Entrance hall of the ICMS

Statistical and computational methods for relatedness and relationship inference from genetic marker data

Sep 22, 2014 - Sep 26, 2014

ICMS, 15 South College Street

Organisers

Name Institution
Cussens, James University of York
Sheehan, Nuala University of Leicester

 

The problem of estimating relationships amongst a group of individuals from genetic marker data is highly relevant to areas as diverse as evolution and conservation research, forensic science identification problems, and epidemiological and genealogical research. In the current climate where increasingly large numbers of genetic markers are becoming more readily available, the challenge to improve and develop computationally efficient methods for estimating relatedness and relationships that fully exploit such data raises new research questions that would benefit from an integrated interdisciplinary approach.

This workshop brings together a multidisciplinary range of experts to discuss various approaches to tackling problems of relatedness and relationship estimation and to form collaborative links. The workshop will also provide an opportunity for young researchers to become acquainted with the main research issues in the area and make cross-disciplinary contacts with the leading people in an informal small group setting.
 

Arrangements

This workshop will begin with Registration at 09.00-10.00 on Monday 22 September and close at 12.30 on Friday 26 September 2014.  

 

Participation

  • Speakers and Invitees will already have received invitations issued by ICMS.  

  • PUBLIC APPLICANTS
    Please note that the application period is now closed and all applicants have been informed of the decision regarding their application.  


UK Visas
If you are travelling from overseas you may require an entry visa. A European visa does not guarantee entry to the UK. Please use this link to the UK Visas site to find out if you need a visa and if so how to apply for one.

 

Venue
The workshop will be held at 15 South College Street, Edinburgh.  All lectures will be held in the Newhaven Lecture Theatre.  In addition, two blackboards have been installed.  The projector and one board may be used simultaneously.   You may also find this MAP useful.

 

Wireless Access
The workshop venue, 15 South College Street, has wireless access throughout. On arrival at Registration you will be given instructions and a code for accessing the wireless network.  For those without laptops, there will also be a couple of computers available for you to check your emails.

 

Travel
Information about travel to the UK and Edinburgh is available here.

Please note that it is your responsibility to have adequate travel insurance to cover medical and other emergencies (volcanic ash disruptions) that may occur on your trip.

A taxi directly from the airport will cost approximately 20.00 to 25.00 GBP to the city centre for a one-way journey.     There is also a bus service direct from the airport to the city centre which will cost 4.00 single or 7.00 GBP return - the Airlink 100.  This is a frequent service (every 10 minutes during peak times) and will bring you close to Waverley Railway Station, only a short walk to the accommodation and the workshop venue (see map in 'Venue' section above). 

Lothian buses charge £1.50 for a single, £3.50 for a day ticket. Please note that the exact fare is required and no change is given.

If travelling by train, please note that Edinburgh has several railway stations - Waverley Railway Station being the main station and closest to the workshop venue at 15 South College Street. If you alight at Edinburgh Waverley, the workshop venue is an easy 10 minute walk over North and South Bridge. The second large railway station is called Haymarket and is at the West End of the city centre.    Please be aware that there is also an Edinburgh Park railway station but this is at the west side of the city some way from the city centre.  For ICMS, use Edinburgh Waverley.

 

Accommodation

  • Invited Speakers:  ICMS will organise accommodation for Invited Speakers and full details will be emailed.
  • Public Applicants:  Please await the Organisers decision about your application before making any accommodation or travel arrangements as there may be some limited financial assistance available.  Some suggested places to stay can be found here

 

Poster Session
A Poster Session will take place on Monday 22 September along with an informal Wine Reception.   Please see here for further information about the Poster Session.  Pizzas will be served at 18.30.  

 

Human Cohort Applications Session
Following the afternoon coffee break on Thursday 25th September (from 15.50-17.50) there will be a Human Cohort Applications Session, which will be open to non-delegates.  This session will include talks by George Davey Smith (University of Bristol) and David Porteous (University of Edinburgh).   A further talk by Susan Wallace (University of Leeds) will take place on Friday 26 September.

