phenotype prediction methods incorporating NDRs as additional information.
O-19
STATISTICAL METHODS FOR THE GENETIC ANALYSIS OF ARBITRARILY STRUCTURED POPULATIONS
John Storey
Princeton University, US
No Abstract
O-20
CLIP TEST: A NEW FAST AND SIMPLE METHOD TO DISTINGUISH BETWEEN LINKED OR PLEIOTROPIC QUANTITATIVE TRAIT LOCI IN LINKAGE DISEQUILIBRIUM ANALYSIS
Ingrid David1,2, Jean-Michel Elsen1, Didier Concordet2
1INRA UR631, Castanet Tolosan, France, 2INRA-ENVT UMR1331, Toulouse, France
Or
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fact that, since the LD between a marker and the QTL is the same for the correlated traits studied under the pleiotropic assumption, the pattern of the SNP effects (i.e. the change in SNP effects when moving along the tested genomic region) should be similar for all these traits whereas it should be different under the close-linked QTL assumption. The Close Linkage versus Pleiotropism (CLIP) test that we propose is based on this consideration. It is a fast, simple and powerful method that compares the square of the observed correlation between a combination of apparent effects at the marker level, to the minimal value it can take under the pleiotropic assumption. A simulation study was performed to estimate the power and alpha risk of the CLIP test in a linkage disequilibrium analysis with dense SNP assays and complex pedigree structure. Performances of the test were compared to the ones of a test that evaluated whether the confidence intervals of the two QTLs overlapped or not (CI test). On average, the CLIP test showed a higher power (68%) to detect close-linked QTLs than the CI test (43%) and a same alpha risk (4%).
O-21
SPARSE FACTOR MODELS FOR ESTIMATING THE GENETIC ARCHITECTURE OF GENE EXPRESSION TRAITS
Daniel Runcie, Sayan Mukherjee Duke University, Durham, NC, USA