 

Catering
The workshop grants will provide refreshments during the breaks in the Programme, lunch on several days, an informal Wine Reception and pizzas on the Monday evening (to coincide with the Poster Session), an informal evening meal at Blonde Restaurant on the Tuesday evening, and a workshop dinner at the Magnum Restaurant on Thursday at 19.00.  

 

Registration Fee
A registration fee of 70.00 GBP is payable by all.  This registration fee should be paid on arrival at ICMS.

At Registration we will accept:

  •  payment by sterling cash;
  •  payment by credit/debit card. Please note that a 1.75% administration fee is added to credit card payments and that we do not accept American Express or Discover cards;
  • payment by sterling cheque.  Please make your cheque payable to “Heriot-Watt University”.  Please do NOT send cheques in advance directly to Heriot-Watt University. 

 

Reimbursement of Travel Expenses (if agreed in your invitation email)
The Organisers have agreed to reimburse some participants with a contribution towards travel costs.   This will have been stated in the invitation email.   Reimbursement will take place after the workshop.  On arrival at ICMS you will be given a claim form and the money will be reimbursed directly into your bank account.   It would be helpful, therefore, if you could bring your bank details to the workshop. In addition to the bank name, address and bank account number, participants from the USA will also require their bank routing number, those from the UK will be asked for the bank sort code, and those from the rest of the world, an IBAN and SWIFT/BIC code.  Please note that I cannot reimburse any item without a signed claim form and original receipts (although electronic tickets for flights can simply be emailed to me if they contain your name and the amount paid).

 

If you have any questions regarding arrangements for this workshop please email Audrey Brown

 

Programme

PLEASE NOTE:  This Programme may be subject to alteration.  You are advised to continue to check the Programme until the time of the workshop as any alterations will be notified here. 

 

Monday 22 September 2014

09.00-10.00

Registration & coffee in the Chapterhouse, Level 1

10.00-10.40

Eric Anderson (NOAA, Southwest Fisheries Science Center & University of California, Santa Cruz)
A pseudo-Gibbs sampler for computationally efficient pedigree inference from SNPs in molecular ecology applications
pdf of presentation

10.40-11.20

Anthony Almudevar (University of Rochester)
An information theoretic approach to pedigree reconstruction
pdf of presentation

11.20-11.50

Coffee/Tea in the Chapterhouse

11.50-12.30

Klaas Slooten (Netherlands Forensic Institute)
Forensic DNA mixtures: donors and relatives
pdf of presentation

12.30-14.00

Lunch provided in the Chapterhouse

14.00-14.40

Pirmin Nietlisbach (University of Zurich)
Heritability of heterozygosity revealed by a multi-generation pedigree and microsatellite genotypes of a wild bird population
pdf of presentation

14.40-15.20

Discussion: planning the rest of the workshop

15.20-15.50

Coffee/Tea in the Chapterhouse

15.50-16.30

Bruce Weir (University of Washington)
Characterizing population structure with F-statistics: relatedness on an evolutionary time scale
pdf of presentation

16.30-17.10

Jinliang Wang (Institute of Zoology)
Pedigrees or markers: which are better in estimating relatedness and inbreeding coefficient?
pdf of presentation

17.10-19.30

Poster session and informal wine reception (with pizzas served at 18.30)

 

Tuesday 23 September 2014

09.00-09.40

David Balding (University College London)
Kinship in the era of genome-wide sequencing
pdf of presentation

09.40-10.30

Breakout sessions

10.30-11.00

Coffee/Tea in the Chapterhouse

11.00-11.50

Group discussion: What is meant by 'relatedness' in the genomic era?

11.50-12.30

Anne-Louise Leutenegger (INSERM, Paris)
Genetic relatedness inference and disease gene mapping
pdf of presentation

12.30-14.00

Lunch provided in the Chapterhouse

14.00-14.40

Mark Bartlett (University of York)
Pedigree reconstruction using integer linear programming
pdf of presentation

14.40-15.20

Discussion: Are pedigrees still useful in the genomic era?

15.20-15.50

Coffee/Tea in the Chapterhouse

15.50-16.30

Gregory Nuel (CNRS and Sorbonne Universities)
Stratification of founders in large pedigrees
pdf of presentation

16.30-17.10

Stefanie Muff (University of Zurich)
On the importance of uncertainty quantification of relatedness and relationship estimates
pdf of presentation

17.10-17.50

Breakout sessions

19.00

Informal evening meal at Blonde Restaurant, 75 St Leonard's Street, Edinburgh

 

Wednesday 24 September 2014

09.00-09.40

Marco Bink (Wageningen UR)
The use of genome-wide and locus-specific relatedness in QTL mapping and association studies in plants
pdf of presentation

09.40-10.20

Breakout sessions

10.20-11.00

Coffee/Tea in the Chapterhouse

11.00-11.40

Itsik Pe'er (Columbia University)
Renewal theory approximation for identity by descent under Sequential Markov Coalescent (SMC & SMC') models

11.40-12.20

Group discussion: Relatedness inference in inbred populations

12.20-13.00

Andrés Legarra (INRA)
A relationship matrix combining pedigree and markers when some individuals are not genotyped
pdf of presentation

13.00

Free afternoon

 

Thursday 25 September 2014

09.00-09.40

Manuel García Magariños (Universidade de Santiago de Compostela & Norwegian University of Life Sciences)
Hypothesis testing of family relationships using identity-by-descent (IBD) parameters
pdf of presentation

09.40-10.20

Group discussion: Computational methods in pedigree reconstruction

10.20-11.00

Coffee/Tea in the Chapterhouse

11.00-11.50

Bill Hill (University of Edinburgh)
Utilising variation in realised relationship
pdf of presentation

11.50-12.30

Breakout sessions

12.30-14.00

Lunch provided in the Chapterhouse

14.00-14.40

Emmanuelle Génin (INSERM, Brest)
Genetic relatedness inference and fine-scale stratification between and within French regions

14.40-15.20

Feedback from breakout groups

15.20-15.50

Coffee/Tea in the Chapterhouse

15.50-16.30

George Davey Smith (University of Bristol)
ALSPAC – from a birth cohort to a multi-generational study
pdf of presentation

16.30-17.10

David Porteous (University of Edinburgh)
Generation Scotland: the Scottish family study
pdf of presentation

17.10-17.50

Discussion: Relatedness issues and applications in Human Cohorts

19.00

Workshop dinner at Magnum Restaurant, 1 Albany Street, Edinburgh

 

Friday 26 September 2014

09.00-09.40

Carmen Amador (MRC IGMM)
Recent genomic heritage in today’s Scotland
pdf of presentation

09.40-10.30

Susan Wallace (University of Leicester)
Relatedness and pedigree reconstruction - ethical, social and legal issues
pdf of presentation

10.30-11.00

Coffee/Tea in the Chapterhouse

11.00-11.40

Group discussion: ESLI: privacy issues in analyses of relatedness

11.40-12.30

Final wrap-up: key problems

12.30

Close of workshop

 

 

Presentations:

Presentation Details
Almudevar, Anthony
An information theoretic approach to pedigree reconstruction
View Abstract Down
Amador, Carmen
Recent genomic heritage in today’s Scotland
View Abstract Down
Anderson, Eric
A pseudo-Gibbs sampler for computationally efficient pedigree inference from SNPs in molecular ecology applications
View Abstract Down
Balding, David
Kinship in the era of genome-wide sequencing
View Abstract Down
Bartlett, Mark
Pedigree reconstruction using integer linear programming
View Abstract Down
Bink, Marco
The use of genome-wide and locus-specific relatedness in QTL mapping and association studies in plants
View Abstract Down
Davey Smith, George
ALSPAC – from a birth cohort to a multi-generational study
View Abstract Down
Fernández, Jesús
POSTER: Genomic estimates of inbreeding and coancestry in commercial and local cattle breeds
View Abstract Down
García-Magariños, Manuel
Hypothesis testing of family relationships using identity-by-descent (IBD) parameters
View Abstract Down
Génin, Emmanuelle
Genetic relatedness inference and fine-scale stratification between and within French regions
View Abstract Down
Hill, Bill
Utilising variation in realised relationship
View Abstract Down
Huisman, Jisca
POSTER: Reconstructing wild pedigrees from SNP data when sampling is incomplete
View Abstract Down
Kruijver, Maarten
POSTER: A population genetic analysis of the Dutch National DNA database
View Abstract Down
Legarra, Andrés
A relationship matrix combining pedigree and markers when some individuals are not genotyped
View Abstract Down
Leutenegger, Anne-Louise
Genetic relatedness inference and disease gene mapping
View Abstract Down
Muff, Stefanie
On the importance of uncertainty quantification of relatedness and relationship estimates
View Abstract Down
Nietlisbach, Pirmin
Heritability of heterozygosity revealed by a multi-generation pedigree and microsatellite genotypes of a wild bird population
View Abstract Down
Nuel, Gregory
Stratification of founders in large pedigrees
View Abstract Down
Pe'er, Itsik
Renewal theory approximation for identity by descent under Sequential Markov Coalescent (SMC & SMC') models
View Abstract Down
Porteous, David
Generation Scotland: the Scottish family study
View Abstract Down
Ranola, John Michael
POSTER: Fast spatial ancestry via flexible allele frequency surfaces
View Abstract Down
Scutari, Marco
POSTER: Predictive accuracy: a function of genetic distance
View Abstract Down
Slooten, Klaas
Forensic DNA mixtures: donors and relatives
View Abstract Down
Sun, Meng
POSTER: Detecting relatives from genome-wide data
View Abstract Down
Wallace, Susan
Relatedness and pedigree reconstruction - ethical, social and legal issues
View Abstract Down
Wang, Jinliang
Pedigrees or markers: which are better in estimating relatedness and inbreeding coefficient?
View Abstract Down
Weir, Bruce
Characterizing population structure with F-statistics: relatedness on an evolutionary time scale
View Abstract Down
Zheng, Xiuwen
POSTER: Eigenanalysis on SNP data with an interpretation of identity by descent
View Abstract Down

Participants

Name Institution
Almudevar, Anthony University of Rochester
Amador, Carmen MRC IGMM
Anderson, Eric NOAA, Southwest Fisheries Science Center & University of California, Santa Cruz
Balding, David University College London
Bartlett, Mark University of York
Beaumont, Mark University of Bristol
Bink, Marco Wageningen UR
Cowell, Robert City University London
Cussens, James University of York
Davey Smith, George University of Bristol
Duthie, Alexander University of Aberdeen
Egeland, Thore Norwegian University of Life Sciences
Fernández, Jesús Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
García-Magariños, Manuel Universidade de Santiago de Compostela & Norwegian University of Life Sciences
Génin, Emmanuelle INSERM, Brest
Hadfield, Jarrod University of Edinburgh
Hill, Bill University of Edinburgh
Huisman, Jisca Institure for Evolutionary Biology
Keller, Lukas University of Zurich
Kruijver, Maarten VU University Amsterdam
Legarra, Andrés INRA
Leutenegger, Anne-Louise INSERM, Paris
Muff, Stefanie University of Zurich
Nietlisbach, Pirmin University of Zurich
Nuel, Gregory CNRS and Sorbonne Universities
Pe'er, Itsik Columbia University
Porteous, David University of Edinburgh
Ranola, John Michael University of Washington
Reid, Jane University of Aberdeen
Scutari, Marco University of Oxford
Sheehan, Nuala University of Leicester
Slooten, Klaas Netherlands Forensic Institute
Smith, Jim University of Warwick
Studený, Milan Academy of Sciences of the Czech Republic
Sun, Meng University of Leicester
Vigeland, Magnus Dehli University of Oslo
Wallace, Susan University of Leicester
Wang, Jinliang Institute of Zoology
Weir, Bruce University of Washington
Zheng, Xiuwen University of Washington at Seattle